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Mitochondrial Genomes: Genetic and Transcriptomic Studies
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Mitochondrial Genomes: Genetic and Transcriptomic Studies

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

Deadline for manuscript submissions: closed (15 January 2019) | Viewed by 25408

Special Issue Editors

Prof. Dr. Yan Guo

grade E-Mail Website1 Website2
Guest Editor
Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
Interests: genomics; genetics; bioinformatics; mitochondria; data mining; machine learning; high throughput genomic data
Special Issues, Collections and Topics in MDPI journals
Dr. Sergey Ivanov

E-Mail Website
Guest Editor
Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Interests: genome evolution; cancer genetics and metabolism; mitochondria; diabetes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mitochondria are small double membraned bound organelles found in almost every cell of all organisms. They are primarily responsible for energy production. Typically, there are approximately 100 mitochondria in each mammalian cell, and each mitochondrion harbors 2–10 copies of mitochondrial DNA. The human mitochondria genome is a double-stranded circular DNA molecule, consisting of 16,569 nucleotides. It contains 13 protein-coding genes, 22 transfer RNAs (tRNAs), and two ribosomal RNAs. Mitochondrial DNA (mtDNA) is maternally inherited, thus its genome is haploid. However, many sites in mitochondria DNA are heteroplasmic, containing two alleles. Mitochondrial DNA variants have been linked to various diseases and important biological processes, such as cancer, aging, etc. Mitochondrial research is on the rise across multiple fields in the medical sciences. Especially with the rise of high throughput sequencing, researchers now can examine mitochondria genome in unprecedented detail. In this Special Issue, we would like to invite researchers to share their latest work on the following mitochondria related (without being limited to) topics:

  • Mitochondrial sequence analysis
  • Mitochondrial mutations related to diseases or trait
  • Mitochondrial mechanisms related to diseases or trait
  • Mitochondrial heteroplasmy analysis
  • Biotechnology aspects related to mitochondria research
  • Bioinformatics, statistical aspects of mitochondria research

Prof. Yan Guo
Dr. Sergey Ivanov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mitochondrial sequence analysis
  • mitochondrial mutations related to diseases or trait
  • mitochondrial mechanisms related to diseases or trait
  • mitochondrial heteroplasmy analysis
  • biotechnology aspects related to mitochondria research
  • bioinformatics, statistical aspects of mitochondria research

Published Papers (6 papers)

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Research

14 pages, 660 KiB  
Communication
Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins
by Evgeniy S. Balakirev
Genes 2019, 10(8), 592; https://doi.org/10.3390/genes10080592 - 05 Aug 2019
Viewed by 3079
Abstract
Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference [...] Read more.
Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes. Full article
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
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13 pages, 3492 KiB  
Article
The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis
by Tiezhu Yang, Guolyu Xu, Bingning Gu, Yanmei Shi, Hellen Lucas Mzuka and Heding Shen
Genes 2019, 10(3), 198; https://doi.org/10.3390/genes10030198 - 05 Mar 2019
Cited by 13 | Viewed by 5034
Abstract
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA [...] Read more.
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus. Full article
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
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16 pages, 1434 KiB  
Article
On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia
by Guillaume Besnard, Ngan Thi-Phan, Hai Ho-Bich, Alexis Dereeper, Hieu Trang Nguyen, Patrick Quénéhervé, Jamel Aribi and Stéphane Bellafiore
Genes 2019, 10(2), 175; https://doi.org/10.3390/genes10020175 - 25 Feb 2019
Cited by 14 | Viewed by 3988
Abstract
Meloidogyne graminicola is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different [...] Read more.
Meloidogyne graminicola is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different environments. Previous studies on nuclear ribosomal DNA (nrDNA) suggested a close phylogenetic relationship between M. graminicola and Meloidogyne oryzae, despite their different modes of reproduction and geographical distribution. In order to clarify the evolutionary history of these two species and explore their molecular intraspecific diversity, we sequenced the genome of 12 M. graminicola isolates, representing populations of worldwide origins, and two South American isolates of M. oryzae. k-mer analysis of their nuclear genome and the detection of divergent homologous genomic sequences indicate that both species show a high proportion of heterozygous sites (ca. 1–2%), which had never been previously reported in facultative meiotic parthenogenetic RKNs. These analyses also point to a distinct ploidy level in each species, compatible with a diploid M. graminicola and a triploid M. oryzae. Phylogenetic analyses of mitochondrial genomes and three nuclear genomic sequences confirm close relationships between these two species, with M. graminicola being a putative parent of M. oryzae. In addition, comparative mitogenomics of those 12 M. graminicola isolates with a Chinese published isolate reveal only 15 polymorphisms that are phylogenetically non-informative. Eight mitotypes are distinguished, the most common one being shared by distant populations from Asia and America. This low intraspecific diversity, coupled with a lack of phylogeographic signal, suggests a recent worldwide expansion of M. graminicola. Full article
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
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19 pages, 3356 KiB  
Article
The Mitochondrial Genomes of Neuropteridan Insects and Implications for the Phylogeny of Neuroptera
by Nan Song, Xin-Xin Li, Qing Zhai, Hakan Bozdoğan and Xin-Ming Yin
Genes 2019, 10(2), 108; https://doi.org/10.3390/genes10020108 - 01 Feb 2019
Cited by 14 | Viewed by 3284
Abstract
The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out [...] Read more.
The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae. Full article
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
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11 pages, 971 KiB  
Article
Characterization of the Complete Mitochondrial Genome of Ostertagia trifurcata of Small Ruminants and its Phylogenetic Associations for the Trichostrongyloidea Superfamily
by Awais Ali Ahmad, Xin Yang, Ting Zhang, Chunqun Wang, Caixian Zhou, Xingrun Yan, Mubashar Hassan, Muhammad Ikram and Min Hu
Genes 2019, 10(2), 107; https://doi.org/10.3390/genes10020107 - 31 Jan 2019
Cited by 10 | Viewed by 3958
Abstract
The complete mitochondrial (mt) genome of Ostertagia trifurcata, a parasitic nematode of small ruminants, has been sequenced and its phylogenetic relationship with selected members from the superfamily Trichostrongyloidea was investigated on the basis of deduced datasets of mt amino acid sequences. The [...] Read more.
The complete mitochondrial (mt) genome of Ostertagia trifurcata, a parasitic nematode of small ruminants, has been sequenced and its phylogenetic relationship with selected members from the superfamily Trichostrongyloidea was investigated on the basis of deduced datasets of mt amino acid sequences. The entire mt genome of Ostertagia trifurcata is circular and 14,151 bp in length. It consists of a total of 36 genes comprising 12 genes coding for proteins (PCGs), 2 genes for ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes and 2 non-coding regions, since all genes are transcribed in the same direction. The phylogenetic analysis based on the concatenated datasets of predicted amino acid sequences of the 12 protein coding genes supported monophylies of the Haemonchidae, Dictyocaulidae and Molineidae families, but rejected monophylies of the Trichostrongylidae family. The complete characterization and provision of the mtDNA sequence of Ostertagia trifurcata provides novel genetic markers for molecular epidemiological investigations, systematics, diagnostics and population genetics of Ostertagia trifurcata and its correspondents. Full article
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
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13 pages, 3463 KiB  
Article
Assembly of the Mitochondrial Genome in the Campanulaceae Family Using Illumina Low-Coverage Sequencing
by Hyun-Oh Lee, Ji-Weon Choi, Jeong-Ho Baek, Jae-Hyeon Oh, Sang-Choon Lee and Chang-Kug Kim
Genes 2018, 9(8), 383; https://doi.org/10.3390/genes9080383 - 30 Jul 2018
Cited by 18 | Viewed by 5361
Abstract
Platycodon grandiflorus (balloon flower) and Codonopsis lanceolata (bonnet bellflower) are important herbs used in Asian traditional medicine, and both belong to the botanical family Campanulaceae. In this study, we designed and implemented a de novo DNA sequencing and assembly strategy to map the [...] Read more.
Platycodon grandiflorus (balloon flower) and Codonopsis lanceolata (bonnet bellflower) are important herbs used in Asian traditional medicine, and both belong to the botanical family Campanulaceae. In this study, we designed and implemented a de novo DNA sequencing and assembly strategy to map the complete mitochondrial genomes of the first two members of the Campanulaceae using low-coverage Illumina DNA sequencing data. We produced a total of 28.9 Gb of paired-end sequencing data from the genomic DNA of P. grandiflorus (20.9 Gb) and C. lanceolata (8.0 Gb). The assembled mitochondrial genome of P. grandiflorus was found to consist of two circular chromosomes; the master circle contains 56 genes, and the minor circle contains 42 genes. The C. lanceolata mitochondrial genome consists of a single circle harboring 54 genes. Using a comparative genome structure and a pattern of repeated sequences, we show that the P. grandiflorus minor circle resulted from a recombination event involving the direct repeats of the master circle. Our dataset will be useful for comparative genomics and for evolutionary studies, and will facilitate further biological and phylogenetic characterization of species in the Campanulaceae. Full article
(This article belongs to the Special Issue Mitochondrial Genomes: Genetic and Transcriptomic Studies)
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