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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: closed (30 November 2021) | Viewed by 9774

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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

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 five to ~100 genes (usually 37 genes in metazoans). In recent decades, due to the rapid advance of 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

mitochondrial genome
eukaryote phylogeny and evolution
next-generation sequencing
gene arrangement
population genetics
DNA barcoding

Published Papers (4 papers)

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Research

17 pages, 12156 KiB

Open AccessArticle

Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats

by Zhenming Lü, Yantao Liu, Shijie Zhao, Jiaqi Fang, Kehua Zhu, Jing Liu, Li Gong, Liqin Liu and Bingjian Liu

Int. J. Mol. Sci. 2023, 24(5), 4362; https://doi.org/10.3390/ijms24054362 - 22 Feb 2023

Cited by 5 | Viewed by 1561

Abstract

The water-to-land transition is one of the most important events in evolutionary history of vertebrates. However, the genetic basis underlying many of the adaptations during this transition remains unclear. Mud-dwelling gobies in the subfamily Amblyopinae are one of the teleosts lineages that show terrestriality and provide a useful system for clarifying the genetic changes underlying adaptations to terrestrial life. Here, we sequenced the mitogenome of six species in the subfamily Amblyopinae. Our results revealed a paraphyletic origin of Amblyopinae with respect to Oxudercinae, which are the most terrestrial fishes and lead an amphibious life in mudflats. This partly explains the terrestriality of Amblyopinae. We also detected unique tandemly repeated sequences in the mitochondrial control region in Amblyopinae, as well as in Oxudercinae, which mitigate oxidative DNA damage stemming from terrestrial environmental stress. Several genes, such as ND2, ND4, ND6 and COIII, have experienced positive selection, suggesting their important roles in enhancing the efficiency of ATP production to cope with the increased energy requirements for life in terrestrial environments. These results strongly suggest that the adaptive evolution of mitochondrial genes has played a key role in terrestrial adaptions in Amblyopinae, as well as in Oxudercinae, and provide new insights into the molecular mechanisms underlying the water-to-land transition in vertebrates. Full article

(This article belongs to the Special Issue Mitochondria Genome)

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13 pages, 836 KiB

Open AccessArticle

Changes of Gut Microbiota by Natural mtDNA Variant Differences Augment Susceptibility to Metabolic Disease and Ageing

by Axel Künstner, Paul Schilf, Hauke Busch, Saleh M. Ibrahim and Misa Hirose

Int. J. Mol. Sci. 2022, 23(3), 1056; https://doi.org/10.3390/ijms23031056 - 19 Jan 2022

Cited by 2 | Viewed by 1893

Abstract

We recently reported on two mouse strains carrying different single nucleotide variations in the mitochondrial complex I gene, i.e., B6-mt^BPL mice carrying m.11902T>C and B6-mt^ALR carrying m.4738C>A. B6-mt^BPL mice exhibited a longer lifespan and a lower metabolic disease susceptibility despite mild mitochondrial functional differences in steady-state. As natural polymorphisms in the mitochondrial DNA (mtDNA) are known to be associated with distinct patterns of gut microbial composition, we further investigated the gut microbiota composition in these mice strains. In line with mouse phenotypes, we found a significantly lower abundance of Proteobacteria, which is positively associated with pathological conditions, in B6-mt^BPL compared to B6-mt^ALR mice. A prediction of functional profile of significantly differential bacterial genera between these strains revealed an involvement of glucose metabolism pathways. Whole transcriptome analysis of liver samples from B6-mt^BPL and B6-mt^ALR mice confirmed these findings. Thus, both host gene expression and gut microbial changes caused by the mtDNA variant differences may contribute to the ageing and metabolic phenotypes observed in these mice strains. Since gut microbiota are easier to modulate, compared with mtDNA variants, identification of such mtDNA variants, specific gut bacterial species and bacterial metabolites may be a potential intervention to modulate common diseases, which are differentially susceptible to individuals with different mtDNA variants. Full article

(This article belongs to the Special Issue Mitochondria Genome)

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16 pages, 3392 KiB

Open AccessArticle

Comparative Mitogenomics of Fungal Species in Stachybotryaceae Provides Evolutionary Insights into Hypocreales

by Li-Yuan Ren, Shu Zhang and Yong-Jie Zhang

Int. J. Mol. Sci. 2021, 22(24), 13341; https://doi.org/10.3390/ijms222413341 - 12 Dec 2021

Cited by 10 | Viewed by 2204

Abstract

Stachybotrys chartarum is one of the world’s ten most feared fungi within the family Stachybotryaceae, although to date, not a single mitogenome has been documented for Stachybotryaceae. Herein, six mitogenomes of four different species in Stachybotryaceae are newly reported. The S. chartarum mitogenome was 30.7 kb in length and contained two introns (one each in rnl and cox1). A comparison of the mitogenomes of three different individuals of S. chartarum showed few nucleotide variations and conservation of gene content/order and intron insertion. A comparison of the mitogenomes of four different Stachybotryaceae species (Memnoniella echinata, Myrothecium inundatum, S. chartarum, and S. chlorohalonata), however, revealed variations in intron insertion, gene order/content, and nad2/nad3 joining pattern. Further investigations on all Hypocreales species with available mitogenomes showed greater variabilities in gene order (six patterns) and nad2/nad3 joining pattern (five patterns) although a dominant pattern always existed in each case. Ancestral state estimation showed that in each case the dominant pattern was always more ancestral than those rare patterns. Phylogenetic analyses based on mitochondrion-encoded genes supported the placement of Stachybotryaceae in Hypocreales. The crown age of Stachybotryaceae was estimated to be approximately the Early Cretaceous (141–142 Mya). This study greatly promotes our understanding of the evolution of fungal species in Hypocreales. Full article

(This article belongs to the Special Issue Mitochondria Genome)

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15 pages, 4519 KiB

Open AccessArticle

Comparative Analysis of Mitochondrial Genome Features among Four Clonostachys Species and Insight into Their Systematic Positions in the Order Hypocreales

by Zhiyuan Zhao, Kongfu Zhu, Dexiang Tang, Yuanbing Wang, Yao Wang, Guodong Zhang, Yupeng Geng and Hong Yu

Int. J. Mol. Sci. 2021, 22(11), 5530; https://doi.org/10.3390/ijms22115530 - 24 May 2021

Cited by 7 | Viewed by 2709

Abstract

The mycoparasite fungi of Clonostachys have contributed to the biological control of plant fungal disease and nematodes. The Clonostachys fungi strains were isolated from Ophiocordyceps highlandensis, Ophiocordycepsnigrolla and soil, which identified as Clonostachyscompactiuscula, Clonostachysrogersoniana, Clonostachyssolani and Clonostachys sp. To explore the evolutionary relationship between the mentioned species, the mitochondrial genomes of four Clonostachys species were sequenced and assembled. The four mitogenomes consisted of complete circular DNA molecules, with the total sizes ranging from 27,410 bp to 42,075 bp. The GC contents, GC skews and AT skews of the mitogenomes varied considerably. Mitogenomic synteny analysis indicated that these mitogenomes underwent gene rearrangements. Among the 15 protein-coding genes within the mitogenomes, the nad4L gene exhibited the least genetic distance, demonstrating a high degree of conservation. The selection pressure analysis of these 15 PCGs were all below 1, indicating that PCGs were subject to purifying selection. Based on protein-coding gene calculation of the significantly supported topologies, the four Clonostachys species were divided into a group in the phylogenetic tree. The results supplemented the database of mitogenomes in Hypocreales order, which might be a useful research tool to conduct a phylogenetic analysis of Clonostachys. Additionally, the suitable molecular marker was significant to study phylogenetic relationships in the Bionectriaceae family. Full article

(This article belongs to the Special Issue Mitochondria Genome)

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