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Mitochondrial Genome 2024
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Mitochondrial Genome 2024

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Biochemistry, Molecular and Cellular Biology".

Deadline for manuscript submissions: 31 July 2024 | Viewed by 10097

Special Issue Editor

Prof. Dr. Ui Wook Hwang

E-Mail Website
Guest Editor
Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
Interests: mitochondrial genome evolution; animal phylogeny (focusing on arthropods); population genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mitochondria possess a remnant of the endosymbiont’s genome that varies considerably in size throughout eukaryotes, ranging from ~15 kb to 11 Mbp. Mitochondrial genomes are mostly circular, containing 5 to ~100 genes (usually 37 genes in metazoans). In recent decades, due to the rapid advances in next-generation sequencing technology and compact structure of mitochondrial genomes, complete mitochondrial genome data have been exponentially increased and accumulated. Extensive sequencing of mitochondrial genomes has established meaningful and unique features in gene arrangements and genetic codes as well as nucleotide sequence substitutions, shedding light on enigmatic phylogenetic relationships and evolutionary histories in eukaryotes, especially metazoans. Additionally, a mitochondrial gene component, COI is known for the most promising metazoan DNA barcoding marker, which has been frequently employed for molecular species identification. Mitochondrial genomes are small but powerful in a variety of aspects, such as eukaryote phylogeny, evolution, population genetics, etc.

Prof. Dr. Ui Wook Hwang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at mdpi.longhoe.net 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.

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 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

  • mitochondria
  • mitochondrial genomes
  • mitochondrial genome data

 

Published Papers (5 papers)

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Research

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13 pages, 2682 KiB  
Article
Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae)
by Quanheng Li, Peiyue Jiang, Mingxuan Li, **g**g Du, Jianxiang Sun, Nuo Chen, Yu Wu, Qing Chang and Chaochao Hu
Curr. Issues Mol. Biol. 2024, 46(6), 6186-6198; https://doi.org/10.3390/cimb46060369 - 19 Jun 2024
Viewed by 323
Abstract
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and [...] Read more.
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and partial mtDNA from Numenius arquata, Limosa limosa, and Limnodromus semipalmatus. The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, T--). In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that ATP8 was the least conserved while COX3 had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera Xenus and Actitis were clustered into another sister group, while the genus Phalaropus is more closely related to the genus Tringa. The genera Limnodromus, Gallinago, and Scolopax form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae. Full article
(This article belongs to the Special Issue Mitochondrial Genome 2024)
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17 pages, 2626 KiB  
Article
Molecular Approaches Detect Early Signals of Programmed Cell Death in Hippolyte inermis Leach
by Francesca Glaviano, Roberta Esposito, Emanuele Somma, Amir Sagi, Eliahu D. Aflalo, Maria Costantini and Valerio Zupo
Curr. Issues Mol. Biol. 2024, 46(6), 6169-6185; https://doi.org/10.3390/cimb46060368 - 18 Jun 2024
Viewed by 342
Abstract
The protandric shrimp Hippolyte inermis is the only known marine invertebrate whose sex determination is strongly influenced by the composition of its food. In H. inermis, a sex reversal is triggered by the ingestion of diatoms of the genus Cocconeis associated with [...] Read more.
The protandric shrimp Hippolyte inermis is the only known marine invertebrate whose sex determination is strongly influenced by the composition of its food. In H. inermis, a sex reversal is triggered by the ingestion of diatoms of the genus Cocconeis associated with leaves of the seagrass Posidonia oceanica. These diatoms contain compounds that promote programmed cell death (PCD) in H. inermis and also in human cancer cells. Transcriptomic analyses suggested that ferroptosis is the primary trigger of the shrimp’s sex reversal, leading to the rapid destruction of the androgen gland (AG) followed by a chain of apoptotic events transforming the testes into ovaries. Here, we propose a molecular approach to detect the effects of compounds stimulating the PCD. An RNA extraction method, suitable for young shrimp post-larvae (five days after metamorphosis; PL5 stage), was established. In addition, six genes involved in apoptosis, four involved in ferroptosis, and seven involved in the AG switch were mined from the transcriptome, and their expression levels were followed using real-time qPCR in PL5 fed on Cocconeis spp., compared to PL5 fed on a basic control feed. Our molecular approach, which detected early signals of sex reversal, represents a powerful instrument for investigating physiological progression and patterns of PCD in marine invertebrates. It exemplifies the physiological changes that may start a few days after the settlement of post-larvae and determine the life destiny of an individual. Full article
(This article belongs to the Special Issue Mitochondrial Genome 2024)
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12 pages, 3454 KiB  
Communication
Complete Mitogenome of “Pumpo” (Bos taurus), a Top Bull from a Peruvian Genetic Nucleus, and Its Phylogenetic Analysis
by Richard Estrada, Deyanira Figueroa, Yolanda Romero, Wuesley Yusmein Alvarez-García, Diorman Rojas, Wigoberto Alvarado, Jorge L. Maicelo, Carlos Quilcate and Carlos I. Arbizu
Curr. Issues Mol. Biol. 2024, 46(6), 5352-5363; https://doi.org/10.3390/cimb46060320 - 28 May 2024
Viewed by 756
Abstract
The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim [...] Read more.
The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices. Full article
(This article belongs to the Special Issue Mitochondrial Genome 2024)
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14 pages, 3972 KiB  
Article
Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes
by Gaoji Zhang, Tangjun Xu, Yukun Chen, Wei Xu, Yinuo Wang, Yuanyuan Li, Fuyuan Zhu, Hongyi Liu and Honghua Ruan
Curr. Issues Mol. Biol. 2024, 46(3), 2514-2527; https://doi.org/10.3390/cimb46030159 - 15 Mar 2024
Viewed by 775
Abstract
There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of [...] Read more.
There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes. Full article
(This article belongs to the Special Issue Mitochondrial Genome 2024)
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Review

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22 pages, 770 KiB  
Review
Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders
by Shafi Mahmud, Suvro Biswas, Shamima Afrose, Mohasana Akter Mita, Md. Robiul Hasan, Mst. Sharmin Sultana Shimu, Gobindo Kumar Paul, Sanghyun Chung, Md. Abu Saleh, Sultan Alshehri, Momammed M. Ghoneim, Maha Alruwaily and Bonglee Kim
Curr. Issues Mol. Biol. 2022, 44(3), 1127-1148; https://doi.org/10.3390/cimb44030074 - 27 Feb 2022
Cited by 8 | Viewed by 7260
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial [...] Read more.
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications. Full article
(This article belongs to the Special Issue Mitochondrial Genome 2024)
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