Genes

2024

Jump to: 2023, 2022, 2021

11 pages, 305 KiB

Open AccessArticle

Genomic Analysis of the Giant Red Shrimp (Aristaeomorpha foliacea) Using Next-Generation Sequencing: Set of Tools for Population Studies

by Sandra Heras, Alba Abras, Aleix Palahí, Jose-Luis García-Marín and María Inés Roldán

Genes 2024, 15(11), 1360; https://doi.org/10.3390/genes15111360 - 23 Oct 2024

Viewed by 510

Abstract

Background/Objectives: The giant red shrimp, Aristaeomorpha foliacea, is a valuable marine fishing resource. The conservation of species, especially exploited ones, depends on a good knowledge of their biology, as well as the development of appropriate management plans based on the identification of [...] Read more.

Background/Objectives: The giant red shrimp, Aristaeomorpha foliacea, is a valuable marine fishing resource. The conservation of species, especially exploited ones, depends on a good knowledge of their biology, as well as the development of appropriate management plans based on the identification of genetically differentiated units or genetic stocks. Microsatellites are widely used molecular markers to detect genetic stocks in penaeoid shrimps and prawns. This study aimed to develop and characterize new microsatellites for A. foliacea. Methods: Next-generation sequencing based on 454 pyrosequencing revealed 58 candidate microsatellite loci for A. foliacea. These were tested on a panel of 8 individuals representative of its worldwide geographical distribution, and 19 polymorphic loci were identified and subsequently validated and characterized in 30 individuals from a single population in the Mediterranean Sea. Results: As a result, 10 polymorphic loci were identified, which did not present linkage disequilibrium and showed a range of alleles per locus and an observed and expected heterozygosity of 2–10, 0.0667–0.5567, and 0.0661–0.8511, respectively. Nine out of these loci were under Hardy–Weinberg equilibrium and showed a combined exclusion probability of 0.9202 and 0.9968 in parentage and identity analysis, respectively. Conclusions: This set of loci will provide a strong set of tools to (i) perform parentage studies and (ii) examine connectivity patterns (horizontal and vertical), including examining the population structure of this species at a variety of geographical scales and, particularly, between exploited populations in shallow waters and deeper unexploited populations. Full article

11 pages, 715 KiB

Open AccessReview

Selected Monogenic Genetic Diseases in Holstein Cattle—A Review

by Marta Gozdek, Sebastian Mucha, Adam Prostek and Tomasz Sadkowski

Genes 2024, 15(8), 1052; https://doi.org/10.3390/genes15081052 - 10 Aug 2024

Cited by 1 | Viewed by 930

Abstract

Genetic disorders arise from alterations in the hereditary information encoded in DNA, leading to potential detrimental effects on the well-being and vitality of organisms. Within the bovine population, genetic conditions inherited in an autosomal recessive manner are frequently associated with particular breeds. In [...] Read more.

Genetic disorders arise from alterations in the hereditary information encoded in DNA, leading to potential detrimental effects on the well-being and vitality of organisms. Within the bovine population, genetic conditions inherited in an autosomal recessive manner are frequently associated with particular breeds. In recent years, several recessive haplotypes and a few causative mutations have been discovered in Holstein cattle: CDH (Holstein cholesterol deficiency), haplotypes with a homozygous deficiency in Holstein (HH1, HH3, HH4, HH5, HH6 and HH7), BLAD (bovine leukocyte adhesion deficiency) and DUMPS (deficiency of uridine monophosphate synthase). All of these diseases are inherited in an autosomal recessive manner. From a breeding perspective, recessive mutations specifically exhibit considerable detrimental effects and are a significant problem for breeders, exposing them to economic losses. Individual mutations can cause embryo death at any stage of pregnancy. Only genetic research and conscious selection of animals for mating will lead to a reduction in the number of carriers and elimination of mutations from the population. Full article

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17 pages, 2947 KiB

Open AccessArticle

New Insights into the Mechanism by Which the Pituitary Gland Copes with Hypoxia Stress Based on a Transcriptomic Analysis of Megalobrama amblycephala

by Ruilin Xie, Huandi Guo, Yuanyuan Luo, Wen Huang, Zhuohao Ruan and Wensheng Liu

Genes 2024, 15(8), 987; https://doi.org/10.3390/genes15080987 - 26 Jul 2024

Viewed by 842

Abstract

Hypoxia is a common environmental stressor in aquatic ecosystems, and during the cultivation process, Megalobrama amblycephala is prone to death because it is hypoxia-intolerant, which brings huge economic losses to farmers. The pituitary gland is a crucial endocrine gland in fish, and it [...] Read more.

Hypoxia is a common environmental stressor in aquatic ecosystems, and during the cultivation process, Megalobrama amblycephala is prone to death because it is hypoxia-intolerant, which brings huge economic losses to farmers. The pituitary gland is a crucial endocrine gland in fish, and it is mainly involved in the secretion, storage, and regulation of hormones. In the present study, we compared the transcriptional responses to serious hypoxia in the pituitary gland among hypoxia-sensitive (HS) and hypoxia-tolerant (HT) M. amblycephala and a control group that received a normal oxygen supply (C0). The fish were categorized according to the time required to lose balance during a hypoxia treatment. A total of 129,251,170 raw reads were obtained. After raw sequence filtering, 43,461,745, 42,609,567, and 42,730,282 clean reads were obtained for the HS, HT, and C0 groups, respectively. A transcriptomic comparison revealed 1234 genes that were differentially expressed in C0 vs. HS, while 1646 differentially expressed genes were obtained for C0 vs. HT. In addition, the results for HS vs. HT showed that 367 upregulated and 41 downregulated differentially expressed genes were obtained for a total of 408 differentially expressed genes. A KEGG analysis of C0 vs. HS, C0 vs. HT, and HS vs. HT identified 315, 322, and 219 enriched pathways, respectively. Similar hypoxia-induced transcription patterns suggested that the downregulated DEGs and enriched pathways were related to pathways of neurodegeneration in multiple diseases, pathways in cancer, thermogenesis, microRNAs in cancer, diabetic cardiomyopathy, and renin secretion. However, in the upregulated DEGs, the PI3K-Akt signaling pathway (C0 vs. HS), microRNAs in cancer (C0 vs. HT), and HIF-1 signaling pathway (HS vs. HT) were significantly enriched. There is a lack of clarity regarding the role of the pituitary gland in hypoxic stress. These results not only provide new insights into the mechanism by which pituitary tissue copes with hypoxia stress in M. amblycephala but also offer a basis for breeding M. amblycephala with hypoxia-resistant traits. Full article

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13 pages, 7064 KiB

Open AccessArticle

A Single-Cell Transcriptome of Bovine Milk Somatic Cells

by Minja Zorc, Mateja Dolinar and Peter Dovč

Genes 2024, 15(3), 349; https://doi.org/10.3390/genes15030349 - 10 Mar 2024

Cited by 3 | Viewed by 2020

Abstract

The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The [...] Read more.

The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The process of lactation in cows serves as an excellent model for studying the biological aspects of lactation with the aim of exploring the mechanistic base of this complex trait at the cellular level. In this study, we analyzed the milk transcriptome at the single-cell level by conducting scRNA-seq analysis on milk samples from two Holstein Friesian cows at mid-lactation (75 and 93 days) using the 10× Chromium platform. Cells were pelleted and fat was removed from milk by centrifugation. The cell suspension from each cow was loaded on separate channels, resulting in the recovery of 9313 and 14,544 cells. Library samples were loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument. After filtering at the cell and gene levels, a total of 7988 and 13,973 cells remained, respectively. We were able to reconstruct different cell types (milk-producing cells, progenitor cells, macrophages, monocytes, dendritic cells, T cells, B cells, mast cells, and neutrophils) in bovine milk. Our findings provide a valuable resource for identifying regulatory elements associated with various functions of the mammary gland such as lactation, tissue renewal, native immunity, protein and fat synthesis, and hormonal response. Full article

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18 pages, 5631 KiB

Open AccessArticle

A Chromosome-Level Genome Assembly of the Non-Hematophagous Leech Whitmania pigra (Whitman 1884): Identification and Expression Analysis of Antithrombotic Genes

by Zichao Liu, Fang Zhao, Zuhao Huang, Bo He, Kaiqing Liu, Feng Shi, Zheng Zhao and Gonghua Lin

Genes 2024, 15(2), 164; https://doi.org/10.3390/genes15020164 - 26 Jan 2024

Cited by 1 | Viewed by 1431

Abstract

Despite being a non-hematophagous leech, Whitmania pigra is widely used in traditional Chinese medicine for the treatment of antithrombotic diseases. In this study, we provide a high quality genome of W. pigra and based on which, we performed a systematic identification of the [...] Read more.

Despite being a non-hematophagous leech, Whitmania pigra is widely used in traditional Chinese medicine for the treatment of antithrombotic diseases. In this study, we provide a high quality genome of W. pigra and based on which, we performed a systematic identification of the potential antithrombotic genes and their corresponding proteins. We identified twenty antithrombotic gene families including thirteen coagulation inhibitors, three platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. Unexpectedly, a total of 79 antithrombotic genes were identified, more than a typical blood-feeding Hirudinaria manillensis, which had only 72 antithrombotic genes. In addition, combining with the RNA-seq data of W. pigra and H. manillensis, we calculated the expression levels of antithrombotic genes of the two species. Five and four gene families had significantly higher and lower expression levels in W. pigra than in H. manillensis, respectively. These results showed that the number and expression level of antithrombotic genes of a non-hematophagous leech are not always less than those of a hematophagous leech. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from a non-hematophagous leech to date and will significantly enhance the investigation and utilization of leech derivatives in thrombosis therapy research and pharmaceutical applications. Full article

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2023

Jump to: 2024, 2022, 2021

20 pages, 9118 KiB

Open AccessArticle

The Genome of the Yellow Mealworm, Tenebrio molitor: It’s Bigger Than You Think

by Brenda Oppert, Aaron T. Dossey, Fu-Chyun Chu, Eva Šatović-Vukšić, Miroslav Plohl, Timothy P. L. Smith, Sergey Koren, Morgan L. Olmstead, Dewey Leierer, Gail Ragan and J. Spencer Johnston

Genes 2023, 14(12), 2209; https://doi.org/10.3390/genes14122209 - 14 Dec 2023

Cited by 7 | Viewed by 8637

Abstract

Background: Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide. Methods: Long [...] Read more.

Background: Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide. Methods: Long and short reads and long-range data were obtained from a T. molitor male pupa. Sequencing transcripts from 12 T. molitor life stages resulted in 279 million reads for gene prediction and genetic engineering. A unique plasmid delivery system containing guide RNAs targeting the eye color gene vermilion flanking the muscle actin gene promoter and EGFP marker was used in CRISPR/Cas9 transformation. Results: The assembly is approximately 53% of the genome size of 756.8 ± 9.6 Mb, measured using flow cytometry. Assembly was complicated by a satellitome of at least 11 highly conserved satDNAs occupying 28% of the genome. The injection of the plasmid into embryos resulted in knock-out of Tm vermilion and knock-in of EGFP. Conclusions: The genome of T. molitor is longer than current assemblies (including ours) due to a substantial amount (26.5%) of only one highly abundant satellite DNA sequence. Genetic sequences and transformation tools for an insect important to the food and feed industries will promote the sustainable utilization of mealworms and other farmed insects. Full article

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14 pages, 2564 KiB

Open AccessArticle

The Expansion of House Mouse Major Urinary Protein Genes Likely Did Not Facilitate Commensalism with Humans

by Miloš Macholán, Kristina Daniszová and Zuzana Hiadlovská

Genes 2023, 14(11), 2090; https://doi.org/10.3390/genes14112090 - 17 Nov 2023

Viewed by 1353

Abstract

Mouse wild-derived strains (WDSs) combine the advantages of classical laboratory stocks and wild animals, and thus appear to be promising tools for diverse biomedical and evolutionary studies. We employed 18 WDSs representing three non-synanthropic species (Mus spretus, Mus spicilegus, and [...] Read more.

Mouse wild-derived strains (WDSs) combine the advantages of classical laboratory stocks and wild animals, and thus appear to be promising tools for diverse biomedical and evolutionary studies. We employed 18 WDSs representing three non-synanthropic species (Mus spretus, Mus spicilegus, and M. macedonicus) and three house mouse subspecies (Mus musculus musculus, M. m. domesticus, M. m. castaneus), which are all important human commensals to explore whether the number of major urinary protein (MUP) genes and their final protein levels in urine are correlated with the level of commensalism. Contrary to expectations, the MUP copy number (CN) and protein excretion in the strains derived from M. m. castaneus, which is supposed to be the strongest commensal, were not significantly different from the non-commensal species. Regardless of an overall tendency for higher MUP amounts in taxa with a higher CN, there was no significant correlation at the strain level. Our study thus suggests that expansion of the Mup cluster, which appeared before the house mouse diversification, is unlikely to facilitate commensalism with humans in three house mouse subspecies. Finally, we found considerable variation among con(sub)specific WDSs, warning against generalisations of results based on a few strains. Full article

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12 pages, 5043 KiB

Open AccessFeature PaperArticle

Independent COL17A1 Variants in Cats with Junctional Epidermolysis Bullosa

by Sarah Kiener, Heather Troyer, Daniel Ruvolo, Paula Grest, Sara Soto, Anna Letko, Vidhya Jagannathan, Tosso Leeb, Elizabeth A. Mauldin, Ching Yang and Ana Rostaher

Genes 2023, 14(10), 1835; https://doi.org/10.3390/genes14101835 - 22 Sep 2023

Viewed by 2736

Abstract

Epidermolysis bullosa (EB), characterized by defective adhesion of the epidermis to the dermis, is a heterogeneous disease with many subtypes in human patients and domestic animals. We investigated two unrelated cats with recurring erosions and ulcers on ear pinnae, oral mucosa, and paw [...] Read more.

Epidermolysis bullosa (EB), characterized by defective adhesion of the epidermis to the dermis, is a heterogeneous disease with many subtypes in human patients and domestic animals. We investigated two unrelated cats with recurring erosions and ulcers on ear pinnae, oral mucosa, and paw pads that were suggestive of EB. Histopathology confirmed the diagnosis of EB in both cats. Case 1 was severe and had to be euthanized at 5 months of age. Case 2 had a milder course and was alive at 11 years of age at the time of writing. Whole genome sequencing of both affected cats revealed independent homozygous variants in COL17A1 encoding the collagen type XVII alpha 1 chain. Loss of function variants in COL17A1 lead to junctional epidermolysis bullosa (JEB) in human patients. The identified splice site variant in case 1, c.3019+1del, was predicted to lead to a complete deficiency in collagen type XVII. Case 2 had a splice region variant, c.769+5G>A. Assessment of the functional impact of this variant on the transcript level demonstrated partial aberrant splicing with residual expression of wildtype transcript. Thus, the molecular analyses provided a plausible explanation of the difference in clinical severity between the two cases and allowed the refinement of the diagnosis in the affected cats to JEB. This study highlights the complexity of EB in animals and contributes to a better understanding of the genotype-phenotype correlation in COL17A1-related JEB. Full article

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18 pages, 10388 KiB

Open AccessArticle

Metabolomic Profiling of Female Mink Serum during Early to Mid-Pregnancy to Reveal Metabolite Changes

by Yuxin Luo, Yiqiu Huang, Liang Deng, Zheng Li and Chunjin Li

Genes 2023, 14(9), 1759; https://doi.org/10.3390/genes14091759 - 4 Sep 2023

Viewed by 1148

Abstract

Mink embryos enter a period of diapause after the embryo develops into the blastocyst, and its reactivation is mainly caused by an increase in polyamine. The specific process of embryo diapause regulation and reactivation remains largely unexamined. This study aimed to identify changes [...] Read more.

Mink embryos enter a period of diapause after the embryo develops into the blastocyst, and its reactivation is mainly caused by an increase in polyamine. The specific process of embryo diapause regulation and reactivation remains largely unexamined. This study aimed to identify changes in metabolites in the early pregnancy of mink by comparing and analyzing in serum metabolites up to twenty-nine days after mating. Blood samples were taken on the first day of mating, once a week until the fifth week. Metabolomic profiles of the serum samples taken during this period were analyzed by ultra-performance liquid chromatography/mass spectrometry. Multivariate statistical analyses identified differential metabolite expression at different time points in both positive and negative ion modes. The levels of dopamine, tyramine, L-phenylalanine, L-tyrosine, tyrosine, L-kynurenine, L-lysine, L-arginine, D-ornithine, and leucine changed significantly. These metabolites may be associated with the process of embryo diapause and subsequent reactivation. Full article

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14 pages, 2939 KiB

Open AccessArticle

Genetic History of the Altai Breed Horses: From Ancient Times to Modernity

by Mariya A. Kusliy, Anna A. Yurlova, Alexandra I. Neumestova, Nadezhda V. Vorobieva, Natalya V. Gutorova, Anna S. Molodtseva, Vladimir A. Trifonov, Kseniya O. Popova, Natalia V. Polosmak, Vyacheslav I. Molodin, Sergei K. Vasiliev, Vladimir P. Semibratov, Tumur-O. Iderkhangai, Alexey A. Kovalev, Diimaajav Erdenebaatar, Alexander S. Graphodatsky and Alexey A. Tishkin

Genes 2023, 14(8), 1523; https://doi.org/10.3390/genes14081523 - 26 Jul 2023

Cited by 1 | Viewed by 2289

Abstract

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, [...] Read more.

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age. Full article

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14 pages, 2320 KiB

Open AccessArticle

Investigating the Migratory Behavior of Soybean Looper, a Major Pest of Soybean, through Comparisons with the Corn Pest Fall Armyworm Using Mitochondrial Haplotypes and a Sex-Linked Marker

by Rodney N. Nagoshi, Jeffrey A. Davis, Robert L. Meagher, Fred R. Musser, Graham P. Head, Hector Portillo and Henry Teran

Genes 2023, 14(7), 1495; https://doi.org/10.3390/genes14071495 - 22 Jul 2023

Viewed by 1629

Abstract

The Noctuid moth soybean looper (SBL), Chrysodeixis includens (Walker), is an economically important pest of soybean (Glycine max (Linnaeus) Merrill). Because it is not known to survive freezing winters, permanent populations in the United States are believed to be limited to the [...] Read more.

The Noctuid moth soybean looper (SBL), Chrysodeixis includens (Walker), is an economically important pest of soybean (Glycine max (Linnaeus) Merrill). Because it is not known to survive freezing winters, permanent populations in the United States are believed to be limited to the southern regions of Texas and Florida, yet its geographical range of infestations annually extend to Canada. This indicates annual migrations of thousands of kilometers during the spring and summer growing season. This behavior is like that of the fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), also a Noctuid that is a major global pest of corn. SBL and FAW are projected to have very similar distributions of permanent populations in North America based on climate suitability modeling and the overlap in the distribution of their preferred host plants (corn and soybean). It therefore seems likely that the two species will display similar migratory behavior in the United States. This was tested by identifying genetic markers in SBL analogous to those successfully used to delineate FAW migratory pathways and comparing the distribution patterns of the markers from the two species. Contrary to expectations, the results indicate substantial differences in migratory behavior that appear to be related to differences in the timing of corn and soybean plantings. These findings underscore the importance of agricultural practices in influencing pest migration patterns, in particular the timing of host availability relative to mean seasonal air transport patterns. Full article

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17 pages, 4768 KiB

Open AccessArticle

Chromosomal Evolution of the Talpinae

by Larisa S. Biltueva, Nadezhda V. Vorobieva, Natalya A. Lemskya, Polina L. Perelman, Vladimir A. Trifonov, Victor V. Panov, Alexey V. Abramov, Shin-ichiro Kawada, Natalya A. Serdukova and Alexandr S. Graphodatsky

Genes 2023, 14(7), 1472; https://doi.org/10.3390/genes14071472 - 19 Jul 2023

Viewed by 1271

Abstract

In recent years, the number of mole species with species status confirmed by genetic methods has been continuously increasing. Unfortunately, cytogenetic data are not yet available for all species. Here, for the first time, a GTG-banded karyotype of the small-toothed mole from Vietnam, [...] Read more.

In recent years, the number of mole species with species status confirmed by genetic methods has been continuously increasing. Unfortunately, cytogenetic data are not yet available for all species. Here, for the first time, a GTG-banded karyotype of the small-toothed mole from Vietnam, Euroscaptor parvidens, a representative of the Eastern clade of the genus Euroscaptor, has been described. Through comparative analysis of available Euroscaptor (Euroscaptor parvidens, Euroscaptor klossi, and Euroscaptor malayana) and Oreoscaptor (Oreoscaptor mizura) karyotypes, we found cytogenetic signatures for each of the studied species. Zoo-FISH with sorted chromosomes of the Siberian mole (Talpa altaica) on chromosome sets of the small-toothed mole (E. parvidens), the small Japanese mole (Mogera imaizumii) from the closely related genus, and the Japanese shrew mole (Urotrichus talpoides) from the tribe Urotrichini made it possible to identify syntenic regions between these species. We propose a possible ancestral karyotype of the tribe and, based on it, traced the features of chromosomal rearrangements accompanying the divergence of moles. The low rates of chromosomal evolution within the species of the genus Talpa—T. altaica and T. europaea—and the high rates of karyotypic reshuffling within the Asian genera of the tribe were confirmed. The karyotype of the Japanese mountain mole O. mizura seems to be the most conserved among the Asian moles. The most frequently occurring types of chromosomal rearrangements in moles are the pericentric inversions and amplification of heterochromatin. The pericentric inversions on four pairs of autosomes are shared between the closely related genera Euroscaptor, Oreoscaptor, and Mogera, while many more apomorphic rearrangements have occurred in each lineage additionally. The highest rate of chromosomal changes, with five rearrangements occurring over approximately 7 million years, was recorded in the lineage of the small-toothed mole. Full article

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17 pages, 4604 KiB

Open AccessArticle

Two Complete Mitochondrial Genomes of Leptobrachium (Anura: Megophryidae: Leptobrachiinae): Characteristics, Population Divergences, and Phylogenetic Implications

by Qiang Zhou, Hong-Mei Xiang, Ming-Yao Zhang, Ying Liu, Zhi-Rong Gu, Xiang-Ying Lan, Jin-Xiu Wang and Wan-Sheng Jiang

Genes 2023, 14(3), 768; https://doi.org/10.3390/genes14030768 - 21 Mar 2023

Cited by 3 | Viewed by 2022

Abstract

The mustache toads Leptobrachium boringii and Leptobrachium liui are two attractive species in Megophryidae, in which adult males have mustache-like keratinized nuptial spines on their upper lip. However, both are under threat due to multiple factors, of which scientific studies are still very limited. [...] Read more.

The mustache toads Leptobrachium boringii and Leptobrachium liui are two attractive species in Megophryidae, in which adult males have mustache-like keratinized nuptial spines on their upper lip. However, both are under threat due to multiple factors, of which scientific studies are still very limited. In this study, two new complete mitochondrial genomes of L. boringii and L. liui were sequenced, assembled, and annotated based on next-generation sequencing. The mitogenome lengths of L. boringii and L. liui were found to be 17,100 and 17,501 bp, respectively, with both containing 13 protein coding genes, 23 tRNAs, 2 rRNAs, and 1 non-coding control region. Nucleotide diversity analyses indicate that atp8, atp6, and nad2 showed higher nucleotide diversity than cox1, cox3, and cytb. The intraspecific genetic distances among three different populations of L. boringii exceed 4%, and those between two populations of L. liui reach 7%. Phylogenetic relationships support their division into two subfamilies of Megophryidae (Leptobrachiinae and Megophryinae) as well as two species groups within Leptobrachium, corresponding to the number of keratinized nuptial spines (10–48 in the L. boringii species group vs. 2–6 in the L. liui species group). The two new mitogenomes reported in this study provide valuable data for future molecular evolutionary and conservation studies of the genus Leptobrachium and other Megophryidae toads. Full article

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13 pages, 1772 KiB

Open AccessArticle

Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions

by Minjin Han, Jianyu Ren, Haipeng Guo, Xiaoling Tong, Hai Hu, Kunpeng Lu, Zongrui Dai and Fangyin Dai

Genes 2023, 14(3), 649; https://doi.org/10.3390/genes14030649 - 4 Mar 2023

Cited by 2 | Viewed by 1956

Abstract

Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents–progeny sequencing to investigate the [...] Read more.

Mutation rate is a crucial parameter in evolutionary genetics. However, the mutation rate of most species as well as the extent to which the environment can alter the genome of multicellular organisms remain poorly understood. Here, we used parents–progeny sequencing to investigate the mutation rate and spectrum of the domestic silkworm (Bombyx mori) among normal and two temperature stress conditions (32 °C and 0 °C). The rate of single-nucleotide mutations in the normal temperature rearing condition was 0.41 × 10⁻⁸ (95% confidence interval, 0.33 × 10⁻⁸–0.49 × 10⁻⁸) per site per generation, which was up to 1.5-fold higher than in four previously studied insects. Moreover, the mutation rates of the silkworm under the stresses are significantly higher than in normal conditions. Furthermore, the mutation rate varies less in gene regions under normal and temperature stresses. Together, these findings expand the known diversity of the mutation rate among eukaryotes but also have implications for evolutionary analysis that assumes a constant mutation rate among species and environments. Full article

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22 pages, 2896 KiB

Open AccessArticle

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

by Aliya Yakupova, Andrey Tomarovsky, Azamat Totikov, Violetta Beklemisheva, Maria Logacheva, Polina L. Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, Natalia A. Serdyukova, Mike Rayko, Tatiana Bulyonkova, Nikolay Cherkasov, Vladimir Pylev, Vladimir Peterfeld, Aleksey Penin, Elena Balanovska, Alla Lapidus, DNA Zoo Consortium, Stephen J. OBrien, Alexander Graphodatsky, Klaus-Peter Koepfli and Sergei Kliver Show full author list Hide full author list

Genes 2023, 14(3), 619; https://doi.org/10.3390/genes14030619 - 28 Feb 2023

Cited by 2 | Viewed by 4836

Abstract

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic [...] Read more.

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions. Full article

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12 pages, 2815 KiB

Open AccessEditor’s ChoiceArticle

Aliens on Boats? The Eastern and Western Expansion of the African House Gecko

by Catarina Jesus Pinho, Luís Cardoso, Sara Rocha and Raquel Vasconcelos

Genes 2023, 14(2), 381; https://doi.org/10.3390/genes14020381 - 31 Jan 2023

Cited by 4 | Viewed by 1969

Abstract

Invasive species disrupt relations between endemics and their ecosystem and are an increasing biodiversity conservation problem. The Hemidactylus genus comprises the most successful invasive reptile species, including the worldwide-distributed Hemidactylus mabouia. In this study, we used 12S and ND2 sequences to taxonomically [...] Read more.

Invasive species disrupt relations between endemics and their ecosystem and are an increasing biodiversity conservation problem. The Hemidactylus genus comprises the most successful invasive reptile species, including the worldwide-distributed Hemidactylus mabouia. In this study, we used 12S and ND2 sequences to taxonomically identify and tentatively determine the diversity and origin of these invaders in Cabo Verde while also clarifying this for several Western Indian Ocean (WIO) populations. By comparing our sequences to recently published ones, we showed, for the first time, that Cabo Verde individuals belong to the H. mabouia sensu stricto lineage and that both of its sublineages (a and b) occur there. Both haplotypes are also in Madeira, which indicates a connection between these archipelagos, possibly related to the past Portuguese trading routes. Across the WIO, results clarified the identity of many island and coastal populations, showing that this likely invasive H. mabouia lineage is widespread in the region, including northern Madagascar, with important conservation implications. Colonisation origins were difficult to access due to the wide geographical spread of these haplotypes; thus, several possible scenarios were outlined. The introduction of this species throughout western and eastern Africa may threaten endemic taxa and needs to be closely monitored. Full article

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17 pages, 2978 KiB

Open AccessArticle

Seasonal Adaptation: Geographic Photoperiod–Temperature Patterns Explain Genetic Variation in the Common Vole Tsh Receptor

by Laura van Rosmalen, Robin Schepers, Wensi Hao, Anna S. Przybylska-Piech, Jeremy S. Herman, Joanna Stojak, Jan M. Wójcik, Louis van de Zande, Jeremy B. Searle and Roelof A. Hut

Genes 2023, 14(2), 292; https://doi.org/10.3390/genes14020292 - 22 Jan 2023

Cited by 1 | Viewed by 2039

Abstract

The vertebrate photoperiodic neuroendocrine system uses the photoperiod as a proxy to time the annual rhythms in reproduction. The thyrotropin receptor (TSHR) is a key protein in the mammalian seasonal reproduction pathway. Its abundance and function can tune sensitivity to the photoperiod. To [...] Read more.

The vertebrate photoperiodic neuroendocrine system uses the photoperiod as a proxy to time the annual rhythms in reproduction. The thyrotropin receptor (TSHR) is a key protein in the mammalian seasonal reproduction pathway. Its abundance and function can tune sensitivity to the photoperiod. To investigate seasonal adaptation in mammals, the hinge region and the first part of the transmembrane domain of the Tshr gene were sequenced for 278 common vole (Microtus arvalis) specimens from 15 localities in Western Europe and 28 localities in Eastern Europe. Forty-nine single nucleotide polymorphisms (SNPs; twenty-two intronic and twenty-seven exonic) were found, with a weak or lack of correlation with pairwise geographical distance, latitude, longitude, and altitude. By applying a temperature threshold to the local photoperiod–temperature ellipsoid, we obtained a predicted critical photoperiod (pCPP) as a proxy for the spring onset of local primary food production (grass). The obtained pCPP explains the distribution of the genetic variation in Tshr in Western Europe through highly significant correlations with five intronic and seven exonic SNPs. The relationship between pCPP and SNPs was lacking in Eastern Europe. Thus, Tshr, which plays a pivotal role in the sensitivity of the mammalian photoperiodic neuroendocrine system, was targeted by natural selection in Western European vole populations, resulting in the optimized timing of seasonal reproduction. Full article

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9 pages, 1185 KiB

Open AccessCommunication

Sorted Bulls’ X-Chromosome-Bearing Spermatozoa Show Increased GAPDHS Activity Correlating with Motility

by Anna A. Kapitonova, Vladimir I. Muronetz and Denis V. Pozdyshev

Genes 2023, 14(1), 235; https://doi.org/10.3390/genes14010235 - 16 Jan 2023

Viewed by 2094

Abstract

Sperm sexing is a technique for spermatozoa sorting into populations enriched with X- or Y-chromosome-bearing cells and is widely used in the dairy industry. Investigation of the characteristics of sorted semen is of practical interest, because it could contribute to the enhancement of [...] Read more.

Sperm sexing is a technique for spermatozoa sorting into populations enriched with X- or Y-chromosome-bearing cells and is widely used in the dairy industry. Investigation of the characteristics of sorted semen is of practical interest, because it could contribute to the enhancement of sexed semen fertility characteristics, which are currently lower than those of conventional semen. Comparison of a spermatozoa population enriched with X-chromosome-bearing cells to a mixed population is also intriguing in the context of potential differences that drive the mechanisms of primary sex-ratio determination. In this work, sexed (X spermatozoa) and conventional spermatozoa of Holstein bulls were analyzed for the content and enzymatic activity of GAPDHS, a sperm-specific isoform of glyceraldehyde-3-phosphate dehydrogenase that plays a significant role in the regulation of flagellar activity. No difference in the amount of this glycolysis enzyme per cell was revealed, but, notably, GAPDHS enzymatic activity in the sexed samples was significantly higher. Enzymatic activity among the group of sexed but not conventional sperm samples positively correlated with spermatozoa motility, which indicates the significant role of this enzyme for the sorted cells population. Full article

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12 pages, 2327 KiB

Open AccessEditor’s ChoiceArticle

Cytogenetic Analysis of Seven Species of Gekkonid and Phyllodactylid Geckos

by Gabriela Chrostek, Aleksandra Domaradzka, Alona Yurchenko, Lukáš Kratochvíl, Sofia Mazzoleni and Michail Rovatsos

Genes 2023, 14(1), 178; https://doi.org/10.3390/genes14010178 - 9 Jan 2023

Cited by 5 | Viewed by 2627

Abstract

Geckos (Gekkota), the species-rich clade of reptiles with more than 2200 currently recognized species, demonstrate a remarkable variability in diploid chromosome numbers (2n = 16–48) and mode of sex determination. However, only a small fraction of gekkotan species have been studied with cytogenetic [...] Read more.

Geckos (Gekkota), the species-rich clade of reptiles with more than 2200 currently recognized species, demonstrate a remarkable variability in diploid chromosome numbers (2n = 16–48) and mode of sex determination. However, only a small fraction of gekkotan species have been studied with cytogenetic methods. Here, we applied both conventional (karyotype reconstruction and C-banding) and molecular (fluorescence in situ hybridization with probes for rDNA loci and telomeric repeats) cytogenetic analyses in seven species of geckos, namely Blaesodactylus boivini, Chondrodactylus laevigatus, Gekko badenii, Gekko cf. lionotum, Hemidactylus sahgali, Homopholis wahlbergii (Gekkonidae) and Ptyodactylus togoensis (Phyllodactylidae), in order to provide further insights into the evolution of karyotypes in geckos. Our analysis revealed the presence of interstitial telomeric repeats in four species, but we were not able to conclude if they are remnants of previous chromosome rearrangements or were formed by an accumulation of telomeric-like satellite motifs. Even though sex chromosomes were previously identified in several species from the genera Hemidactylus and Gekko by cytogenetic and/or genomic methods, they were not detected by us in any examined species. Our examined species either have poorly differentiated sex chromosomes or, possibly, environmental sex determination. Future studies should explore the effect of temperature and conduct genome-wide analyses in order to identify the mode of sex determination in these species. Full article

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2022

Jump to: 2024, 2023, 2021

15 pages, 2062 KiB

Open AccessArticle

Sex Differences in Response to Marek’s Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome

by Ehud Lipkin, Jacqueline Smith, Morris Soller, David W. Burt and Janet E. Fulton

Genes 2023, 14(1), 20; https://doi.org/10.3390/genes14010020 - 21 Dec 2022

Viewed by 2042

Abstract

Marek’s Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome [...] Read more.

Marek’s Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome (GGZ) a particularly attractive target to study the chicken MD response. Previously, we used a Hy-Line F₆ population from a full-sib advanced intercross line to map MD QTL regions (QTLRs) on all chicken autosomes. Here, we mapped MD QTLRs on GGZ in the previously utilized F₆ population with individual genotypes and phenotypes, and in eight elite commercial egg production lines with daughter-tested sires and selective DNA pooling (SDP). Four MD QTLRs were found from each analysis. Some of these QTLRs overlap regions from previous reports. All QTLRs were tested by individuals from the same eight lines used in the SDP and genotyped with markers located within and around the QTLRs. All QTLRs were confirmed. The results exemplify the complexity of MD resistance in chickens and the complex distribution of p-values and Linkage Disequilibrium (LD) pattern and their effect on localization of the causative elements. Considering the fragments and interdigitated LD blocks while using LD to aid localization of causative elements, one must look beyond the non-significant markers, for possible distant markers and blocks in high LD with the significant block. The QTLRs found here may explain at least part of the gender differences in MD tolerance, and provide targets for mitigating the effects of MD. Full article

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14 pages, 1705 KiB

Open AccessArticle

Characterising Mitochondrial Capture in an Iberian Shrew

by Henry D. Kunerth, Joaquim T. Tapisso, Raul Valente, Maria da Luz Mathias, Paulo C. Alves, Jeremy B. Searle, Rodrigo Vega and Joana Paupério

Genes 2022, 13(12), 2228; https://doi.org/10.3390/genes13122228 - 27 Nov 2022

Cited by 3 | Viewed by 1811

Abstract

Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of [...] Read more.

Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus. Full article

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13 pages, 2844 KiB

Open AccessArticle

Characterization, Comparison of Two New Mitogenomes of Crocodile Newts Tylototriton (Caudata: Salamandridae), and Phylogenetic Implications

by Jin-Xiu Wang, Xiang-Ying Lan, Qing-Hua Luo, Zhi-Rong Gu, Qiang Zhou, Ming-Yao Zhang, You-Xiang Zhang and Wan-Sheng Jiang

Genes 2022, 13(10), 1878; https://doi.org/10.3390/genes13101878 - 17 Oct 2022

Cited by 5 | Viewed by 2028

Abstract

Mitochondrial genomes (mitogenomes) are valuable resources in molecular and evolutionary studies, such as phylogeny and population genetics. The complete mitogenomes of two crocodile newts, Tylototriton broadoridgus and Tylototriton gaowangjienensis, were sequenced, assembled, and annotated for the first time using next-generation sequencing. The [...] Read more.

Mitochondrial genomes (mitogenomes) are valuable resources in molecular and evolutionary studies, such as phylogeny and population genetics. The complete mitogenomes of two crocodile newts, Tylototriton broadoridgus and Tylototriton gaowangjienensis, were sequenced, assembled, and annotated for the first time using next-generation sequencing. The complete mitogenomes of T. broadoridgus and T. gaowangjienensis were 16,265 bp and 16,259 bp in lengths, which both composed of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 control region. The two mitogenomes had high A + T content with positive AT-skew and negative GC-skew patterns. The ratio of non-synonymous and synonymous substitutions showed that, relatively, the ATP8 gene evolved the fastest and COI evolved the slowest among the 13 PCGs. Phylogenetic trees from BI and ML analyses resulted in identical topologies, where the Tylototriton split into two groups corresponding to two subgenera. Both T. broadoridgus and T. gaowangjienensis sequenced here belonged to the subgenus Yaotriton, and these two species shared a tentative sister group relationship. The two mitogenomes reported in this study provided valuable data for future molecular and evolutionary studies of the genus Tylotoriton and other salamanders. Full article

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10 pages, 739 KiB

Open AccessArticle

Expression and Variations in EPAS1 Associated with Oxygen Metabolism in Sheep

by Qiming Xi, Fangfang Zhao, Jiang Hu, Jiqing Wang, Xiu Liu, Pengju Dang, Yuzhu Luo and Shaobin Li

Genes 2022, 13(10), 1871; https://doi.org/10.3390/genes13101871 - 15 Oct 2022

Cited by 1 | Viewed by 2293

Abstract

Endothelial PAS domain protein 1 gene (EPAS1) is a member of the HIF gene family. This gene encodes a transcription factor subunit that is involved in the induction of oxygen-regulated genes. Several studies have demonstrated that a mutation in EPAS1 could [...] Read more.

Endothelial PAS domain protein 1 gene (EPAS1) is a member of the HIF gene family. This gene encodes a transcription factor subunit that is involved in the induction of oxygen-regulated genes. Several studies have demonstrated that a mutation in EPAS1 could affect oxygen sensing, polycythemia, and hemoglobin level. However, whether EPAS1 mutation affects sheep oxygen metabolism is still unknown. Therefore, we explored the relationship between the variation of EPAS1 and oxygen metabolism in sheep. In this study, variations in ovine EPAS1 exon 15 were investigated in 332 Tibetan sheep and 339 Hu sheep by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. In addition, we studied the effect of these variations on blood gas in 176 Tibetan sheep and 231 Hu sheep. Finally, the mRNA expression of EPAS1 in six tissues of Hu sheep and Tibetan sheep living at different altitudes (2500 m, 3500 m, and 4500 m) was analyzed by real-time quantitative PCR (RT-qPCR). Four alleles (A, B, C, and D) were detected, and their distributions highly differed between Tibetan sheep and Hu sheep. In Tibetan sheep, B was the dominant allele, and C and D alleles were rare, whereas all four alleles were common in Hu sheep. Six single nucleotide polymorphisms (SNPs) were identified between the four alleles and one of them was non-synonymous (p.F606L). While studying the blood gas levels in Tibetan sheep and Hu sheep, one variant region was found to be associated with an elevated pO₂ and sO₂, which suggested that variations in EPAS1 are associated with oxygen metabolism in sheep. RT-qPCR results showed that EPAS1 was expressed in the six tissues of Hu sheep and Tibetan sheep at different altitudes. In addition, the expression of EPAS1 in four tissues (heart, liver, spleen, and longissimus dorsi muscle) of Hu sheep was lower than that in Tibetan sheep from three different altitudes, and the expression of EPAS1 was positively correlated with the altitude. These results indicate that the variations and expression of EPAS1 is closely related to oxygen metabolism. Full article

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16 pages, 3126 KiB

Open AccessArticle

Population Genetics of California Gray Foxes Clarify Origins of the Island Fox

by Benjamin N. Sacks, Mark J. Statham, Laurel E. K. Serieys and Seth P. D. Riley

Genes 2022, 13(10), 1859; https://doi.org/10.3390/genes13101859 - 14 Oct 2022

Cited by 3 | Viewed by 2586

Abstract

We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands <13,000 years ago and [...] Read more.

We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands <13,000 years ago and in the southern Channel Islands <6000 years ago. It is unclear whether island foxes evolved directly from mainland gray foxes transported to the islands one or more times or from a now-extinct mainland population, already diverged from the gray fox. Our 345 mitochondrial sequences, combined with previous data, confirmed island foxes to be monophyletic, tracing to a most recent common ancestor approximately 85,000 years ago. Our rooted nuclear DNA tree additionally indicated genome-wide monophyly of island foxes relative to western gray foxes, although we detected admixture in northern island foxes from adjacent mainland gray foxes, consistent with some historical gene flow. Southern California gray foxes also bore a genetic signature of admixture and connectivity to a desert population, consistent with partial replacement by a late-Holocene range expansion. Using our outgroup analysis to root previous nuclear sequence-based trees indicated reciprocal monophyly of northern versus southern island foxes. Results were most consistent with island fox origins through multiple introductions from a now-extirpated mainland population. Full article

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13 pages, 2398 KiB

Open AccessArticle

Long-Read Transcriptome of Equine Bronchoalveolar Cells

by Sophie Elena Sage, Pamela Nicholson, Tosso Leeb, Vinzenz Gerber and Vidhya Jagannathan

Genes 2022, 13(10), 1722; https://doi.org/10.3390/genes13101722 - 25 Sep 2022

Viewed by 2016

Abstract

We used Pacific Biosciences long-read isoform sequencing to generate full-length transcript sequences in equine bronchoalveolar lavage fluid (BALF) cells. Our dataset consisted of 313,563 HiFi reads comprising 805 Mb of polished sequence information. The resulting equine BALF transcriptome consisted of 14,234 full-length transcript [...] Read more.

We used Pacific Biosciences long-read isoform sequencing to generate full-length transcript sequences in equine bronchoalveolar lavage fluid (BALF) cells. Our dataset consisted of 313,563 HiFi reads comprising 805 Mb of polished sequence information. The resulting equine BALF transcriptome consisted of 14,234 full-length transcript isoforms originating from 7017 unique genes. These genes consisted of 6880 previously annotated genes and 137 novel genes. We identified 3428 novel transcripts in addition to 10,806 previously known transcripts. These included transcripts absent from existing genome annotations, transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. We provide transcript-level data for equine BALF cells as a resource to the scientific community. Full article

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13 pages, 4538 KiB

Open AccessArticle

Comparative Mitogenomics of Two Sympatric Catfishes of Exostoma (Siluriformes: Sisoridae) from the Lower Yarlung Tsangpo River and Its Application for Phylogenetic Consideration

by Zheng Gong, Wanxiang Jiang, Huizhe Feng, Yanchao Liu and Tianshun Zhu

Genes 2022, 13(9), 1615; https://doi.org/10.3390/genes13091615 - 8 Sep 2022

Cited by 1 | Viewed by 1855

Abstract

The genus Exostoma is a group of stenotopic and rheophilic glyptosternine catfishes distributed in South and Southeast Asia. So far, comprehensive studies on mitogenomics referring to this genus are very scarce. In this study, we first sequenced and annotated the complete mitochondrial genomes [...] Read more.

The genus Exostoma is a group of stenotopic and rheophilic glyptosternine catfishes distributed in South and Southeast Asia. So far, comprehensive studies on mitogenomics referring to this genus are very scarce. In this study, we first sequenced and annotated the complete mitochondrial genomes of Exostoma tibetanum and Exostoma tenuicaudatum—two sympatric congeners from the lower Yarlung Tsangpo River, Tibet, China. The mitogenomes of both species contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one light-strand origin of replication, and one control region, with lengths of 16,528 bp and 16,533 bp, respectively. The mitogenome architecture, nucleotide composition, and codon usage of protein-coding genes were almost identical between the two Exostoma species, although some estimated parameters varied. Phylogenetic analysis strongly supported the monophyly of Exostoma in the subfamily Glyptosternae, and Exostoma tibetanum had the closest relationship to Exostoma tenuicaudatum. The divergence time estimation demonstrated that these two species diverged approximately 1.51 Ma during the early Pleistocene, which was speculated to be triggered by the river system changes caused by the uplift of the southeastern Tibetan Plateau. Selection pressure analyses indicated that all protein-coding genes of Exostoma species underwent a strong purifying selection, while minority positive sites from NADH dehydrogenase complex genes were detected. These findings are expected to promote our understanding of the molecular phylogeny of the genus Exostoma and provide valuable mitogenomic resources for the subfamily Glyptosternae. Full article

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16 pages, 2643 KiB

Open AccessArticle

Genome-Wide Association Study of Parasite Resistance to Gastrointestinal Nematodes in Corriedale Sheep

by Beatriz Carracelas, Elly A. Navajas, Brenda Vera and Gabriel Ciappesoni

Genes 2022, 13(9), 1548; https://doi.org/10.3390/genes13091548 - 27 Aug 2022

Cited by 11 | Viewed by 3355

Abstract

Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sheep by single-step genome-wide association studies (ssGWAS) [...] Read more.

Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sheep by single-step genome-wide association studies (ssGWAS) using 170, 507 and 50K single nucleotide polymorphisms (SNPs). Analysis included 19,547 lambs with faecal egg counts (FEC) records, a pedigree file of 40,056 animals and 454, 711 and 383 genotypes from 170, 507 and 50K SNPs, respectively. Genomic estimated breeding values (GEBV) were obtained with single-step genomic BLUP methodology (ssGBLUP), using a univariate animal model, which included contemporary group, type of birth and age of dam as class fixed effects and age at FEC recording as covariate. The SNP effects as wells as p-values were estimated with POSTGSF90 program. Significance level was defined by a chromosome-wise False Discovery Rate of 5%. Significant genomic regions were identified in chromosomes 1, 3, 12 and 19 with the 170 SNP set, in chromosomes 7, 12 and 24 using the 507 SNP chip and only in chromosome 7 with the 50K SNP chip. Candidate genes located in these regions, using Oar_v4.0 as reference genome, were TIMP3, TLR5, LEPR and TLR9 (170 SNPs), SYNDIG1L and MGRN1 (507 SNP chip) and INO80, TLN2, TSHR and EIF2AK4 (50K SNP chip). These results validate genomic regions associated with FEC previously identified in Corriedale and other breeds and report new candidate regions for further investigation. Full article

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12 pages, 2557 KiB

Open AccessEditor’s ChoiceBrief Report

Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea

by Juan Antonio Baeza, Mei Lin Neo and Danwei Huang

Genes 2022, 13(5), 903; https://doi.org/10.3390/genes13050903 - 18 May 2022

Cited by 4 | Viewed by 2949

Abstract

The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read [...] Read more.

The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31–1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate. Full article

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13 pages, 3211 KiB

Open AccessArticle

Activation of Esterase D by FPD5 Inhibits Growth of A549 Lung Cancer Cells via JAB1/p53 Pathway

by Wen Yao, Yuejun Yang, Xinpeng Chen, Xiaoling Cui, Bangzhao Zhou, Baoxiang Zhao, Zhaomin Lin and Junying Miao

Genes 2022, 13(5), 786; https://doi.org/10.3390/genes13050786 - 28 Apr 2022

Cited by 7 | Viewed by 3309

Abstract

Esterase D (ESD) is widely distributed in mammals, and it plays an important role in drug metabolism, detoxification, and biomarkers and is closely related to the development of tumors. In our previous work, we found that a chemical small-molecule fluorescent pyrazoline derivative, FPD5, [...] Read more.

Esterase D (ESD) is widely distributed in mammals, and it plays an important role in drug metabolism, detoxification, and biomarkers and is closely related to the development of tumors. In our previous work, we found that a chemical small-molecule fluorescent pyrazoline derivative, FPD5, an ESD activator, could inhibit tumor growth by activating ESD, but its molecular mechanism is still unclear. Here, by using RNA interference (RNAi), andco-immunoprecipitation techniques, we found that ESD suppressed the nucleus exportation of p53 through reducing the interaction between p53 and JAB1. The protein level of p53 in the nucleus was upregulated and the downstream targets of p53 were found by Human Gene Expression Array. p53 inhibited the expression of CDCA8 and CDC20. Lastly, the cell cycle of A549 cells was arrested at the G0/G1 phase. Together, our data suggest that ESD inhibited the cancer cell growth by arresting the cell cycle of A549 cells via the JAB1/p53 signaling pathway. Our findings provide a new insight into how to inhibit the growth of lung cancer with the activation of ESD by FPD5. Full article

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16 pages, 1480 KiB

Open AccessArticle

Transcriptomics of Wet Skin Biopsies Predict Early Radiation-Induced Hematological Damage in a Mouse Model

by Abdulnaser Alkhalil, John Clifford, Stacy Ann Miller, Aarti Gautam, Marti Jett, Rasha Hammamieh, Lauren T. Moffatt and Jeffrey W. Shupp

Genes 2022, 13(3), 538; https://doi.org/10.3390/genes13030538 - 18 Mar 2022

Viewed by 2485

Abstract

The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using [...] Read more.

The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using wet skin (blood/skin) biopsies obtained at hour 2 and days 4, 7, 21, and 28 from a mouse radiation model. Analysis of significantly differentially transcribed genes (SDTG; p ≤ 0.05 and FC ≥ 2) during the first post-exposure week identified the glycoprotein 6 (GP-VI) signaling, the dendritic cell maturation, and the intrinsic prothrombin activation pathways as the top modulated pathways with stable inactivation after lethal exposures (20 Gy) and intermittent activation after sublethal (1, 3, 6 Gy) exposure time points (TPs). Interestingly, these pathways were inactivated in the late TPs after sublethal exposure in concordance with a delayed deleterious effect. Modulated transcription of a variety of collagen types, laminin, and peptidase genes underlay the modulated functions of these hematologically important pathways. Several other SDTGs related to platelet and leukocyte development and functions were identified. These results outlined genetic determinants that were crucial to clinically documented radiation-induced hematological and skin damage with potential countermeasure applications. Full article

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2021

Jump to: 2024, 2023, 2022

18 pages, 4896 KiB

Open AccessArticle

Transcriptome Analysis of Neuroendocrine Regulation of Ovine Hypothalamus-Pituitary-Ovary Axis during Ovine Anestrus and the Breeding Season

by Yingjie Zhong, Ran Di, Yang Yang, Qiuyue Liu and Mingxing Chu

Genes 2021, 12(12), 1861; https://doi.org/10.3390/genes12121861 - 24 Nov 2021

Cited by 9 | Viewed by 2691

Abstract

Most sheep are seasonal estrus, and they breed in autumn when the days get shorter. Seasonal estrus is an important factor that affects the productivity and fertility of sheep. The key point to solve this problem is to explore the regulation mechanism of [...] Read more.

Most sheep are seasonal estrus, and they breed in autumn when the days get shorter. Seasonal estrus is an important factor that affects the productivity and fertility of sheep. The key point to solve this problem is to explore the regulation mechanism of estrus in sheep. Therefore, in this study, transcriptomic sequencing technology was used to identify differentially expressed mRNAs in the hypothalamus, pituitary and ovary of Small Tail Han sheep (year-round estrus) and tan sheep (seasonal estrus) among luteal, proestrus and estrus stages. There were 256,923,304,156 mRNAs being identified in the hypothalamus, pituitary and ovary, respectively. Functional analysis showed that the photosensor, leucine and isoleucine biosynthesis pathways were enriched significantly. It is speculated that photoperiod may initiate estrus by stimulating the corresponding pathways in hypothalamus. ODC1, PRLH, CRYBB2, SMAD5, OPN1SW, TPH1 are believed to be key genes involved in the estrogen process. In conclusion, this study expanded the database of indigenous sheep breeds, and also provided new candidate genes for future genetic and molecular studies on the seasonal estrus trait in sheep. Full article

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14 pages, 2246 KiB

Open AccessArticle

Insights into the Evolution of Spermatogenesis-Related Ubiquitin–Proteasome System Genes in Abdominal Testicular Laurasiatherians

by Xiaoyue Ding, Li Cao, Yu Zheng, Xu Zhou, Xiaofang He, Shixia Xu and Wenhua Ren

Genes 2021, 12(11), 1780; https://doi.org/10.3390/genes12111780 - 10 Nov 2021

Cited by 1 | Viewed by 2570

Abstract

During embryonic development in mammals, the testicles generally descend into the scrotum, making the testicular temperature 2–4 °C lower than the core temperature via heat exchange and clearance, and thus more beneficial for normal spermatogenesis. Failure to descend, known as cryptorchidism, carries a [...] Read more.

During embryonic development in mammals, the testicles generally descend into the scrotum, making the testicular temperature 2–4 °C lower than the core temperature via heat exchange and clearance, and thus more beneficial for normal spermatogenesis. Failure to descend, known as cryptorchidism, carries a series of risks such as infertility and testicular cancer. However, some mammals have evolved abdominal testes while maintaining healthy reproduction. To explore the underlying molecular mechanism, we conducted comparative genomic analyses and functional assays on the spermatogenesis-related ubiquitin–proteasome system (UPS) genes essential to sperm formation in representative laurasiatherians. Here, positive selection and rapid evolution of spermatogenesis-related UPS genes were identified in the abdominal testicular laurasiatherians. Moreover, potential convergent amino acids were found between distantly related species with similar abdominal testicles and functional analyses showed RNF8 (V437I) in abdominal testicular species (437I) has a stronger ubiquitination ability, which suggests that the mammals with abdominal testes might exhibit enhanced sperm cell histone clearance to maintain sperm formation. This evidence implies that, in response to “cryptorchidism injury”, spermatogenesis-related UPS genes in the abdominal testicular species might have undergone adaptive evolution to stabilize sperm formation. Thus, our study could provide some novel insights into the reproductive adaptation in abdominal testicular mammals. Full article

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