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Advanced Research on Mitochondrial Genome
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Advanced Research on Mitochondrial Genome

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

Deadline for manuscript submissions: closed (20 November 2023) | Viewed by 18902

Special Issue Editor

Dr. J. Antonio Baeza

E-Mail Website
Guest Editor
Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
Interests: mitochondrial genomics; long reads; transcriptomics; phylogenomics

Special Issue Information

Dear Colleagues, 

The expansion of high-throughput sequencing into the life sciences, together with the diminishing costs of short-read sequencing, explains why complete or nearly complete mitochondrial genomes are quickly and steadily becoming markers of choice for the examination of within-species population structures and among-species phylogenetic relationships. The accurate assembly, in silico annotation, manual curation, and detailed characterization of mitochondrial genomic features is highly relevant for phylomitogenomic and many other downstream analyses. Unfortunately, many studies assembling and characterizing mitochondrial genomes are published as (extremely) short genome announcement reports that lack detailed descriptions of the pipeline used for the assembling, annotation, and manual curation of mitochondrial chromosomes, in turn making it difficult to reproduce the analyses reported in these studies. The present Special Issue of the journal Genes, entitled “Advanced Research on Mitochondrial Genome”, will host articles in which the authors provide an accurate and detailed characterization of mitochondrial genomes from a wide variety of marine, freshwater, and terrestrial vertebrate and invertebrate animals. Studies that provide an accurate assembly of mitochondrial genomes and a detailed characterization of their features will result in relevant biological insight.

Dr. J. Antonio Baeza
Guest Editor

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Keywords

  • phylomitogenomics
  • selective pressure analysis
  • mitochondrial genome
  • annotation

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Published Papers (9 papers)

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Research

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13 pages, 2128 KiB  
Article
The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae
by Hui Xu, Ziyi Zhu, Zeyuan Tian, Cuiyuan Wei, Qi Fan, Yuanbing Wang, Shikang Shen, Gang Deng and Mingliang Ding
Genes 2024, 15(1), 111; https://doi.org/10.3390/genes15010111 - 17 Jan 2024
Viewed by 1485
Abstract
Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is [...] Read more.
Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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9 pages, 2792 KiB  
Communication
Characterization and Comparison of the Two Mitochondrial Genomes in the Genus Rana
by Yan-Mei Wang, Chi-Ying Zhang, Si-Te Luo, Guo-Hua Ding and Fen Qiao
Genes 2023, 14(9), 1786; https://doi.org/10.3390/genes14091786 - 11 Sep 2023
Viewed by 1343
Abstract
The mitochondrial genome (mitogenome) possesses several invaluable attributes, including limited recombination, maternal inheritance, a fast evolutionary rate, compact size, and relatively conserved gene arrangement, all of which make it particularly useful for applications in phylogenetic reconstruction, population genetics, and evolutionary research. In this [...] Read more.
The mitochondrial genome (mitogenome) possesses several invaluable attributes, including limited recombination, maternal inheritance, a fast evolutionary rate, compact size, and relatively conserved gene arrangement, all of which make it particularly useful for applications in phylogenetic reconstruction, population genetics, and evolutionary research. In this study, we aimed to determine the complete mitogenomes of two morphologically similar Rana species (Rana hanluica and Rana longicrus) using next-generation sequencing. The entire circular mitogenome was successfully identified, with a length of 19,395 bp for R. hanluica and 17,833 bp for R. longicrus. The mitogenomes of both species contained 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and one control region; mitogenome size varied predominantly with the length of the control region. The two synonymous codon usages in 13 PCGs showed that T and A were used more frequently than G and C. The ratios of non-synonymous to synonymous substitutions of all 13 PCGs were <1 in the Rana species, indicating that the PCGs were under purifying selection. Finally, phylogenetic relationship analyses suggested that R. hanluica and R. longicrus were classified in the R. japonica group. Our study provides valuable reference material for the taxonomy of the genus Rana. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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12 pages, 2275 KiB  
Article
A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae
by Jiaqiao Wang, Weiyi He, Hao Huang, Danyun Ou, Lei Wang, Jun Li, Weiwen Li and Site Luo
Genes 2023, 14(8), 1612; https://doi.org/10.3390/genes14081612 - 11 Aug 2023
Cited by 2 | Viewed by 1158
Abstract
Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using [...] Read more.
Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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16 pages, 5719 KiB  
Article
Mitogenomes of Eight Nymphalidae Butterfly Species and Reconstructed Phylogeny of Nymphalidae (Nymphalidae: Lepidoptera)
by Zhen-Tian Yan, Zhen-Huai Fan, Shu-Lin He, Xue-Qian Wang, Bin Chen and Si-Te Luo
Genes 2023, 14(5), 1018; https://doi.org/10.3390/genes14051018 - 29 Apr 2023
Cited by 3 | Viewed by 2258
Abstract
The Nymphalidae family of cosmopolitan butterflies (Lepidoptera) comprises approximately 7200 species found on all continents and in all habitats. However, debate persists regarding the phylogenetic relationships within this family. In this study, we assembled and annotated eight mitogenomes of Nymphalidae, constituting the first [...] Read more.
The Nymphalidae family of cosmopolitan butterflies (Lepidoptera) comprises approximately 7200 species found on all continents and in all habitats. However, debate persists regarding the phylogenetic relationships within this family. In this study, we assembled and annotated eight mitogenomes of Nymphalidae, constituting the first report of complete mitogenomes for this family. Comparative analysis of 105 mitochondrial genomes revealed that the gene compositions and orders were identical to the ancestral insect mitogenome, except for Callerebia polyphemus trnV being before trnL and Limenitis homeyeri having two trnL genes. The results regarding length variation, AT bias, and codon usage were consistent with previous reports on butterfly mitogenomes. Our analysis indicated that the subfamilies Limenitinae, Nymphalinae, Apaturinae, Satyrinae, Charaxinae, Heliconiinae, and Danainae are monophyletic, while the subfamily the subfamily Cyrestinae is polyphyletic. Danainae is the base of the phylogenetic tree. At the tribe level, Euthaliini in Limenitinae; Melitaeini and Kallimini in Nymphalinae; Pseudergolini in Cyrestinae; Mycalesini, Coenonymphini, Ypthimini, Satyrini, and Melanitini in Satyrinae; and Charaxini in Charaxinae are regarded as monophyletic groups. However, the tribe Lethini in Satyrinae is paraphyletic, while the tribes Limenitini and Neptini in Limenitinae, Nymphalini and Hypolimni in Nymphalinae, and Danaini and Euploeini in Danainae are polyphyletic. This study is the first to report the gene features and phylogenetic relationships of the Nymphalidae family based on mitogenome analysis, providing a foundation for future studies of population genetics and phylogenetic relationships within this family. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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15 pages, 2864 KiB  
Article
Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals
by J. Antonio Baeza, Ryan Barata, Dilani Rajapakse, Jayra Penaloza, Preston Harrison and Adam Haberski
Genes 2023, 14(3), 657; https://doi.org/10.3390/genes14030657 - 5 Mar 2023
Cited by 3 | Viewed by 3111
Abstract
The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population’s health non-intrusively and inform strategies for [...] Read more.
The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population’s health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered ‘vulnerable’, ‘endangered’, and/or ‘critically endangered’ by the IUCN Red List of Threatened Species. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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9 pages, 2646 KiB  
Communication
The Mitochondrial Genomes of Two Parasitoid Wasps Protapanteles immunis and Parapanteles hyposidrae (Hymenoptera: Braconidae) with Phylogenetic Implications and Novel Gene Rearrangements
by Dandan Xiao, Ziqi Wang, Jiachen Zhu, Xiaogui Zhou, Pu Tang and Xuexin Chen
Genes 2023, 14(1), 230; https://doi.org/10.3390/genes14010230 - 16 Jan 2023
Viewed by 1816
Abstract
Parapanteles hypsidrae (Wilkinson, 1928) and Protapanteles immunis (Haliday, 1834) are the most important parasitic wasps of Ectropis grisescens Warren and Ectropis obliqua (Prout). We sequenced and annotated the mitochondrial genomes of Pa. hyposidrae and Pr. immunis, which are 17,063 bp and 16,397 [...] Read more.
Parapanteles hypsidrae (Wilkinson, 1928) and Protapanteles immunis (Haliday, 1834) are the most important parasitic wasps of Ectropis grisescens Warren and Ectropis obliqua (Prout). We sequenced and annotated the mitochondrial genomes of Pa. hyposidrae and Pr. immunis, which are 17,063 bp and 16,397 bp in length, respectively, and possess 37 mitochondrial genes. We discovered two novel types of gene rearrangement, the local inversion of nad4L in Pa. hyposidrae and the remote inversion of the block cox3-nad3-nad5-nad4 in Pr. immunis, within the mitogenomes of Braconidae. The phylogenetic analysis supported the subfamily Microgastrinae is a monophyletic group, but the tribes Apantelini and Cotesiini within this subfamily are paraphyletic groups. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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11 pages, 1297 KiB  
Article
Complete Mitogenome of the Triplophysa bombifrons: Comparative Analysis and Phylogenetic Relationships among the Members of Triplophysa
by Xinyue Wang, Yong Song, Haoyang Xie, Fangze Zi, Shengao Chen and Site Luo
Genes 2023, 14(1), 128; https://doi.org/10.3390/genes14010128 - 2 Jan 2023
Cited by 4 | Viewed by 2643
Abstract
In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. [...] Read more.
In the last decade, the phylogenetic relationships within the genus Triplophysa have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of Triplophysa bombifrons via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the Triplophysa genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of T. bombifrons was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for cox1, and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the Triplophysa genus can be divided into 4 main clades and demonstrated that T. bombifrons and T. tenuis are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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14 pages, 5890 KiB  
Article
A Compositional Heterogeneity Analysis of Mitochondrial Phylogenomics in Chalcidoidea Involving Two Newly Sequenced Mitogenomes of Eupelminae (Hymenoptera: Chalcidoidea)
by Jingtao Jiang, Tong Wu, Jun Deng and Lingfei Peng
Genes 2022, 13(12), 2340; https://doi.org/10.3390/genes13122340 - 11 Dec 2022
Cited by 1 | Viewed by 1662
Abstract
As next-generation sequencing technology becomes more mature and the cost of sequencing continues to fall, researchers are increasingly using mitochondrial genomes to explore phylogenetic relationships among different groups. In this study, we sequenced and analyzed the complete mitochondrial genomes of Eupelmus anpingensis and [...] Read more.
As next-generation sequencing technology becomes more mature and the cost of sequencing continues to fall, researchers are increasingly using mitochondrial genomes to explore phylogenetic relationships among different groups. In this study, we sequenced and analyzed the complete mitochondrial genomes of Eupelmus anpingensis and Merostenus sp. We predicted the secondary-structure tRNA genes of these two species and found that 21 of the 22 tRNA genes in Merostenus sp. exhibited typical clover-leaf structures, with trnS1 being the lone exception. In E. anpingensis, we found that, in addition to trnS1, the secondary structure of trnE was also incomplete, with only DHU arms and anticodon loop remaining. In addition, we found that compositional heterogeneity and variable rates of evolution are prevalent in Chalcidoidea. Under the homogeneity model, a Eupelmidae + Encyrtidae sister group relationship was proposed. Different datasets based on the heterogeneity model produced different tree topologies, but all tree topologies contained Chalcididae and Trichogrammatidae in the basal position of the tree. This is the first study to consider the phylogenetic relationships of Chalcidoidea by comparing a heterogeneity model with a homogeneity model. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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Review

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12 pages, 2004 KiB  
Review
Genetic Diversity in the mtDNA of Physarum polycephalum
by Freya Hammar and Dennis L. Miller
Genes 2023, 14(3), 628; https://doi.org/10.3390/genes14030628 - 2 Mar 2023
Viewed by 2406
Abstract
The mtDNA of the myxomycete Physarum polycephalum can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are classically found on the mtDNA of many organisms. However, 43 of these genes [...] Read more.
The mtDNA of the myxomycete Physarum polycephalum can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are classically found on the mtDNA of many organisms. However, 43 of these genes are cryptogenes that require a unique type of RNA editing (MICOTREM). A second category of gene is putative protein-coding genes represented by 26 significant open reading frames. However, these genes do not appear to be transcribed during the growth of the plasmodium and are currently unassigned since they do not have any apparent similarity to other classical mitochondrial protein-coding genes. The third category of gene is found in the mtDNA of some strains of P. polycephalum. These genes derive from a linear mitochondrial plasmid with nine significant, but unassigned, open reading frames which can integrate into the mitochondrial DNA by recombination. Here, we review the mechanism and evolution of the RNA editing necessary for cryptogene expression, discuss possible origins for the 26 unassigned open reading frames based on tentative identification of their protein product, and discuss the implications to mtDNA structure and replication of the integration of the linear mitochondrial plasmid. Full article
(This article belongs to the Special Issue Advanced Research on Mitochondrial Genome)
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