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Mitochondrial Genome of Aquatic Animals: Analysis of Structure, Evolution and Diversity

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 6489

Special Issue Editors


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Guest Editor
A.V. Zhirmunsky National Scientific Center of Marine Biology (NSCMB), Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
Interests: molecular biology; genomics; mitogenomics; molecular phylogenetics; biostatistics & bioinformatics; population biometry; genetics and breeding of fish & shellfish; conservation genetics

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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,

We gladly invite colleagues to submit papers to the Special Issue of IJMS that should be published within the current year.

Aim and Background of the Issue: The focus of this Special Issue is on the analysis of the structure, evolution, and diversity of mitogenomes in aquatic animals. Submissions with biomolecular experiments are especially welcomed due to the IJMS policy.

Guidance for potential authors: In recent years, genomics, including mitogenomics, has become a vast science frontier and is having significant scientific, social, and economic impacts along with the rapidly adopting technologies in many research fields in molecular science and biology. Submissions should be recent investigations related to the main directions defined above, representing the following: analysis of structure, evolution and diversity of mitogenomes in aquatic animals. Experimental evidence should contain some examples of the use of mitogenomes and other mtDNA molecular markers for the needs of basic biology and modern society. The structure, evolution, phylogenetic informativeness, diversity, and functioning of mitogenomes, along with the organism’s biology and lifestyle variability and mitonuclear relations, may also be included.

Prof. Dr. Yuri Kartavtsev
Prof. Dr. Ui Wook Hwang
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • aquatic animals
  • genomics
  • mitogenomes
  • structure
  • phylogenetic informativeness
  • evolution
  • comparative genomics
  • diversity
  • biomarker
  • function
  • mitonuclear relations

Published Papers (5 papers)

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Research

15 pages, 2691 KiB  
Article
Comparative Mitogenome Analyses of Fifteen Ramshorn Snails and Insights into the Phylogeny of Planorbidae (Gastropoda: Hygrophila)
by Kexin Tao, Yue Gao, Haofei Yin, Qichao Liang, Qianqian Yang and Xiaoping Yu
Int. J. Mol. Sci. 2024, 25(4), 2279; https://doi.org/10.3390/ijms25042279 - 14 Feb 2024
Viewed by 697
Abstract
Ramshorn snails from the family Planorbidae are important freshwater snails due to their low trophic level, and some of them act as intermediate hosts for zoonotic trematodes. There are about 250 species from 40 genera of Planorbidae, but only 14 species from [...] Read more.
Ramshorn snails from the family Planorbidae are important freshwater snails due to their low trophic level, and some of them act as intermediate hosts for zoonotic trematodes. There are about 250 species from 40 genera of Planorbidae, but only 14 species from 5 genera (Anisus, Biomphalaria, Bulinus, Gyraulus, and Planorbella) have sequenced complete mitochondrial genomes (mitogenomes). In this study, we sequenced and assembled a high-quality mitogenome of a ramshorn snail, Polypylis sp. TS-2018, which represented the first mitogenome of the genus. The mitogenome of Polypylis sp. TS-2018 is 13,749 bp in length, which is shorter than that of most gastropods. It contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA). We compared mitogenome characteristics, selection pressure, and gene rearrangement among all of the available mitogenomes of ramshorn snails. We found that the nonsynonymous and synonymous substitution rates (Ka/Ks) of most PCGs indicated purifying and negative selection, except for atp8 of Anisus, Biomphalaria, and Gyraulus, which indicated positive selection. We observed that transpositions and reverse transpositions occurred on 10 tRNAs and rrnS, which resulted in six gene arrangement types. We reconstructed the phylogenetic trees using the sequences of PCGs and rRNAs and strongly supported the monophyly of each genus, as well as three tribes in Planorbidae. Both the gene rearrangement and phylogenetic results suggested that Polypylis had a close relationship with Anisus and Gyraulus, while Bulinus was the sister group to all of the other genera. Our results provide useful data for further investigation of species identification, population genetics, and phylogenetics among ramshorn snails. Full article
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19 pages, 19929 KiB  
Article
Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)
by Shantanu Kundu, Hye-Eun Kang, Ah Ran Kim, Soo Rin Lee, Eun-Bi Kim, Muhammad Hilman Fu’adil Amin, Sapto Andriyono, Hyun-Woo Kim and Kyoungmi Kang
Int. J. Mol. Sci. 2024, 25(3), 1822; https://doi.org/10.3390/ijms25031822 - 2 Feb 2024
Viewed by 1226
Abstract
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The [...] Read more.
The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost’s, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses. Full article
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11 pages, 4455 KiB  
Communication
The Complete Mitochondrial Genome and Phylogenetic Analysis of the Freshwater Shellfish Novaculina chinensis (Bivalvia: Pharidae)
by Ziquan Zhou, Yuxin Song, Zewen Zheng, Yunguang Liu, Haiyan Yao, Xiaozhen Rao and Gang Lin
Int. J. Mol. Sci. 2024, 25(1), 67; https://doi.org/10.3390/ijms25010067 - 20 Dec 2023
Cited by 1 | Viewed by 872
Abstract
Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the [...] Read more.
Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the Pharidae family. In order to understand the phylogenetic relationships of N. chinensis, we sequenced the mitochondrial genome of the genus Novaculina, which is 16,262 bp in length and consists of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The phylogenetic relationships of 69 Imparidentian mitochondrial genomes (mitogenomes) indicated that N. chineisis is closely related to Sinonovacula constricta of the order Adapedonta. Our study also found that the Ka/Ks ratios of 12 protein-coding genes in the Pharidae family are lower than one, indicating the occurrence of negative purification selection. Morphological observations of the siphons of N. chinensis, Novaculina myanmarensis, and Novaculina gangetica indicate that N. chinensis may be the ancestral clade of the genus Novaculina, which has not been proposed in previous studies. Our study provides useful molecular information on the phylogenetic and evolutionary relationships of Pharidae and also contributes to the conservation and management of the germplasm resources of N. chinensis. Full article
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12 pages, 2171 KiB  
Article
The Complete Mitochondrial Genomes of Two Rock Scallops (Bivalvia: Spondylidae) Indicate Extensive Gene Rearrangements and Adaptive Evolution Compared with Pectinidae
by Fengping Li, Yu Zhang, Tao Zhong, Xin Heng, Tiancheng Ao, Zhifeng Gu, Aimin Wang, Chunsheng Liu and Yi Yang
Int. J. Mol. Sci. 2023, 24(18), 13844; https://doi.org/10.3390/ijms241813844 - 8 Sep 2023
Cited by 2 | Viewed by 1073
Abstract
Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the [...] Read more.
Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the present study, the complete mitochondrial genomes of Spondylus versicolor and S. spinosus were sequenced and compared with those of pectinids. The mtDNA of S. versicolor and S. spinosus show similar patterns with respect to genome size, AT content, AT skew, GC skew, and codon usage, and their mitogenomic sizes are longer than most pectinid species. The mtDNA of S. spinosus is 27,566 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, while an additional tRNA-Met was found in the mtDNA of S. versicolor, which is 28,600 bp in length. The monophylies of Spondylidae and Pectinidae were well supported, but the internal relationships within Pectinidae remain unresolved due to the paraphyly of the genus Mimachlamy and the controversial position of the tribe Aequipectinini. The gene orders of S. versicolor and S. spinosus are almost identical but differ greatly from species of the Pectinidae, indicating extensive gene rearrangements compared with Pectinidae. Positive selection analysis revealed evidence of adaptive evolution in the branch of Spondylidae. The present study could provide important information with which to understand the evolutionary progress of the diverse and economically significant marine bivalve Pectinoidea. Full article
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17 pages, 5517 KiB  
Article
Expression of Hairpin-Enriched Mitochondrial DNA in Two Hairworm Species (Nematomorpha)
by Olga V. Nikolaeva, Aleksandra M. Beregova, Boris D. Efeykin, Tatiana S. Miroliubova, Andrey Yu. Zhuravlev, Andrey Yu. Ivantsov, Kirill V. Mikhailov, Sergei E. Spiridonov and Vladimir V. Aleoshin
Int. J. Mol. Sci. 2023, 24(14), 11411; https://doi.org/10.3390/ijms241411411 - 13 Jul 2023
Viewed by 1292
Abstract
Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. [...] Read more.
Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes—a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species—Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the ‘blind spots’ of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes. Full article
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