Genes

13 pages, 2604 KiB

Open AccessArticle

Basal Levels of CD18 Antigen Presenting Cells in Cow Milk Associate with Copy Number Variation of Fc Gamma Receptors

by Eyal Seroussi, Shlomo E. Blum, Oleg Krifucks, Andrey Shirak, Shamay Jacoby and Gabriel Leitner

Genes 2020, 11(8), 952; https://doi.org/10.3390/genes11080952 - 18 Aug 2020

Cited by 4 | Viewed by 2613

Abstract

Differentiation of cells by flow cytometry provides informative somatic cell counts (SCCs) that allow analyzing leukocyte population patterns in udder infections of different etiologies. Postulating that this approach also enhances the statistical power to detect genetic variants linked to cell levels in milk [...] Read more.

Differentiation of cells by flow cytometry provides informative somatic cell counts (SCCs) that allow analyzing leukocyte population patterns in udder infections of different etiologies. Postulating that this approach also enhances the statistical power to detect genetic variants linked to cell levels in milk of healthy mammary glands, we used monoclonal antibodies anti-CD18, anti-CD4, anti--CD14, and anti-PMN to count cells presenting these surface antigens, and performed a genome-wide association study of these counts in 125 Israeli Holsteins genotyped using SNP BeadChips. We identified an informative haplotype of 15 SNPs in the centromeric end of BTA3 that was strongly associated with CD18 cells (p < 2.3 × 10⁻⁹). Within this region, examination of the network of genes interacting with ITGB2 (CD18) indicated an Fc-γ-receptor gene cluster, including FCGR2A (CD32). Sanger-sequence analysis of FCGR2s-linked exon 3 variation to CD18 counts. Meta-analysis of RNA-Seq data revealed a significant negative correlation (R = −0.51) between expression of CD32 and CD18 in milk. Assembly of DNA-Seq reads uncovered FCGR copy-number variation and a variant, designated V7, was abundant in dairy cattle, probably reflecting adaptation to selection pressure for low SCC in Holstein milk. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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14 pages, 2426 KiB

Open AccessArticle

Generation of Marker-Free pbd-2 Knock-in Pigs Using the CRISPR/Cas9 and Cre/loxP Systems

by Jing Huang, Antian Wang, Chao Huang, Yufan Sun, Bingxiao Song, Rui Zhou and Lu Li

Genes 2020, 11(8), 951; https://doi.org/10.3390/genes11080951 - 18 Aug 2020

Cited by 19 | Viewed by 6574

Abstract

Porcine β-defensin 2 (PBD-2), expressed by different tissues of pigs, is a multifunctional cationic peptide with antimicrobial, immunomodulatory and growth-promoting abilities. As the latest generation of genome-editing tool, CRISPR/Cas9 system makes it possible to enhance the expression of PBD-2 in pigs by site-specific [...] Read more.

Porcine β-defensin 2 (PBD-2), expressed by different tissues of pigs, is a multifunctional cationic peptide with antimicrobial, immunomodulatory and growth-promoting abilities. As the latest generation of genome-editing tool, CRISPR/Cas9 system makes it possible to enhance the expression of PBD-2 in pigs by site-specific knock-in of pbd-2 gene into the pig genome. In this study, we aimed to generate marker-free pbd-2 knock-in pigs using the CRISPR/Cas9 and Cre/loxP systems. Two copies of pbd-2 gene linked by a T2A sequence were inserted into the porcine Rosa26 locus through CRISPR/Cas9-mediated homology-directed repair. The floxed selectable marker gene neoR, used for G418 screening of positive cell clones, was removed by cell-penetrating Cre recombinase with a recombination efficiency of 48.3%. Cloned piglets were produced via somatic cell nuclear transfer and correct insertion of pbd-2 genes was confirmed by PCR and Southern blot. Immunohistochemistry and immunofluorescence analyses indicated that expression levels of PBD-2 in different tissues of transgenic (TG) piglets were significantly higher than those of their wild-type (WT) littermates. Bactericidal assays demonstrated that there was a significant increase in the antimicrobial properties of the cell culture supernatants of porcine ear fibroblasts from the TG pigs in comparison to those from the WT pigs. Altogether, our study improved the protein expression level of PBD-2 in pigs by site-specific integration of pbd-2 into the pig genome, which not only provided an effective pig model to study the anti-infection mechanisms of PBD-2 but also a promising genetic material for the breeding of disease-resistant pigs. Full article

(This article belongs to the Special Issue Pig Genomics and Genetics)

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12 pages, 1840 KiB

Open AccessArticle

Manganese Ions Individually Alter the Reverse Transcription Signature of Modified Ribonucleosides

by Marco Kristen, Johanna Plehn, Virginie Marchand, Kristina Friedland, Yuri Motorin, Mark Helm and Stephan Werner

Genes 2020, 11(8), 950; https://doi.org/10.3390/genes11080950 - 18 Aug 2020

Cited by 15 | Viewed by 4209

Abstract

Reverse transcription of RNA templates containing modified ribonucleosides transfers modification-related information as misincorporations, arrest or nucleotide skipping events to the newly synthesized cDNA strand. The frequency and proportion of these events, merged from all sequenced cDNAs, yield a so-called RT signature, characteristic for [...] Read more.

Reverse transcription of RNA templates containing modified ribonucleosides transfers modification-related information as misincorporations, arrest or nucleotide skipping events to the newly synthesized cDNA strand. The frequency and proportion of these events, merged from all sequenced cDNAs, yield a so-called RT signature, characteristic for the respective RNA modification and reverse transcriptase (RT). While known for DNA polymerases in so-called error-prone PCR, testing of four different RTs by replacing Mg²⁺ with Mn²⁺ in reaction buffer revealed the immense influence of manganese chloride on derived RT signatures, with arrest rates on m¹A positions dropping from 82% down to 24%. Additionally, we observed a vast increase in nucleotide skipping events, with single positions rising from 4% to 49%, thus implying an enhanced read-through capability as an effect of Mn²⁺ on the reverse transcriptase, by promoting nucleotide skipping over synthesis abortion. While modifications such as m¹A, m²₂G, m¹G and m³C showed a clear influence of manganese ions on their RT signature, this effect was individual to the polymerase used. In summary, the results imply a supporting effect of Mn²⁺ on reverse transcription, thus overcoming blockades in the Watson-Crick face of modified ribonucleosides and improving both read-through rate and signal intensity in RT signature analysis. Full article

(This article belongs to the Special Issue Functions and Dynamics of RNA Modifications)

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13 pages, 1725 KiB

Open AccessArticle

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

by Sureshnee Pillay, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Stacey Mattison, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyile, James Emmanuel San, Vagner Fonseca, Marta Giovanetti, Luiz Carlos Alcantara, Jr. and Tulio de Oliveira

Genes 2020, 11(8), 949; https://doi.org/10.3390/genes11080949 - 17 Aug 2020

Cited by 56 | Viewed by 13780

Abstract

The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [...] Read more.

The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium. Full article

(This article belongs to the Special Issue Sequencing Techniques and Genomics Technologies to Help with Diagnostics and Virus Characterization – Focus on COVID 19)

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2 pages, 159 KiB

Open AccessCorrection

Correction: Kim, N.K., et al. Study of the Association between microRNA (miR-25T>C, miR-32C>A, miR-125C>T, and miR-222G>T) Polymorphisms and the Risk of Recurrent Pregnancy Loss in Korean Women. Genes 2020, 11, 354

by Jeong Yong Lee, Jung Oh Kim, Han Sung Park, Chang Soo Ryu, Ji Hyang Kim, Young Ran Kim, Woo Sik Lee, Jung Ryeol Lee and Nam Keun Kim

Genes 2020, 11(8), 948; https://doi.org/10.3390/genes11080948 - 17 Aug 2020

Cited by 3 | Viewed by 1935

Abstract

The authors wish to make a correction to the published version of their paper [...] Full article

(This article belongs to the Special Issue Genetic Aspects of Female Infertility)

6 pages, 529 KiB

Open AccessCase Report

Combined PTPN11 and MYBPC3 Gene Mutations in an Adult Patient with Noonan Syndrome and Hypertrophic Cardiomyopathy

by Martina Caiazza, Marta Rubino, Emanuele Monda, Annalisa Passariello, Adelaide Fusco, Annapaola Cirillo, Augusto Esposito, Anna Pierno, Federica De Fazio, Roberta Pacileo, Eloisa Evangelista, Giuseppe Pacileo, Maria Giovanna Russo and Giuseppe Limongelli

Genes 2020, 11(8), 947; https://doi.org/10.3390/genes11080947 - 17 Aug 2020

Cited by 19 | Viewed by 4516

Abstract

In this report, an atypical case of Noonan syndrome (NS) associated with sarcomeric hypertrophic cardiomyopathy (HCM) in a 33-year-old patient was described. Genetic testing revealed two different disease-causing mutations: a mutation in the PTPN11 gene, explaining NS, and a mutation in the MYBPC3 [...] Read more.

In this report, an atypical case of Noonan syndrome (NS) associated with sarcomeric hypertrophic cardiomyopathy (HCM) in a 33-year-old patient was described. Genetic testing revealed two different disease-causing mutations: a mutation in the PTPN11 gene, explaining NS, and a mutation in the MYBPC3 gene, known to be associated with HCM. This case exemplifies the challenge in achieving a definite etiological diagnosis in patients with HCM and the need to exclude other diseases mimicking this condition (genocopies or phenocopies). Compound heterozygous mutations are rare but possible in HCM patients. In conclusion, this study highlights the important role of genetic testing as a necessary diagnostic tool for performing a definitive etiological diagnosis of HCM. Full article

(This article belongs to the Special Issue Cardiovascular Genetics)

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11 pages, 447 KiB

Open AccessArticle

Assembling Reads Improves Taxonomic Classification of Species

by Quang Tran and Vinhthuy Phan

Genes 2020, 11(8), 946; https://doi.org/10.3390/genes11080946 - 17 Aug 2020

Cited by 15 | Viewed by 3348

Abstract

Most current approach to metagenomic classification employ short next generation sequencing (NGS) reads that are present in metagenomic samples to identify unique genomic regions. NGS reads, however, might not be long enough to differentiate similar genomes. This suggests a potential for using longer [...] Read more.

Most current approach to metagenomic classification employ short next generation sequencing (NGS) reads that are present in metagenomic samples to identify unique genomic regions. NGS reads, however, might not be long enough to differentiate similar genomes. This suggests a potential for using longer reads to improve classification performance. Presently, longer reads tend to have a higher rate of sequencing errors. Thus, given the pros and cons, it remains unclear which types of reads is better for metagenomic classification. We compared two taxonomic classification protocols: a traditional assembly-free protocol and a novel assembly-based protocol. The novel assembly-based protocol consists of assembling short-reads into longer reads, which will be subsequently classified by a traditional taxonomic classifier. We discovered that most classifiers made fewer predictions with longer reads and that they achieved higher classification performance on synthetic metagenomic data. Generally, we observed a significant increase in precision, while having similar recall rates. On real data, we observed similar characteristics that suggest that the classifiers might have similar performance of higher precision with similar recall with longer reads. We have shown a noticeable difference in performance between assembly-based and assembly-free taxonomic classification. This finding strongly suggests that classifying species in metagenomic environments can be achieved with higher overall performance simply by assembling short reads. Further, it also suggests that long-read technologies might be better for species classification. Full article

(This article belongs to the Special Issue Microbiome Analysis Techniques and Discovery)

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15 pages, 1108 KiB

Open AccessArticle

Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution

by Michelle Jonika, Johnathan Lo and Heath Blackmon

Genes 2020, 11(8), 945; https://doi.org/10.3390/genes11080945 - 16 Aug 2020

Cited by 8 | Viewed by 5448

Abstract

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. [...] Read more.

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes. Full article

(This article belongs to the Special Issue Causes and Consequences of Chromosomal Aberrations)

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18 pages, 3149 KiB

Open AccessArticle

Sexual Difference in the Optimum Environmental Conditions for Growth and Maturation of the Brown Alga Undaria pinnatifida in the Gametophyte Stage

by Yoichi Sato, Hikaru Endo, Hiroki Oikawa, Koichi Kanematsu, Hiroyuki Naka, Miho Mogamiya, Shigeyuki Kawano and Yusuke Kazama

Genes 2020, 11(8), 944; https://doi.org/10.3390/genes11080944 - 16 Aug 2020

Cited by 9 | Viewed by 4900

Abstract

Undaria pinnatifida is an annual brown kelp growing naturally in coastal areas as a major primary producer in temperate regions and is cultivated on an industrial scale. Kelps have a heteromorphic life cycle characterized by a macroscopic sporophyte and microscopic sexual gametophytes. The [...] Read more.

Undaria pinnatifida is an annual brown kelp growing naturally in coastal areas as a major primary producer in temperate regions and is cultivated on an industrial scale. Kelps have a heteromorphic life cycle characterized by a macroscopic sporophyte and microscopic sexual gametophytes. The sex-dependent effects of different environmental factors on the growth and maturation characteristics of the gametophyte stage were investigated using response surface methodology. Gametophytes were taken from three sites in Japan: Iwate Prefecture, Tokushima Prefecture, and Kagoshima Prefecture in order to confirm the sexual differences in three independent lines. Optimum temperature and light intensity were higher for males (20.7–20.9 °C and 28.6–33.7 µmol m⁻² s⁻¹, respectively) than females (16.5–19.8 °C and 26.9–32.5 µmol m⁻² s⁻¹), and maturity progressed more quickly in males than females. Optimum wavelengths of light for growth and maturation of the gametophytes were observed for both blue (400–500 nm, λ_max 453 nm) and green (500–600 nm; λ_max 525 nm) lights and were sex-independent. These characteristics were consistent among the three regional lines. Slower growth optima and progress of maturation could be important for female gametophytes to restrict fertilization and sporophyte germination to the lower water temperatures of autumn and winter, and suggest that the female gametophyte may be more sensitive to temperature than the male. The sexual differences in sensitivity to environmental factors improved the synchronicity of sporeling production. Full article

(This article belongs to the Special Issue Unraveling the Genetic Control of Sexual Reproduction in Wild Plants and Their Domesticated Cousins)

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13 pages, 1660 KiB

Open AccessArticle

Distinct Alteration of Gene Expression Programs in the Small Intestine of Male and Female Mice in Response to Ablation of Intestinal Fabp Genes

by Yiheng Chen and Luis B. Agellon

Genes 2020, 11(8), 943; https://doi.org/10.3390/genes11080943 - 15 Aug 2020

Cited by 8 | Viewed by 3056

Abstract

Fatty acid-binding proteins (Fabps) make up a family of widely distributed cytoplasmic lipid-binding proteins. The small intestine contains three predominant Fabp species, Fabp1, Fabp2, and Fabp6. Our previous studies showed that Fabp2 and Fabp6 gene-disrupted mice exhibited sexually dimorphic phenotypes. In this study, [...] Read more.

Fatty acid-binding proteins (Fabps) make up a family of widely distributed cytoplasmic lipid-binding proteins. The small intestine contains three predominant Fabp species, Fabp1, Fabp2, and Fabp6. Our previous studies showed that Fabp2 and Fabp6 gene-disrupted mice exhibited sexually dimorphic phenotypes. In this study, we carried out a systematic comparative analysis of the small intestinal transcriptomes of 10 week-old wild-type (WT) and Fabp gene-disrupted male and female mice. We found that the small intestinal transcriptome of male and female mice showed key differences in the gene expression profiles that affect major biological processes. The deletion of specific Fabp genes induced unique and sex-specific changes in the gene expression program, although some differentially expressed genes in certain genotypes were common to both sexes. Functional annotation and interaction network analyses revealed that the number and type of affected pathways, as well as the sets of interacting nodes in each of the Fabp genotypes, are partitioned by sex. To our knowledge, this is the first time that sex differences were identified and categorized at the transcriptome level in mice lacking different intestinal Fabps. The distinctive transcriptome profiles of WT male and female small intestine may predetermine the nature of transcriptional reprogramming that manifests as sexually dimorphic responses to the ablation of intestinal Fabp genes. Full article

(This article belongs to the Special Issue Sex/Gender Differences in Health from Omics Approaches)

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19 pages, 258 KiB

Open AccessReview

Advances in Genomics for Drug Development

by Roberto Spreafico, Leah B. Soriaga, Johannes Grosse, Herbert W. Virgin and Amalio Telenti

Genes 2020, 11(8), 942; https://doi.org/10.3390/genes11080942 - 15 Aug 2020

Cited by 26 | Viewed by 7782

Abstract

Drug development (target identification, advancing drug leads to candidates for preclinical and clinical studies) can be facilitated by genetic and genomic knowledge. Here, we review the contribution of population genomics to target identification, the value of bulk and single cell gene expression analysis [...] Read more.

Drug development (target identification, advancing drug leads to candidates for preclinical and clinical studies) can be facilitated by genetic and genomic knowledge. Here, we review the contribution of population genomics to target identification, the value of bulk and single cell gene expression analysis for understanding the biological relevance of a drug target, and genome-wide CRISPR editing for the prioritization of drug targets. In genomics, we discuss the different scope of genome-wide association studies using genotyping arrays, versus exome and whole genome sequencing. In transcriptomics, we discuss the information from drug perturbation and the selection of biomarkers. For CRISPR screens, we discuss target discovery, mechanism of action and the concept of gene to drug mapping. Harnessing genetic support increases the probability of drug developability and approval. Full article

(This article belongs to the Section Technologies and Resources for Genetics)

24 pages, 4080 KiB

Open AccessArticle

The Role of APOSTART in Switching between Sexuality and Apomixis in Poa pratensis

by Gianpiero Marconi, Domenico Aiello, Bryan Kindiger, Loriano Storchi, Alessandro Marrone, Lara Reale, Niccolò Terzaroli and Emidio Albertini

Genes 2020, 11(8), 941; https://doi.org/10.3390/genes11080941 - 14 Aug 2020

Cited by 10 | Viewed by 4246

Abstract

The production of seeds without sex is considered the holy grail of plant biology. The transfer of apomixis to various crop species has the potential to transform plant breeding, since it will allow new varieties to retain valuable traits thorough asexual reproduction. Therefore, [...] Read more.

The production of seeds without sex is considered the holy grail of plant biology. The transfer of apomixis to various crop species has the potential to transform plant breeding, since it will allow new varieties to retain valuable traits thorough asexual reproduction. Therefore, a greater molecular understanding of apomixis is fundamental. In a previous work we identified a gene, namely APOSTART, that seemed to be involved in this asexual mode of reproduction, which is very common in Poa pratensis L., and here we present a detailed work aimed at clarifying its role in apomixis. In situ hybridization showed that PpAPOSTART is expressed in reproductive tissues from pre-meiosis to embryo development. Interestingly, it is expressed early in few nucellar cells of apomictic individuals possibly switching from a somatic to a reproductive cell as in aposporic apomixis. Moreover, out of 13 APOSTART members, we identified one, APOSTART_6, as specifically expressed in flower tissue. APOSTART_6 also exhibited delayed expression in apomictic genotypes when compared with sexual types. Most importantly, the SCAR (Sequence Characterized Amplified Region) derived from the APOSTART_6 sequence completely co-segregated with apomixis. Full article

(This article belongs to the Special Issue Molecular Basis of Apomixis in Plants)

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15 pages, 1431 KiB

Open AccessArticle

Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis

by Alexandra S. Abdelmanova, Veronika R. Kharzinova, Valeria V. Volkova, Arina I. Mishina, Arsen V. Dotsev, Alexander A. Sermyagin, Oxana I. Boronetskaya, Lidia V. Petrikeeva, Roman Yu Chinarov, Gottfried Brem and Natalia A. Zinovieva

Genes 2020, 11(8), 940; https://doi.org/10.3390/genes11080940 - 14 Aug 2020

Cited by 20 | Viewed by 4580

Abstract

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century [...] Read more.

Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r² = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of F_ST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle. Full article

(This article belongs to the Special Issue Research Progress and Application Prospects of Microsatellites)

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18 pages, 1322 KiB

Open AccessReview

Wnt/β-catenin Signaling in Tissue Self-Organization

by Kelvin W. Pond, Konstantin Doubrovinski and Curtis A. Thorne

Genes 2020, 11(8), 939; https://doi.org/10.3390/genes11080939 - 14 Aug 2020

Cited by 23 | Viewed by 6018

Abstract

Across metazoans, animal body structures and tissues exist in robust patterns that arise seemingly out of stochasticity of a few early cells in the embryo. These patterns ensure proper tissue form and function during early embryogenesis, development, homeostasis, and regeneration. Fundamental questions are [...] Read more.

Across metazoans, animal body structures and tissues exist in robust patterns that arise seemingly out of stochasticity of a few early cells in the embryo. These patterns ensure proper tissue form and function during early embryogenesis, development, homeostasis, and regeneration. Fundamental questions are how these patterns are generated and maintained during tissue homeostasis and regeneration. Though fascinating scientists for generations, these ideas remain poorly understood. Today, it is apparent that the Wnt/β-catenin pathway plays a central role in tissue patterning. Wnt proteins are small diffusible morphogens which are essential for cell type specification and patterning of tissues. In this review, we highlight several mechanisms described where the spatial properties of Wnt/β-catenin signaling are controlled, allowing them to work in combination with other diffusible molecules to control tissue patterning. We discuss examples of this self-patterning behavior during development and adult tissues’ maintenance. The combination of new physiological culture systems, mathematical approaches, and synthetic biology will continue to fuel discoveries about how tissues are patterned. These insights are critical for understanding the intricate interplay of core patterning signals and how they become disrupted in disease. Full article

(This article belongs to the Special Issue Wnt Signaling in Development, Regeneration and Cancer)

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13 pages, 6776 KiB

Open AccessFeature PaperArticle

A Forensic Genomics Approach for the Identification of Sister Marija Crucifiksa Kozulić

by Charla Marshall, Kimberly Sturk-Andreaggi, Erin M. Gorden, Jennifer Daniels-Higginbotham, Sidney Gaston Sanchez, Željana Bašić, Ivana Kružić, Šimun Anđelinović, Alan Bosnar, Miran Čoklo, Anja Petaros, Timothy P. McMahon, Dragan Primorac and Mitchell M. Holland

Genes 2020, 11(8), 938; https://doi.org/10.3390/genes11080938 - 14 Aug 2020

Cited by 7 | Viewed by 4275

Abstract

Sister Marija Krucifiksa Kozulić (1852–1922) was a Croatian nun who is in consideration for beatification by the Vatican, which is facilitated by the identification of her 20th-century remains. Sister Marija was buried in a tomb in Rijeka, Croatia, along with other nuns including [...] Read more.

Sister Marija Krucifiksa Kozulić (1852–1922) was a Croatian nun who is in consideration for beatification by the Vatican, which is facilitated by the identification of her 20th-century remains. Sister Marija was buried in a tomb in Rijeka, Croatia, along with other nuns including her biological sister, Tereza Kozulić (1861–1933). When the remains were exhumed in 2011, they were found in a deteriorated state and commingled with several other sets of remains. Thus, mitochondrial genome sequencing of the long bones was performed to sort the remains by mitochondrial haplotype. Two similar but unique haplotypes belonging to haplogroup H1bu were identified, and samples from these bones were subjected to autosomal short tandem repeat (STR) and single nucleotide polymorphism (SNP) sequencing. Although only partial profiles were obtained, the data were sufficient for kinship analysis with the profile of a paternal niece of Sister Marija (Fides Kozulić). The data indicate that it is 574,195-fold more likely that the two sets of skeletal remains represent 2nd-degree relatives of Fides than sisters who are unrelated to Fides. Although it is impossible to discern which set of remains belongs to Marija and which belongs to Tereza, forensic genomics methods have enabled identification of the sisters. Full article

(This article belongs to the Special Issue Forensic Mitochondrial Genomics)

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17 pages, 2332 KiB

Open AccessArticle

Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer

by Kun-Lung Li, Keisuke Nakashima, Jun Inoue and Noriyuki Satoh

Genes 2020, 11(8), 937; https://doi.org/10.3390/genes11080937 - 13 Aug 2020

Cited by 3 | Viewed by 3098

Abstract

Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, CesA, [...] Read more.

Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, CesA, in which a gene, probably transferred from bacteria, greatly impacted tunicate evolution. A Glycosyl Hydrolase Family 6 (GH6) hydrolase-like domain exists at the C-terminus of tunicate CesA, but not in cellulose synthases of other organisms. The recent discovery of another GH6 hydrolase-like gene (GH6-1) in tunicate genomes further raises the question of how tunicates acquired GH6. To examine the probable origin of these genes, we analyzed the phylogenetic relationship of GH6 proteins in tunicates and other organisms. Our analyses show that tunicate GH6s, the GH6-1 gene, and the GH6 part of the CesA gene, form two independent, monophyletic gene groups. We also compared their sequence signatures and exon splice sites. All tunicate species examined have shared splice sites in GH6-containing genes, implying ancient intron acquisitions. It is likely that the tunicate CesA and GH6-1 genes existed in the common ancestor of all extant tunicates. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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13 pages, 2459 KiB

Open AccessArticle

Stable Longitudinal Methylation Levels at the CpG Sites Flanking the CTG Repeat of DMPK in Patients with Myotonic Dystrophy Type 1

by Mathis Hildonen, Kirsten Lykke Knak, Morten Dunø, John Vissing and Zeynep Tümer

Genes 2020, 11(8), 936; https://doi.org/10.3390/genes11080936 - 13 Aug 2020

Cited by 10 | Viewed by 2705

Abstract

Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystem disorder mainly characterized by gradual muscle loss, weakness, and delayed relaxation after muscle contraction. It is caused by an expanded CTG repeat in the 3′ UTR of DMPK, which is transcribed into [...] Read more.

Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystem disorder mainly characterized by gradual muscle loss, weakness, and delayed relaxation after muscle contraction. It is caused by an expanded CTG repeat in the 3′ UTR of DMPK, which is transcribed into a toxic gain-of-function mRNA that affects the splicing of a range of other genes. The repeat is unstable, with a bias towards expansions both in somatic cells and in the germline, which results in a tendency for earlier onset with each generation, as longer repeat lengths generally correlate with earlier onset. Previous studies have found hypermethylation in the regions flanking the repeat in congenital onset DM1 and in some patients with non-congenital DM1. We used pyrosequencing to investigate blood methylation levels in 68 patients with non-congenital DM1, compare the methylation levels between the blood and muscle, and assess whether methylation levels change over time in the blood. We found higher methylation levels in the blood of DM1 patients than in healthy controls and especially in the patients who had inherited the disease allele maternally. The methylation levels remained relatively stable over time and are a strong biomarker of the disease, as well as of the maternal inheritance of the disease. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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12 pages, 5333 KiB

Open AccessArticle

Comparative Analysis of Mouse Decidualization Models at the Molecular Level

by Chong Wang, Miao Zhao, Wen-Qian Zhang, Ming-Yu Huang, Can Zhu, Jia-Peng He and Ji-Long Liu

Genes 2020, 11(8), 935; https://doi.org/10.3390/genes11080935 - 13 Aug 2020

Cited by 12 | Viewed by 3773

Abstract

The mouse is widely used to study decidualization and there are three well-established mouse models of decidualization, namely natural pregnancy decidualization (NPD), artificial decidualization (AD), and in vitro decidualization (IVD). However, the extent of similarity and difference between these models at the molecular [...] Read more.

The mouse is widely used to study decidualization and there are three well-established mouse models of decidualization, namely natural pregnancy decidualization (NPD), artificial decidualization (AD), and in vitro decidualization (IVD). However, the extent of similarity and difference between these models at the molecular level remains largely unknown. Here, we performed a comparative analysis using the RNA-seq approach. In the NPD model, which is thought to be the golden standard of mouse decidualization, we found a total of 5277 differentially expressed genes, with 3158 genes being up-regulated and 2119 genes being down-regulated. A total of 4294 differentially expressed genes were identified in the AD model: 1127 up-regulated genes and 3167 down-regulated genes. In comparison to NPD, 1977 genes were consistently expressed, whereas only 217 genes were inconsistently expressed, indicating that AD is a reliable model for mouse decidualization. In the IVD model, RNA-seq analysis revealed that 513 genes were up-regulated and 988 genes were down-regulated. Compared to NPD, 310 genes were consistently expressed, whereas 456 genes were inconsistently expressed. Moreover, although the decidualization marker Prl8a2 (prolactin family 8 subfamily a member 2) was up-regulated, the widely-used marker Alpl (alkaline phosphatase liver/bone/kidney) was down-regulated in the IVD model. Therefore, we suggest that the IVD model should be optimized to mimic NPD at the transcriptomic level. Our study contributes to an increase in the knowledge about mouse models of decidualization. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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11 pages, 1027 KiB

Open AccessArticle

Variation in the Caprine Keratin-Associated Protein 27-1 Gene is Associated with Cashmere Fiber Diameter

by Mengli Zhao, Huitong Zhou, Yuzhu Luo, Jiqing Wang, Jiang Hu, Xiu Liu, Shaobin Li, Zhiyun Hao, Xiayang Jin, Yize Song, Xinmiao Wu, Liyan Hu and Jon G. H. Hickford

Genes 2020, 11(8), 934; https://doi.org/10.3390/genes11080934 - 13 Aug 2020

Cited by 16 | Viewed by 2640

Abstract

Variation in some caprine keratin-associated protein (KAP) genes has been associated with cashmere fiber traits, but many KAP genes remain unidentified in goats. In this study, we confirm the identification of a KAP27-1 gene (KRTAP27-1) and describe its effect on cashmere [...] Read more.

Variation in some caprine keratin-associated protein (KAP) genes has been associated with cashmere fiber traits, but many KAP genes remain unidentified in goats. In this study, we confirm the identification of a KAP27-1 gene (KRTAP27-1) and describe its effect on cashmere traits in 248 Longdong cashmere goats. A polymerase chain reaction–single strand conformation polymorphism (PCR-SSCP) analysis was used to screen for sequence variation in this gene, and three sequence variants (named A to C) were found. These sequences have the highest similarity (77% identity) to a human KRTAP27-1 sequence, while sharing some homology with a predicted caprine KRTAP27-1 sequence ENSCHIG00000023347 in the goat genome construct (ARS1:CM004562.1) at chromosome 1 position 3,966,193–3,973,677 in the forward strand. There were two single nucleotide polymorphisms (SNPs) detected in the coding sequence, including one nonsynonymous SNP (c.413C/T; p.Ala138Val) and one synonymous SNP (c.495C/T). The C variant differed from A and B at c.413C/T, having cytosine in its nucleotide sequence, while the B variant differed from A and C at c.495C/T, having thymine in its nucleotide sequence. Goats of the genotypes AB and BB produced cashmere fibers of higher mean fiber diameter (MFD) than goats of genotype AA, but no difference in MFD was detected between the AB and BB goats. These results suggest that B is associated with increased MFD. Expression of the caprine KRTAP27-1 sequence was predominantly detected in the skin tissue of goats but not or only weakly detected in other tissues, including longissimus dorsi muscle, heart, kidney, liver, lung and spleen. Full article

(This article belongs to the Special Issue Complex Genetic Loci, 2nd Edition)

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16 pages, 616 KiB

Open AccessArticle

Effects of CYP1A2 and ADORA2A Genotypes on the Ergogenic Response to Caffeine in Professional Handball Players

by Alejandro Muñoz, Álvaro López-Samanes, Millán Aguilar-Navarro, David Varillas-Delgado, Jesús Rivilla-García, Víctor Moreno-Pérez and Juan Del Coso

Genes 2020, 11(8), 933; https://doi.org/10.3390/genes11080933 - 13 Aug 2020

Cited by 35 | Viewed by 6416

Abstract

Previous investigations have found that several genes may be associated with the interindividual variability to the ergogenic response to caffeine. The aim of this study is to analyze the influence of the genetic variations in CYP1A2 (−163C > A, rs762551; characterized such as [...] Read more.

Previous investigations have found that several genes may be associated with the interindividual variability to the ergogenic response to caffeine. The aim of this study is to analyze the influence of the genetic variations in CYP1A2 (−163C > A, rs762551; characterized such as “fast” (AA genotype) and “slow” caffeine metabolizers (C-carriers)) and ADORA2A (1976T > C; rs5751876; characterized by “high” (TT genotype) or “low” sensitivity to caffeine (C-carriers)) on the ergogenic response to acute caffeine intake in professional handball players. Thirty-one professional handball players (sixteen men and fifteen women; daily caffeine intake = 60 ± 25 mg·d⁻¹) ingested 3 mg·kg⁻¹·body mass (bm) of caffeine or placebo 60 min before undergoing a battery of performance tests consisting of a countermovement jump (CMJ), a sprint test, an agility test, an isometric handgrip test, and several ball throws. Afterwards, the handball players performed a simulated handball match (2 × 20 min) while movements were recorded using inertial units. Saliva samples were analyzed to determine the genotype of each player for the −163C > A polymorphism in the CYP1A2 gene (rs762551) and for the 1976T > C polymorphism in the ADORA2A gene (rs5751876). In the CYP1A2, C-allele carriers (54.8%) were compared to AA homozygotes (45.2%). In the ADORA2A, C-allele carriers (80.6%) were compared to TT homozygotes (19.4%). There was only a genotype x treatment interaction for the ball throwing from 7 m (p = 0.037) indicating that the ergogenic effect of caffeine on this test was higher in CYP1A2 AA homozygotes than in C-allele carriers. In the remaining variables, there were no genotype x treatment interactions for CYP1A2 or for ADORA2A. As a whole group, caffeine increased CMJ height, performance in the sprint velocity test, and ball throwing velocity from 9 m (2.8–4.3%, p = 0.001–0.022, effect size = 0.17–0.31). Thus, pre-exercise caffeine supplementation at a dose of 3 mg·kg⁻¹·bm can be considered as an ergogenic strategy to enhance some neuromuscular aspects of handball performance in professional handball players with low daily caffeine consumption. However, the ergogenic response to acute caffeine intake was not modulated by CYP1A2 or ADORA2A genotypes. Full article

(This article belongs to the Special Issue Genetic Influence in Exercise Performance)

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16 pages, 307 KiB

Open AccessArticle

Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

by Gabriele Senczuk, Lorenzo Guerra, Salvatore Mastrangelo, Claudia Campobasso, Kaouadji Zoubeyda, Meghelli Imane, Donata Marletta, Szilvia Kusza, Taki Karsli, Semir Bachir Souheil Gaouar, Fabio Pilla, Elena Ciani and The Bovita Consortium

Genes 2020, 11(8), 932; https://doi.org/10.3390/genes11080932 - 13 Aug 2020

Cited by 18 | Viewed by 5523

Abstract

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this [...] Read more.

Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort F_ST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle. Full article

(This article belongs to the Special Issue Coat Color Genetics)

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15 pages, 385 KiB

Open AccessArticle

A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data

by Saurav Mallik, Soumita Seth, Tapas Bhadra and Zhongming Zhao

Genes 2020, 11(8), 931; https://doi.org/10.3390/genes11080931 - 12 Aug 2020

Cited by 27 | Viewed by 5484

Abstract

DNA methylation change has been useful for cancer biomarker discovery, classification, and potential treatment development. So far, existing methods use either differentially methylated CpG sites or combined CpG sites, namely differentially methylated regions, that can be mapped to genes. However, such methylation signal [...] Read more.

DNA methylation change has been useful for cancer biomarker discovery, classification, and potential treatment development. So far, existing methods use either differentially methylated CpG sites or combined CpG sites, namely differentially methylated regions, that can be mapped to genes. However, such methylation signal mapping has limitations. To address these limitations, in this study, we introduced a combinatorial framework using linear regression, differential expression, deep learning method for accurate biological interpretation of DNA methylation through integrating DNA methylation data and corresponding TCGA gene expression data. We demonstrated it for uterine cervical cancer. First, we pre-filtered outliers from the data set and then determined the predicted gene expression value from the pre-filtered methylation data through linear regression. We identified differentially expressed genes (DEGs) by Empirical Bayes test using

Limma

. Then we applied a deep learning method, “nnet” to classify the cervical cancer label of those DEGs to determine all classification metrics including accuracy and area under curve (AUC) through 10-fold cross validation. We applied our approach to uterine cervical cancer DNA methylation dataset (NCBI accession ID: GSE30760, 27,578 features covering 63 tumor and 152 matched normal samples). After linear regression and differential expression analysis, we obtained 6287 DEGs with false discovery rate (FDR)

< 0.001

. After performing deep learning analysis, we obtained average classification accuracy

90.69 %

(

\pm 1.97 %

) of the uterine cervical cancerous labels. This performance is better than that of other peer methods. We performed in-degree and out-degree hub gene network analysis using

Cytoscape

. We reported five top in-degree genes (

PAIP 2

,

GRWD 1

,

VPS 4 B

,

CRADD

and

LLPH

) and five top out-degree genes (

MRPL 35

,

FAM 177 A 1

,

STAT 4

,

ASPSCR 1

and

FABP 7

). After that, we performed KEGG pathway and Gene Ontology enrichment analysis of DEGs using tool WebGestalt(WEB-based Gene SeT AnaLysis Toolkit). In summary, our proposed framework that integrated linear regression, differential expression, deep learning provides a robust approach to better interpret DNA methylation analysis and gene expression data in disease study. Full article

(This article belongs to the Special Issue Selected Papers from the International Conference on Intelligent Biology and Medicine (ICIBM 2020))

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19 pages, 12605 KiB

Open AccessArticle

Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1

by Nicolas Carraro, Vladimir Sentchilo, Lenka Polák, Claire Bertelli and Jan Roelof van der Meer

Genes 2020, 11(8), 930; https://doi.org/10.3390/genes11080930 - 12 Aug 2020

Cited by 5 | Viewed by 3784

Abstract

The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such [...] Read more.

The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1′s chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). P. nitroreducens carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICEclc of Pseudomonas knackmussii B13. The variable regions of ICEPni1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICEPni2 (171 kb) encodes complete meta-cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10⁻⁶–10⁻⁸ per P. nitroreducens HBP-1 donor into Pseudomonas putida, where they integrated site specifically into tRNA^Gly-gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments. Full article

(This article belongs to the Special Issue Genomic Islands)

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14 pages, 1124 KiB

Open AccessArticle

Evaluation of the Ion AmpliSeq SARS-CoV-2 Research Panel by Massive Parallel Sequencing

by Federica Alessandrini, Sara Caucci, Valerio Onofri, Filomena Melchionda, Adriano Tagliabracci, Patrizia Bagnarelli, Laura Di Sante, Chiara Turchi and Stefano Menzo

Genes 2020, 11(8), 929; https://doi.org/10.3390/genes11080929 - 12 Aug 2020

Cited by 27 | Viewed by 4953

Abstract

Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion [...] Read more.

Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion AmpliSeq™ SARS-CoV-2 Research Panel by a massively parallel sequencing (MPS) assay. The panel allows for targeted sequencing by overlapping amplicons, thereby providing specific, accurate, and high throughput analysis. A modified reverse transcription reaction, which consists of the use of a SARS-CoV-2 specific primers pool from the Ion AmpliSeq SARS-CoV-2 Research Panel, was assessed in order to promote viral RNA specific reverse transcription. The aim of this study was to evaluate the effectiveness of the Ion AmpliSeq™ SARS-CoV-2 Research Panel in sequencing the entire viral genome in different samples. SARS-CoV-2 sequence data were obtained from ten viral isolates and one nasopharyngeal swab from different patients. The ten isolate samples amplified with 12 PCR cycles displayed high mean depth values compared to those of the two isolates amplified with 20 PCR cycles. High mean depth values were also obtained for the nasopharyngeal swab processed by use of a target-specific reverse transcription. The relative depth of coverage (rDoC) analysis showed that when 12 PCR cycles were used, all target regions were amplified with high sequencing coverage, while in libraries amplified at 20 cycles, a poor uniformity of amplification, with absent or low coverage of many target regions, was observed. Our results show that the Ion AmpliSeq SARS-CoV-2 Research Panel can achieve rapid and high throughput SARS-CoV-2 whole genome sequencing from 10 ng of DNA-free viral RNA from isolates and from 1 ng of DNA-free viral RNA from a nasopharyngeal swab using 12 PCR cycles for library amplification. The modified RT-PCR protocol yielded superior results on the nasopharyngeal swab compared to the reverse transcription reaction set up according to the manufacturer’s instructions. Full article

(This article belongs to the Special Issue Sequencing Techniques and Genomics Technologies to Help with Diagnostics and Virus Characterization – Focus on COVID 19)

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20 pages, 2167 KiB

Open AccessArticle

Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes

by Ling Sze Lee, Beatriz M. Navarro-Domínguez, Zhiqiang Wu, Eugenia E. Montiel, Daleen Badenhorst, Basanta Bista, Thea B. Gessler and Nicole Valenzuela

Genes 2020, 11(8), 928; https://doi.org/10.3390/genes11080928 - 12 Aug 2020

Cited by 5 | Viewed by 4424

Abstract

Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use [...] Read more.

Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider turtles (Trachemys scripta elegans). Optical mapping increased C. picta’s N50 by ~242% compared to the previous assembly. Physical mapping permitted anchoring ~45% of the genome assembly, spanning 5544 genes (including 20 genes related to the sex determination network of turtles and vertebrates). BAC-FISH data revealed assembly errors in C. picta and T. s. elegans assemblies, highlighting the importance of molecular cytogenetic data to complement bioinformatic approaches. We also compared C. picta’s anchored scaffolds to the genomes of other chelonians, chicken, lizards, and snake. Results revealed a mostly one-to-one correspondence between chromosomes of painted and slider turtles, and high homology among large syntenic blocks shared with other turtles and sauropsids. Yet, numerous chromosomal rearrangements were also evident across chelonians, between turtles and squamates, and between avian and non-avian reptiles. Full article

(This article belongs to the Special Issue Vertebrate Karyotype Evolution: How Far Have We Come, and Where Are We Going?)

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19 pages, 7131 KiB

Open AccessArticle

Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica

by Xifang Zong, Qi Yan, Fan Wu, Qian Ma and Jiyu Zhang

Genes 2020, 11(8), 927; https://doi.org/10.3390/genes11080927 - 12 Aug 2020

Cited by 14 | Viewed by 3705

Abstract

Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert [...] Read more.

Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert grass in northwestern China. In this study, 162 NAC genes were found from the Cleistogenes songorica genome, among which 156 C. songoricaNAC (CsNAC) genes (96.3%) were mapped onto 20 chromosomes. The phylogenetic tree constructed by CsNAC and rice NAC TFs can be separated into 14 subfamilies. Syntenic and Ka/Ks analyses showed that CsNACs were primarily expanded by genomewide replication events, and purifying selection was the primary force driving the evolution of CsNAC family genes. The CsNAC gene expression profiles showed that 36 CsNAC genes showed differential expression between cleistogamous (CL) and chasmogamous (CH) flowers. One hundred and two CsNAC genes showed differential expression under heat, cold, drought, salt and ABA treatment. Twenty-three CsNAC genes were commonly differentially expressed both under stress responses and during dimorphic floret development. Gene Ontology (GO) annotation, coexpression network and qRT-PCR tests revealed that these CsNAC genes may simultaneously regulate dimorphic floret development and the response to stress. Our results may help to characterize the NAC transcription factors in C. songorica and provide new insights into the functional research and application of the NAC family in crop improvement, especially in dimorphic floret plants. Full article

(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)

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15 pages, 2293 KiB

Open AccessArticle

Genetic Characterization of Russian Rapeseed Collection and Association Mapping of Novel Loci Affecting Glucosinolate Content

by Rim Gubaev, Lyudmila Gorlova, Stepan Boldyrev, Svetlana Goryunova, Denis Goryunov, Pavel Mazin, Alina Chernova, Elena Martynova, Yakov Demurin and Philipp Khaitovich

Genes 2020, 11(8), 926; https://doi.org/10.3390/genes11080926 - 12 Aug 2020

Cited by 3 | Viewed by 5047

Abstract

Rapeseed is the second most common oilseed crop worldwide. While the start of rapeseed breeding in Russia dates back to the middle of the 20th century, its widespread cultivation began only recently. In contrast to the world’s rapeseed genetic variation, the genetic composition [...] Read more.

Rapeseed is the second most common oilseed crop worldwide. While the start of rapeseed breeding in Russia dates back to the middle of the 20th century, its widespread cultivation began only recently. In contrast to the world’s rapeseed genetic variation, the genetic composition of Russian rapeseed lines remained unexplored. We have addressed this question by performing genome-wide genotyping of 90 advanced rapeseed accessions provided by the All-Russian Research Institute of Oil Crops (VNIIMK). Genome-wide genetic analysis demonstrated a clear difference between Russian rapeseed varieties and the rapeseed varieties from the rest of the world, including the European ones, indicating that rapeseed breeding in Russia proceeded in its own independent direction. Hence, genetic determinants of agronomical traits might also be different in Russian rapeseed lines. To assess it, we collected the glucosinolate content data for the same 90 genotyped accessions obtained during three years and performed an association mapping of this trait. We indeed found that the loci significantly associated with glucosinolate content variation in the Russian rapeseed collection differ from those previously reported for the non-Russian rapeseed lines. Full article

(This article belongs to the Special Issue Selection Methods in Plant Breeding: From Visual Phenotyping to NGS)

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17 pages, 686 KiB

Open AccessArticle

Prevalence and Spectrum of BRCA Germline Variants in Central Italian High Risk or Familial Breast/Ovarian Cancer Patients: A Monocentric Study

by Jennifer Foglietta, Vienna Ludovini, Fortunato Bianconi, Lorenza Pistola, Maria Sole Reda, Antonella Al-Refaie, Francesca Romana Tofanetti, Annamaria Mosconi, Elisa Minenza, Paola Anastasi, Carmen Molica, Fabrizio Stracci and Fausto Roila

Genes 2020, 11(8), 925; https://doi.org/10.3390/genes11080925 - 12 Aug 2020

Cited by 11 | Viewed by 3336

Abstract

Hereditary breast and ovarian cancers are mainly linked to variants in BRCA1/2 genes. Recently, data has shown that identification of BRCA variants has an immediate impact not only in cancer prevention but also in targeted therapeutic approaches. This prospective observational study characterized [...] Read more.

Hereditary breast and ovarian cancers are mainly linked to variants in BRCA1/2 genes. Recently, data has shown that identification of BRCA variants has an immediate impact not only in cancer prevention but also in targeted therapeutic approaches. This prospective observational study characterized the overall germline BRCA variant and variant of uncertain significance (VUS) frequency and spectrum in individuals affected by breast (BC) or ovarian cancer (OC) and in healthy individuals at risk by sequencing the entire BRCA genes. Of the 363 probands analyzed, 50 (13.8%) were BRCA1/2 mutated, 28 (7.7%) at BRCA1 and 23 (6.3%) at BRCA2 gene. The variant c.5266dupC p.(Gln1756Profs) was the most frequent alteration, representing 21.4% of the BRCA1 variants and 12.0% of all variants identified. The variant c.6313delA p.(Ile2105Tyrfs) of BRCA2 was the most frequent alteration observed in 6 patients. Interestingly, two new variants were identified in BRCA2. In addition, 25 different VUS were identified; two were reported for the first time in BRCA1 and two in BRCA2. The number of triple-negative BCs was significantly higher in patients with the pathogenic BRCA1/2-variant (36.4%) than in BRCA1/2 VUS (16.0%) and BRCA1/2 wild-type patients (10.7%) (p < 0.001). Our study reveals that the overall frequency of BRCA germline variants in the selected high-risk Italian population is about 13.8%. We believe that our results could have significant implications for preventive strategies for unaffected BRCA-carriers and effective targeted treatments such as PARP inhibitors for patients with BC or OC. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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13 pages, 1263 KiB

Open AccessArticle

Molecular Analysis of 55 Spanish Patients with Acute Intermittent Porphyria

by María-José Morán-Jiménez, María-José Borrero-Corte, Fátima Jara-Rubio, Inmaculada García-Pastor, Silvia Díaz-Díaz, Francisco-Javier Castelbón-Fernandez, Rafael Enríquez-de-Salamanca and Manuel Méndez

Genes 2020, 11(8), 924; https://doi.org/10.3390/genes11080924 - 12 Aug 2020

Cited by 8 | Viewed by 2989

Abstract

Acute intermittent porphyria (AIP) results from a decreased activity of hepatic hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway. AIP is an autosomal dominant disorder with incomplete penetrance, characterized by acute neurovisceral attacks precipitated by several factors that induce the [...] Read more.

Acute intermittent porphyria (AIP) results from a decreased activity of hepatic hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway. AIP is an autosomal dominant disorder with incomplete penetrance, characterized by acute neurovisceral attacks precipitated by several factors that induce the hepatic 5-aminolevulinic acid synthase, the first enzyme in the heme biosynthesis. Thus, a deficiency in HMBS activity results in an overproduction of porphyrin precursors and the clinical manifestation of the disease. Early diagnosis and counselling are essential to prevent attacks, and mutation analysis is the most accurate method to identify asymptomatic carriers in AIP families. In the present study, we have investigated the molecular defects in 55 unrelated Spanish patients with AIP, identifying 32 HMBS gene mutations, of which six were novel and ten were found in more than one patient. The novel mutations included a missense, an insertion, two deletions, and two splice site variants. Prokaryotic expression studies demonstrated the detrimental effect for the missense mutation, whereas reverse transcription-PCR and sequencing showed aberrant splicing caused by each splice site mutation. These results will allow for an accurate diagnosis of carriers of the disease in these families. Furthermore, they increase the knowledge about the molecular heterogeneity of AIP in Spain. Full article

(This article belongs to the Special Issue The Value of Genetics in the Identification of Treatable Rare Diseases. The Paradigm of Inborn Errors of Metabolism)

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12 pages, 2911 KiB

Open AccessArticle

Progesterone Receptor Coregulators as Factors Supporting the Function of the Corpus Luteum in Cows

by Robert Rekawiecki, Karolina Dobrzyn, Jan Kotwica and Magdalena K. Kowalik

Genes 2020, 11(8), 923; https://doi.org/10.3390/genes11080923 - 12 Aug 2020

Cited by 9 | Viewed by 2833

Abstract

Progesterone receptor (PGR) for its action required connection of the coregulatory proteins, including coactivators and corepressors. The former group exhibits a histone acetyltransferase (HAT) activity, while the latter cooperates with histone deacetylase (HDAC). Regulations of the coregulators mRNA and protein and HAT and [...] Read more.

Progesterone receptor (PGR) for its action required connection of the coregulatory proteins, including coactivators and corepressors. The former group exhibits a histone acetyltransferase (HAT) activity, while the latter cooperates with histone deacetylase (HDAC). Regulations of the coregulators mRNA and protein and HAT and HDAC activity can have an indirect effect on the PGR function and thus progesterone (P4) action on target cells. The highest mRNA expression levels for the coactivators—histone acetyltransferase p300 (P300), cAMP response element-binding protein (CREB), and steroid receptor coactivator-1 (SRC-1)—and nuclear receptor corepressor-2 (NCOR-2) were found in the corpus luteum (CL) on days 6 to 16 of the estrous cycle. The CREB protein level was higher on days 2–10, whereas SRC-1 and NCOR-2 were higher on days 2–5. The activity of HAT and HDAC was higher on days 6–10 of the estrous cycle. All of the coregulators were localized in the nuclei of small and large luteal cells. The mRNA and protein expression levels of the examined coactivators and corepressor changed with the P4 level. Thus, P4 may regulate CL function via the expression of coregulators, which probably affects the activity of the PGR. Full article

(This article belongs to the Special Issue Genomic Studies in the Mammalian Reproductive Tract)

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