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Mitochondrial Genome 2024

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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: closed (31 July 2024) | Viewed by 21612

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Prof. Dr. Ui Wook Hwang

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Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
Interests: mitochondrial genome evolution; animal phylogeny (focusing on arthropods); population genetics
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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

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Keywords

mitochondria
mitochondrial genomes
mitochondrial genome data

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Research

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20 pages, 6007 KiB

Open AccessArticle

Integrative Taxonomy Reveals New Insights into the Species Validity of the Neocaridina davidi-N. denticulata-N. heteropoda Complex and Mitogenomic Phylogeny of Caridean Shrimps

by Mei Yang, Xiaodong Cui, Xinzheng Li, Dong Dong, Xianjiang Kang and Zhibin Gan

Curr. Issues Mol. Biol. 2024, 46(11), 12279-12298; https://doi.org/10.3390/cimb46110729 - 31 Oct 2024

Viewed by 829

Abstract

The genus Neocaridina, originating from East Asia and representing a small-size landlocked shrimp group of the family Atyidae, is an important group of ornamental shrimps and plays significant ecological roles in their natural habitats. Owing to the considerable variability of the taxonomic characters it employed, Neocaridina is constantly under revision, and the validation of several species is currently questionable. In the present study, several Neocaridina shrimps were collected from the Baiyangdian drainage area. Through morphological examination, they exhibited delicately diagnostical differences in the dactyli of the third pereiopod and the endopod of the first and second pleopod and were classified into morph A, morph B and morph C. According to the literature description, morph A and morph C were identified as N. denticulata denticulata and N. denticulata sinensis, respectively. Among them, morph B presents an intermediate state between morph A and morph C. Subsequently, we determined the mitogenomes of morph A, morph B and morph C. Based on the morphological characteristics, genetic variation and phylogenetic tree, we contend that N. davidi, N. d. denticulata, N. d. sinensis and N. heteropoda should belong to the same species, and we propose retaining the name N. denticulata. The reconstructed mitogenomic phylogeny indicated that the monophyly of several genera within Atyidae has been challenged, suggesting that the established classification of Atyidae requires substantial taxonomic revision at all taxonomic levels. Furthermore, the tree’s topologies supported Atyidae at a deeper base within Caridea. More comprehensive taxon sampling is still needed to resolve the explicit internal relationships among Caridea. Full article

(This article belongs to the Special Issue Mitochondrial Genome 2024)

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11 pages, 6107 KiB

Open AccessArticle

The Complete Mitochondrial Genomes of Penthe kochi (Coleoptera: Tetratomidae) with Its Phylogenetic Implications

by Bowen Ouyang, Yingying Li, Jieqiong Wang, Zhonghua Wei and Aimin Shi

Curr. Issues Mol. Biol. 2024, 46(10), 10795-10805; https://doi.org/10.3390/cimb46100641 - 26 Sep 2024

Viewed by 658

Abstract

To explore the mitogenome characteristics of Tetratomidae and the phylogenetic position of this family in Tenebrionoidea, the mitogenome of Penthe kochi Mařan, 1940 was sequenced, annotated, and analyzed. The P. kochi mitogenome is consistent with Tenebrionoidea species in gene length, genomic organization, codon usage, and secondary structures of transfer genes (tRNAs). Most protein-coding genes (PCGs) originate with a typical ATN start codon, except nad1 and nad3, which start with TTG. In total, 10 PCGs are terminated with complete stop codon TAA and TAG, while cox1, cox2, and nad 4 contain an incomplete stop codon T-. Among the 13 PCGs, nad2 (Pi = 0.282) has the most diverse nucleotide composition, and cox2 is the most conserved gene with the lowest value (Pi = 0.154). The Ka/Ks ratio of cox1 (0.076) and cox2 (0.124) has a lower value. All the tRNAs can be folded in a typical clover-leaf secondary structure, except trnS1, which lacked a dihydrouridine arm. And phylogenetic analyses were performed based on 13 PCGs using the Bayesian inference (BI) method. The results showed that the clade of Tenebrionoidea was well separated from the outgroups, and Tetratomidae and Mycetophagidae were not well resolved. Phylogenetic analyses with more mitogenome samplings are needed to resolve the phylogeny of Tenebrionoidea. Full article

(This article belongs to the Special Issue Mitochondrial Genome 2024)

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20 pages, 3422 KiB

Open AccessArticle

Characterization of the Complete Mitochondrial Genome of the Central Highland Grey-Shanked Douc Langur (Pygathrix cinerea), a Critically Endangered Species Endemic to Vietnam (Mammalia: Primates)

by Mai Thi Phuong Nguyen, Tram Thi Thuy Nguyen, Tung Thanh Ha, Chi Nguyen Quynh Ho, Cuong Phan Minh Le, Huy Nghia Quang Hoang, Quynh Thi Nhu Nguyen, Tao Thien Nguyen, Dung Tri Luu, Khoa Dang Dang, Quan Ke Thai and Long Thanh Le

Curr. Issues Mol. Biol. 2024, 46(9), 9928-9947; https://doi.org/10.3390/cimb46090592 - 6 Sep 2024

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Abstract

The grey-shanked douc langur (Pygathrix cinerea) is a recently described, critically endangered primate, endemic to Vietnam. In this study, we describe the Central Highland species’ complete mitochondrial genome (mitogenome—mtDNA). It is a circular molecule with a length of 16,541 base pairs (bp). The genome consists of 37 genes, consistent with those found in most other vertebrates, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs. A comparison with the mitogenomes of more than 50 primates showed that the mitogenome of Vietnamese Central Highland Pygathrix cinerea has a conservative gene order. We identified 43 nucleotide differences when comparing this genome with a previously published mitogenome of Pygathrix cinerea. It is evident that there are distinct differences between the Pygathrix cinerea we are currently studying and other Pygathrix cinerea specimens. These differences are unlikely to be solely the result of sequencing errors, as the mitogenomes were generated using high-quality methods. The genetic divergence observed between the two Pygathrix cinerea mitogenomes implies the potential existence of at least two distinct lineages or forms of this primate species within its native range in Vietnam. Full article

(This article belongs to the Special Issue Mitochondrial Genome 2024)

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14 pages, 2880 KiB

Open AccessArticle

Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae)

by Xuhui Chen, Yudi Zhao, Shenghua Xu, Yingze Zhou, Lijie Zhang, Bo Qu and Yufeng Xu

Curr. Issues Mol. Biol. 2024, 46(9), 9807-9820; https://doi.org/10.3390/cimb46090582 - 3 Sep 2024

Viewed by 880

Abstract

In order to understand the bias and main affecting factors of codon usage in the plastid genome of Diplandrorchis sinica, which is a rare and endangered plant species in the Orchidaceae family, the complete plastid genome sequence of D. sinica was downloaded from the GenBank database and 20 protein-coding sequences that met the analysis requirements were finally selected. The GC content, length of the amino acid (Laa), relative synonymous codon usage (RSCU), and effective number of codon (ENC) of each gene and codon were calculated using the CodonW and EMBOSS online programs. Neutral plot analysis, ENC-plot analysis, PR2-plot analysis, and correspondence analysis were performed using Origin Pro 2024 software, and correlation analysis between various indicators was performed using SPSS 23.0 software. The results showed that the third base of the codon in the plastid genome of D. sinica was rich in A and T, with a GC₃ content of 27%, which was lower than that of GC₁ (45%) and GC₂ (39%). The ENC value ranged from 35 to 57, with an average of 47. The codon usage bias was relatively low, and there was a significant positive correlation between ENC and GC₃. There were a total of 32 codons with RSCU values greater than 1, of which 30 ended with either A or U. There were a total of nine optimal codons identified, namely, UCU, UCC, UCA, GCA, UUG, AUA, CGU, CGA, and GGU. This study indicated that the dominant factor affecting codon usage bias in the plastid genome of D. sinica was natural selection pressure, while the impact of base mutations was limited. The codon usage patterns were not closely related to gene types, and the distribution of photosynthetic system genes and ribosomal protein-coding gene loci was relatively scattered, indicating significant differences in the usage patterns of these gene codons. In addition, the codon usage patterns may not be related to whether the plant is a photosynthetic autotrophic or heterotrophic nutritional type. The results of this study could provide scientific references for the genomic evolution and phylogenetic research of plant species in the family Orchidaceae. Full article

(This article belongs to the Special Issue Mitochondrial Genome 2024)

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7 pages, 1055 KiB

Open AccessCommunication

The Mitogenome of the Subarctic Octocoral Alcyonium digitatum Reveals a Putative tRNA^Pro Gene Nested within MutS

by Alisa Heuchel, Åse Emblem, Tor Erik Jørgensen, Truls Moum and Steinar Daae Johansen

Curr. Issues Mol. Biol. 2024, 46(8), 8104-8110; https://doi.org/10.3390/cimb46080479 - 27 Jul 2024

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Abstract

We sequenced and analyzed the complete mitogenome of a Norwegian isolate of the octocoral Alcyonium digitatum using the Ion Torrent sequencing technology. The 18,790 bp circular mitochondrial genome was found to harbor the same set of 17 genes, which encode 14 protein subunits, two structural ribosomal RNAs and one tRNA, as reported in other octocorals. In addition, we detected a new tRNA^Pro-like gene sequence nested within the MutS protein coding region. This putative tRNA gene feature appears to be conserved among the octocorals but has not been reported previously. The A. digitatum mitogenome was also shown to harbor an optional gene (ORFA) that encodes a putative protein of 191 amino acids with unknown function. A mitogenome-based phylogenetic analysis, presented as a maximum likelihood tree, showed that A. digitatum clustered with high statistical confidence with two other Alcyonium species endemic to the Mediterranean Sea and the Southeast Pacific Ocean. Full article

(This article belongs to the Special Issue Mitochondrial Genome 2024)

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13 pages, 2682 KiB

Open AccessArticle

Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae)

by Quanheng Li, Peiyue Jiang, Mingxuan Li, Jingjing 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 1017

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 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

Open AccessArticle

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

Cited by 1 | Viewed by 3671

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 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

Open AccessCommunication

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 1640

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 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

Open AccessArticle

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 1322

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 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

Open AccessReview

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 11 | Viewed by 8187

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 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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