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Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (15 September 2024) | Viewed by 10154

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Prof. Dr. Jiayong Zhang

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College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
Interests: gene rearrangement; mitochondrial genome; molecular evolution; mitochondrial gene expression
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Jiasheng Hao

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College of Life Sciences, Anhui Normal University, Wuhu 241002, China
Interests: insect phylogeny and phylogeography; mitochondrial genome; molecular evolution; molecular clock
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Due to the great success of our Special Issue "Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals", we decided to set up a second volume: "Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—Volume II".

To obtain more papers related to molecular evolution in using nuclear or mitochondrial DNA and mitochondrial genomics, we decided to expand the range of species in all animals. At the same time, the mitochondrial gene arrangement in different animal species is of great interest. We are encouraging authors to submit the papers focused on the mitochondrial gene expression of animals under different levels of environmental stress.

For this second volume, we are encouraging authors to submit review articles related to the mitochondrial genomes of all kinds of high taxonomy of animals, e.g., reviews on the mitochondrial genomes of Hymenoptera, reviews on the mitochondrial genomes of Lepidoptera, etc.

We invite you to read the Special Issue "Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals", which can be found at https://www.mdpi.com/journal/genes/special_issues/9X18DGL0I6.

Prof. Dr. Jiayong Zhang
Prof. Dr. Jiasheng Hao
Guest Editors

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Keywords

mitochondrial genome
gene arrangement
phylogenetic relationship
mitochondrial gene expression
molecular evolution

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Published Papers (9 papers)

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Research

13 pages, 2724 KiB

Open AccessArticle

Unraveling the Mitogenomic Characteristics and Phylogenetic Implications of Leuciscus merzbacheri (Zugmayer, 1912), an Endangered Fish in the Junggar Basin of Xinjiang, Northwest China

by Yan Sun and Tianyan Yang

Genes 2024, 15(10), 1284; https://doi.org/10.3390/genes15101284 - 30 Sep 2024

Viewed by 778

Abstract

Background: Leuciscus merzbacheri is a rare and endangered fish in Xinjiang, China. As a representative species of the fauna in the Junggar Basin, it is of high economic and scientific value. The genetic data are still limited, and the mitochondrial genomic characteristics remain unexplored. Methods: A high-throughput sequencing method was used to obtain the complete mitogenome of L. merzbacheri. Results: The full length of the circular DNA was 16,609 bp, and it consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs and 2 non-coding regions. The overall nucleotide compositions of both the mitogenome and PCGs showed an obvious AT preference with percentages of 54.20% and 53.60%, respectively. Three commonly used amino acids were Leu (16.43%), Ala (8.95%) and Thr (7.85%) in turn. All tRNAs could form the typical clover structures excluding tRNA-Ser ^AGY. The presumed secondary structures of two rRNAs contained several stem-loop domains, and the structure of 12S rRNA seemed to be more stable than that of 16S rRNA. Extended termination sequence regions (ETASs), central conserved regions (CSB-F, CSB-E and CSB-D), and conserved sequence regions (CSB-1, CSB-2 and CSB-3) were identified in the control region. The phylogenetic tree showed that L. merzbacheri was recovered with strong supports as a sister to the other members of the genus. The location in the outermost branch implied that it might be a relatively ancient species among its congeners. Conclusions: This study would complement the genetic data on L. merzbacheri and contribute to a better understanding of molecular evolution in Leuciscus as well. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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12 pages, 4080 KiB

Open AccessArticle

Complete Mitochondrial Genome of Tanypus chinensis and Tanypus kraatzi (Diptera: Chironomidae): Characterization and Phylogenetic Implications

by Shaobo Gao, Chengyan Wang, Yaning Tang, Yuzhen Zhang, Xinyu Ge, Jiwei Zhang and Wenbin Liu

Genes 2024, 15(10), 1281; https://doi.org/10.3390/genes15101281 - 29 Sep 2024

Viewed by 678

Abstract

Background: Chironomidae occupy a pivotal position within global aquatic ecosystems. The unique structural attributes of the mitochondrial genome provide profound insights and compelling evidence, underpinning the morphological classification of organisms and substantially advancing our understanding of the phylogenetic relationships within Chironomidae. Results: We have meticulously sequenced, assembled, and annotated the mitogenomes of Tanypus chinensis (Wang, 1994) and Tanypus kraatzi (Kieffer, 1912), incorporating an additional 25 previously published mitogenomes into our comprehensive analysis. This extensive dataset enables us to delve deeper into the intricate characteristics and nuances of these mitogenomes, facilitating a more nuanced understanding of their genetic makeup. Conclusions: The genomic nucleotide composition of T. kraatzi was 39.10% A, 36.51% T, 14.33% C, and 10.06% G, with a total length of 1508 bp. The genomic nucleotide composition of T. chinensis was 39.61% A, 36.27% T, 14.55% C, and 9.57% G, with a total length of 1503 bp. This significant enrichment of the chironomid mitogenome library establishes a novel foundation for further exploration in the realm of phylogenetics. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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11 pages, 2445 KiB

Open AccessArticle

Elucidating Scarab Divergence in an Evolutionary-Ecological Context through the Comprehensive Analysis of the Complete Mitogenome of Anomala

by Xianyi Wang, Shuchai Li and Tielong Xu

Genes 2024, 15(8), 1022; https://doi.org/10.3390/genes15081022 - 3 Aug 2024

Viewed by 755

Abstract

Anomala Samouelle, 1819 is one of the specious genera of Coleoptera, with over 1000 known species, and includes some of the most destructive pests of crops or forests. Morphological convergence is a common phenomenon within this genus, making the identification of closely related species very difficult. To explore the phylogenetic placement of Anomalini and provide a basis for the classification and identification of Anomala, we comparatively analyzed the complete mitogenome of three Anomala species (A. exoleta, A. perplexa diana, and A. praecoxalis). Based on all accessible mitogenome data, we performed comparative mitochondrial genomics analysis of this genus and reconstructed the phylogenetic relationships of Scarabaeidae based on two datasets (protein-coding genes and amino acids) and two methods (Bayesian approach and maximum likelihood). The phylogenetic relationships found in this study highly support that the groups of Aphodiinae, Cetoniinae, Dynastinae, Rutelinae and Scarabaeinae are monophyletic. Interestingly, the phylogenetic clustering relationship was highly consistent with the Scarabaeidae diet, indicating that the herbivorous species and dung-eating species are clustered separately. The phylogenetic tree showed that the subfamily Melolonthinae and the genus Anomala are not monophyletic, suggesting that these two groups should be further revised with more data. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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16 pages, 7285 KiB

Open AccessArticle

Interspecific and Intraspecific Transcriptomic Variations Unveil the Potential High-Altitude Adaptation Mechanisms of the Parnassius Butterfly Species

by Chen Ding, Chengyong Su, Yali Li, Youjie Zhao, Yunliang Wang, Ying Wang, Ruie Nie, Bo He, Junye Ma and Jiasheng Hao

Genes 2024, 15(8), 1013; https://doi.org/10.3390/genes15081013 - 1 Aug 2024

Viewed by 1065

Abstract

Parnassius butterflies have significantly advanced our understanding of biogeography, insect–plant interactions, and other fields of ecology and evolutionary biology. However, to date, little is known about the gene expression patterns related to the high-altitude adaptation of Parnassius species. In this study, we obtained high-throughput RNA-seq data of 48 adult Parnassius individuals covering 10 species from 12 localities in China, and deciphered their interspecific and intraspecific expression patterns based on comparative transcriptomic analyses. Though divergent transcriptional patterns among species and populations at different altitudes were found, a series of pathways related to genetic information processing (i.e., recombination, repair, transcription, RNA processing, and ribosome biogenesis), energy metabolism (i.e., oxidative phosphorylation, thermogenesis, and the citrate cycle), and cellular homeostasis were commonly enriched, reflecting similar strategies to cope with the high-altitude environments by activating energy metabolism, enhancing immune defense, and concurrently inhibiting cell growth and development. These findings deepen our understanding about the molecular mechanisms of adaptative evolution to extreme environments, and provide us with some theoretical criteria for the biodiversity conservation of alpine insects. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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18 pages, 5887 KiB

Open AccessArticle

Phylogenetic and Comparative Genomics Study of Papilionidae Based on Mitochondrial Genomes

by Zhen-Tian Yan, Xiao-Ya Tang, Dong Yang, Zhen-Huai Fan, Si-Te Luo and Bin Chen

Genes 2024, 15(7), 964; https://doi.org/10.3390/genes15070964 - 22 Jul 2024

Viewed by 1014

Abstract

Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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12 pages, 2589 KiB

Open AccessArticle

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

by Li-min Yang, Jing-feng Xue, Xiao-man Zhao, Ke Ding, Zhao-wen Liu, Zhou-si-yu Wang, Jian-bing Chen and You-kun Huang

Genes 2024, 15(7), 893; https://doi.org/10.3390/genes15070893 - 8 Jul 2024

Viewed by 949

Abstract

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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12 pages, 3861 KiB

Open AccessArticle

Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China

by Siqi Zhu, Naifan Zhang, Jie Zhang, Xinyue Shao, Yaqi Guo and Dawei Cai

Genes 2024, 15(6), 790; https://doi.org/10.3390/genes15060790 - 15 Jun 2024

Viewed by 1044

Abstract

This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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16 pages, 2740 KiB

Open AccessArticle

Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species

by Zhengfei Wang, Xinyi Xu, Yuqing Zheng, Zhiwen Xu, Yunjie Li and Huohuo Chen

Genes 2024, 15(4), 437; https://doi.org/10.3390/genes15040437 - 29 Mar 2024

Cited by 1 | Viewed by 1141

Abstract

Complete mitochondrial genomes (mitogenomes) can provide important information regarding the molecular evolution and phylogenetic relationships of marine invertebrates, especially in Brachyura. Only one Cancroidea species of mitogenomes has been sequenced before; in this research, the mitogenomic characteristics of Metacarcinus magister (Cancridae: Cancroidea) are newly studied. The length of the M. magister mitogenome was 48,820 bp, and it contained the typical 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. We performed a series of analyses on the characteristics of the mNCR of M. magister. The phylogenetics, life circumstances, and selective pressures were all analyzed to explain the formation of this length, which revealed the length of the M. magister mitogenome to be approximately three times greater than the normal length of Brachyuran mitogenomes. Phylogenetic analyses based on a dataset of 215 Decapodan mitogenomes indicated that all Eriphioidea crabs were clustered together as a group. Moreover, the rearrangement mechanism of the Cancroidea species was predicted to provide stronger evidence for the phylogenetic analysis. In general, the results obtained in this study will contribute to a better understanding of the cause of the unusual length of the M. magister mitogenome and provide new insights into the phylogeny of Brachyura. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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20 pages, 1325 KiB

Open AccessArticle

The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes

by Ke Li, Sheng-Wu Yu, Hao Hu, Yu-Feng Feng, Kenneth B. Storey, Yue Ma, Jia-Yong Zhang and Dan-Na Yu

Genes 2024, 15(1), 13; https://doi.org/10.3390/genes15010013 - 20 Dec 2023

Cited by 1 | Viewed by 1568

Abstract

Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17–22 bp intergenic spacers (IGS) with a ‘TACTA’ motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals—2nd Edition)

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