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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 (25 September 2023) | Viewed by 20881

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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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Guest Editor

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

Special Issue Information

Dear Colleagues,

Molecular evolution in animals using nuclear or mitochondrial DNA, and mitochondrial genomics has transformed phylogeny of animals in recent decades. Still, there is a lot of work ahead. The demand for molecular evolution and mitochondrial genomics in animals is rising. At the same time, the mitochondrial gene arrangement in different orders of animals is of great concern. Understanding the molecular evolution in animals, the molecular mechanisms of gene rearrangement in animals, and even the mitochondrial gene expression of animals under different stress will benefit us all. This Special Issue in Genes on “Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals” will highlight how mitochondrial genomics technologies are paving the way to understand the evolution of animals and the function of mitochondrial gene in animals. The Special Issue will provide an article of recent developments in molecular evolution using nuclear and mitochondrial DNA in animals, or the phylogenetic relationship of animals using mitochondrial genomes, or mitochondrial gene expression of animals under different enviromental stress.

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 (10 papers)

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Research

12 pages, 1627 KiB

Open AccessEditor’s ChoiceArticle

Genetic Analysis Based on Mitochondrial nad2 Gene Reveals a Recent Population Expansion of the Invasive Mussel, Mytella strigata, in China

by Shaojing Yan, Peizhen Ma, Chenxia Zuo, Yi Zhu, Xiaojie Ma and Zhen Zhang

Genes 2023, 14(11), 2038; https://doi.org/10.3390/genes14112038 - 3 Nov 2023

Cited by 3 | Viewed by 1488

Abstract

Mytella strigata is a highly adaptable invasive alien species that has been established in coastal China since 2014. Mitochondrial DNA (mtDNA) is an important tool for studying the evolution and population genetics of invasive species. In this study, the mitochondrial genome of M. strigata from China was sequenced by Illumina high-throughput sequencing and characterized with 13 protein-coding genes (PCGs). By assessing the selective pressure of 13 PCGs, the nad2 gene had the fastest evolutionary rate and was finally selected for population genetic analysis. A total of 285 nad2 sequences from seven M. strigata populations in China were analyzed and showed obviously T-rich and C-rich characteristics. According to population genetic diversity analysis, all the seven populations had haplotype (gene) diversity (Hd) ≥ 0.5 and nucleotide diversity (Pi) < 0.005. Haplotype networks showed a “star” distribution. Population historical dynamic analyses showed that Fu’s Fs and Tajima’s D values of all populations were negative except the Qukou (QK) and Beihai (BH) populations. The Zhangzhou (ZJ) and Xiamen (XM) populations were unimodal while the other populations were multimodal. These results suggested that the population of M. strigata in China may have passed the bottleneck period and is currently in a state of population expansion. Full article

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

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11 pages, 2691 KiB

Open AccessArticle

Structural Characteristics of Mitochondrial Genomes of Eight Treehoppers (Hemiptera: Membracidae: Centrotinae) and Their Phylogenetic Implications

by Haijun Bai, Jinrui Zhang, Christopher H. Dietrich, Yiping Li and Xiangqun Yuan

Genes 2023, 14(7), 1510; https://doi.org/10.3390/genes14071510 - 24 Jul 2023

Viewed by 1531

Abstract

Complete mitochondrial genomes were newly sequenced for eight species of the treehopper subfamily Centrotinae (Hemiptera: Membracidae), four of which represent genera for which mitogenomes were not previously available. The new mitogenomes are generally similar in overall structure, gene order, base composition, and nucleotide content to those of previously sequenced species of the subfamily. Phylogenetic analyses were conducted using both maximum likelihood and Bayesian inference methods based on three separate nucleotide sequence datasets in which RNA gene sequences and/or third codon positions were either included or excluded from the concatenated protein-coding gene alignments. The results are consistent with previous phylogenies based on morphology and partial nuclear genome data, except for the lack of support for the monophyly of Leptocentrini. These results show that mitogenome sequences are informative of both ancient and recent divergence patterns within Centrotinae. Full article

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

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16 pages, 4156 KiB

Open AccessArticle

Comparative Mitochondrial Genomes between the Genera Amiota and Phortica (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability

by Caihong Zhang, Yalian Wang, Hongwei Chen and Jia Huang

Genes 2023, 14(6), 1240; https://doi.org/10.3390/genes14061240 - 9 Jun 2023

Cited by 1 | Viewed by 1417

Abstract

To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143–16,803 bp and 15,933–16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica. Full article

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

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17 pages, 5259 KiB

Open AccessArticle

Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae)

by Yanqiong Yang, Jiajia Wang, Renhuai Dai and Xianyi Wang

Genes 2023, 14(6), 1175; https://doi.org/10.3390/genes14061175 - 28 May 2023

Cited by 7 | Viewed by 1643

Abstract

Krisna species are insects that have piercing–sucking mouthparts and belong to the Krisnini tribe in the Iassinae subfamily of leafhoppers in the Cicadellidae family. In this study, we sequenced and compared the mitochondrial genomes (mitogenomes) of four Krisna species. The results showed that all four mitogenomes were composed of cyclic double-stranded molecules and contained 13 protein-coding genes (PCGs) and 22 and 2 genes coding for tRNAs and rRNAs, respectively. Those mitogenomes exhibited similar base composition, gene size, and codon usage patterns for the protein-coding genes. The analysis of the nonsynonymous substitution rate (Ka)/synonymous substitution rate (Ks) showed that evolution occurred the fastest in ND4 and the slowest in COI. 13 PCGs that underwent purification selection were suitable for studying phylogenetic relationships within Krisna. ND2, ND6, and ATP6 had highly variable nucleotide diversity, whereas COI and ND1 exhibited the lowest diversity. Genes or gene regions with high nucleotide diversity can provide potential marker candidates for population genetics and species delimitation in Krisna. Analyses of parity and neutral plots showed that both natural selection and mutation pressure affected the codon usage bias. In the phylogenetic analysis, all subfamilies were restored to a monophyletic group; the Krisnini tribe is monophyletic, and the Krisna genus is paraphyletic. Our study provides novel insights into the significance of the background nucleotide composition and codon usage patterns in the CDSs of the 13 mitochondrial PCGs of the Krisna genome, which could enable the identification of a different gene organization and may be used for accurate phylogenetic analysis of Krisna species. Full article

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

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13 pages, 17710 KiB

Open AccessArticle

The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea

by Abdur Rehman, Qing-Bo Huo and Yu-Zhou Du

Genes 2023, 14(5), 965; https://doi.org/10.3390/genes14050965 - 24 Apr 2023

Viewed by 1713

Abstract

Capniidae are a family of stoneflies, also known as snow flies, who emerge in winter. The phylogeny of Capniidae is widely accepted to be based on morphological analysis. Until now, only five Capniidae mitochondrial genomes have been sequenced so far. In addition, sampling is required to determine an accurate phylogenetic association because the generic classification of this family is still controversial and needs to be investigated further. In this study, the first mitogenome of genus Isocapnia was sequenced with a length of 16,200 bp and contained 37 genes, including a control region, two rRNAs, 22 tRNAs, and 13 PCGs, respectively. Twelve PCGs originated with the common start codon ATN (ATG, ATA, or ATT), while nad5 used GTG. Eleven PCGs had TAN (TAA or TAG) as their last codon; however, cox1 and nad5 had T as their final codon due to a shortened termination codon. All tRNA genes demonstrated the cloverleaf structure, which is distinctive for metazoans excluding the tRNASer1 (AGN) that missed the dihydrouridine arm. A Phylogenetic analysis of the superfamily Nemouroidea was constructed using thirteen PCGs from 32 formerly sequenced Plecoptera species. The Bayesian inference and maximum likelihood phylogeny tree structures derived similar results across the thirteen PCGs. Our findings strongly supported Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). Ultimately, the best well-supported generic phylogenetic relationship within Capniidae is as follows; (Isocapnia + (Capnia + Zwicknia) + (Apteroperla + Mesocapnia)). These findings will enable us to better understand the evolutionary relationships within the superfamily Nemouroidea and the generic classification and mitogenome structure of the family Capniidae. Full article

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

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11 pages, 2102 KiB

Open AccessArticle

Full-Length Transcriptome Profiling of Coridius chinensis Mitochondrial Genome Reveals the Transcription of Genes with Ancestral Arrangement in Insects

by Shiwen Xu, Yuange Duan, Ling Ma, Fan Song, Li Tian, Wanzhi Cai and Hu Li

Genes 2023, 14(1), 225; https://doi.org/10.3390/genes14010225 - 15 Jan 2023

Cited by 4 | Viewed by 2531

Abstract

Coridius chinensis (Hemiptera: Dinidoridae) is a medicinal insect. Its mitochondrial gene arrangement is consistent with that of Drosophila melanogaster and Erthesina fullo, the two insects with well-studied mitochondrial transcription. To investigate whether the structural consistency of mitochondrial genes leads to similarities in transcription and post-transcriptional processing, we improved the gene annotation and constructed a quantitative transcription map for the C. chinensis mitochondrial genome (mitogenome) using full-length transcriptome sequencing. The size of this mitogenome was 16,214 bp and the proposed model of mitochondrial transcription was similar to that of Drosophila. Both strands were nearly entirely transcribed except for the antisense genes downstream of trnS2 on N strand. The expression of cytochrome c subunit genes is higher than that of NADH-dehydrogenase subunit genes. The post-transcriptional cleavage process followed the “tRNA punctuation” model, and both the “reverse cleavage” model in Drosophila and “forward cleavage” model in E. fullo were found in C. chinensis. In addition, we found that long non-coding RNAs from the control region contained tandem repeats. Polyadenylation was performed after CCA triplet at the 3′ end of tRNA. The isoform diversity of lrRNA was identified. Our study sheds light on the transcriptional regulation and RNA processing of insect mitogenomes with the putative ancestral gene arrangement. Full article

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

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17 pages, 8387 KiB

Open AccessArticle

Spatio-Temporal Evolutionary Patterns of the Pieridae Butterflies (Lepidoptera: Papilionoidea) Inferred from Mitogenomic Data

by Fanyu Wei, Wenxiang Huang, Lin Fang, Bo He, Youjie Zhao, Yingming Zhang, Zufei Shu, Chengyong Su and Jiasheng Hao

Genes 2023, 14(1), 72; https://doi.org/10.3390/genes14010072 - 26 Dec 2022

Cited by 3 | Viewed by 2762

Abstract

Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K–Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth’s history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated. Full article

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

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13 pages, 1252 KiB

Open AccessArticle

Phylogenetic Analysis and Genetic Structure of Schlegel’s Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences

by Longjie Xia, Fengna Cai, Shasha Chen, Yao Cai, Kaiya Zhou, Jie Yan and Peng Li

Genes 2023, 14(1), 18; https://doi.org/10.3390/genes14010018 - 21 Dec 2022

Cited by 1 | Viewed by 2489

Abstract

Gekko japonicus, i.e., Schlegel’s Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of G. japonicus populations from China. Phylogenetic analysis indicated that G. japonicus had a close relationship with Gekko wenxianensis. A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of G. japonicus was comparatively low across different geographic populations. The populations of G. japonicus were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of G. japonicus has occurred as well. Overall, these results demonstrate that the populations of G. japonicus reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of G. japonicus and will provide some insights into the study of origin of populations. Full article

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

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14 pages, 3185 KiB

Open AccessArticle

Complete Mitogenome Analysis of Five Leafhopper Species of Idiocerini (Hemiptera: Cicadellidae)

by Lili Tian, Wenxin Yang, Chengyan Si, Xianguang Guo and Bin Zhang

Genes 2022, 13(11), 2000; https://doi.org/10.3390/genes13112000 - 1 Nov 2022

Cited by 3 | Viewed by 1834

Abstract

Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics, and biogeography. So far, only 12 mitogenomes of the leafhopper tribe Idiocerini have been released in GenBank, although the tribe comprises 488 known species including some agricultural, forestry, and horticultural pests. In order to compare and analyze the mitochondrial genome structure of Idiocerini and even the selective pressure of 13 protein-coding genes (PCGs) of the family Cicadellidae, the complete mitogenomes of five species including Nabicerus dentimus, Sahlbergotettix salicicola, Podulmorinus opacus, Podulmorinus consimilis, and a new species of a new genus were determined by next-generation sequencing. The size of the newly determined mitogenomes ranged from 14,733 bp to 15,044 bp, comprising the standard set of 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a long non-coding control region (CR). The extent of purifying selection presented different pictures in the tribe and the family. The less pronounced genes (0.5 < dN/dS < 1) were nad5 and nad4l in Idiocerin, whereas in the family Cicadellidae including the sequences of Idiocerin, nad1-nad6 and cox1 genes were less pronounced. The codon encoding leucine was the most common in all species, and the codon encoding serine 1 was the most common in all species except for P. opacus. Interestingly, in P. opacus, another of the most common codons is that encoding serine 2. Among the 17 examined species of the Idiocerini, 14 species contained the tandem repeats, and 11 species of them contained the motif “TTATA”. These findings will promote research on the structure and evolution of the mitochondrial genome and highlight the need for more mitogenomes in Cicadellidae. Full article

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

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14 pages, 5834 KiB

Open AccessArticle

A Rearrangement of the Mitochondrial Genes of Centipedes (Arthropoda, Myriapoda) with a Phylogenetic Analysis

by Jia-Jia Wang, Yu Bai and Yan Dong

Genes 2022, 13(10), 1787; https://doi.org/10.3390/genes13101787 - 3 Oct 2022

Cited by 4 | Viewed by 2126

Abstract

Due to the limitations of taxon sampling and differences in results from the available data, the phylogenetic relationships of the Myriapoda remain contentious. Therefore, we try to reconstruct and analyze the phylogenetic relationships within the Myriapoda by examining mitochondrial genomes (the mitogenome). In this study, typical circular mitogenomes of Mecistocephalus marmoratus and Scolopendra subspinipes were sequenced by Sanger sequencing; they were 15,279 bp and 14,637 bp in length, respectively, and a control region and 37 typical mitochondrial genes were annotated in the sequences. The results showed that all 13 PCGs started with ATN codons and ended with TAR codons or a single T; what is interesting is that the gene orders of M. marmoratus have been extensively rearranged compared with most Myriapoda. Thus, we propose a simple duplication/loss model to explain the extensively rearranged genes of M. marmoratus, hoping to provide insights into mitogenome rearrangement events in Myriapoda. In addition, our mitogenomic phylogenetic analyses showed that the main myriapod groups are monophyletic and supported the combination of the Pauropoda and Diplopoda to form the Dignatha. Within the Chilopoda, we suggest that Scutigeromorpha is a sister group to the Lithobiomorpha, Geophilomorpha, and Scolopendromorpha. We also identified a close relationship between the Lithobiomorpha and Geophilomorpha. The results also indicate that the mitogenome can be used as an effective mechanism to understand the phylogenetic relationships within Myriapoda. Full article

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

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