Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

Wang, Jiachen; Xu, Wei; Liu, Yuyao; Bai, Yawen; Liu, Hongyi

doi:10.1016/j.gene.2023.147186

Cited by 5 publications

(14 citation statements)

References 60 publications

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“…The AT-skew were inconspicuously positive (0.002 ~ 0.076), indicating a small difference in the content of A and T in the mitogenomes. This phenomenon is also observed in other published Teleostei genomes ( Liu et al 2020 ; Ruan et al 2020 ; Xu et al 2021a , 2021b ; Wang et al 2023 ). The A nucleotide composition is commonly used to indicate gene direction and replication orientation during transcription and replication ( Wei et al 2010a , 2010b ).…”

Section: Results and Discussionsupporting

confidence: 85%

“…It typically contains 13 protein-coding genes ( PCGs ), two ribosomal RNA genes ( rRNAs ), 22 transfer RNA genes ( tRNAs ), and one control region ( CR ) ( Iwasaki et al 2013 ). Mitogenomes have the characteristics of high evolutionary rate, matrilineal inheritance, low molecular weight, simple structure, and ease of amplification, which makes them a reliable marker for studying phylogenetics ( Ye et al 2022 ; Wang et al 2023 ). Mitogenome components, such as nad2 or rrnL , are widely used for phylogenetic analyses ( Sturmbauer et al 2010 ; Schwarzer et al 2015 ).…”

Section: Introductionmentioning

confidence: 99%

“…Although partial mitochondrial sequences can offer some insights into evolutionary relationships, they are limited in their ability to provide a comprehensive understanding due to the absence of information such as gene rearrangement, genetic code changes, replication, and transcriptional regulation patterns. Therefore, complete mitogenome sequences can be more beneficial as they can provide improved resolution and sensitivity for investigating evolutionary relationships ( Li et al 2019 ; Fiteha et al 2023 ; Wang et al 2023 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

Wang,

Tai,

Zhang

et al. 2023

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In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologus kungweensis, L. meleagris, L. ornatipinnis, Neolamprologus brevis, N. caudopunctatus, N. leleupi, and N. similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A + T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A + T content was higher than the G + C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L. meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species.

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Section: Results and Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

Wang,

Tai,

Zhang

et al. 2023

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“…Invertebrate mitogenome consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and one non-coding control region (CR) 2 , 3 . The mitogenome has characteristics such as small size, simple structure and fast evolution, it has been extensively studied and widely used for species identification and molecular phylogeny researches 4 , 5 .…”

Section: Introductionmentioning

confidence: 99%

Characterization of the complete mitochondrial genome of Spirobolus grahami (Diplopoda: Spirobolidae) with phylogenetic analysis

Zhang,

Gan,

et al. 2024

Sci Rep

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Diplopoda is one of the most diverse and important groups of soil arthropods, but little research has been done on their phylogenetic relationship and evolution. Here, we sequenced and annotated the complete mitochondrial genomes of Spirobolus grahami. The total mitogenome of S. grahami was typical circular, double-stranded molecules, with 14,875 bp in length, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region. Base composition analysis suggested that the mitochondrial sequences were biased toward A and T, with A + T content of 58.68%. The mitogenomes of S. grahami exhibited negative AT and positive GC skews. Most of the 13 PCGs had ATN as the start codon, except COX1 start with CGA, and most PCGs ended with the T stop codon. The dN/dS values for most PCGs were lower than 1, suggesting that purifying selection was likely the main driver of mitochondrial PCG evolution. Phylogenetic analyses based on 13 PCGs using BI and ML methods support the classification of genus Spirobolus and Tropostreptus. Glomeridesmus spelaeus is distantly related to the other Diplopoda species.

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“…In the realm of animals, the mitochondrial genome (mitogenome) is a small, circular genome, ranging in size from 15 to 18 kb [ 10 , 11 ]. It generally contains 13 protein-coding genes (PCGs), 22 transport RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region (CR) [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

Xu,

Tai,

et al. 2024

Animals

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Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial genomes (mitogenomes) from four Nannostomus species for the first time. The four mitogenomes exhibited the typical circular structure, with overall sizes varying from 16,661 bp to 16,690 bp. They contained 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 1 control region (CR). Nucleotide composition analysis suggested that the mitochondrial sequences were biased toward A and T. Bayesian inference and maximum likelihood analyses based on PCGs support the family Lebiasinidae classification, described using four Nannostomus species, clustering together with Lebiasina multimaculata from the same family. The results of this study support the current taxonomic classification of the family Lebiasinidae. Phylogenetic analysis also suggested that gene rearrangement would not significantly impact the phylogenetic relationships within the order Characiformes. These results might provide new data regarding the phylogeny and classification of the order Characiformes, thus providing a theoretical basis for the economic development of aquarium fish markets.

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Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

Cited by 5 publications

References 60 publications

Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

Characterization of the complete mitochondrial genome of Spirobolus grahami (Diplopoda: Spirobolidae) with phylogenetic analysis

Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

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Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

Cited by 5 publications

References 60 publications

﻿Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

﻿Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

Characterization of the complete mitochondrial genome of Spirobolus grahami (Diplopoda: Spirobolidae) with phylogenetic analysis

Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

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Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae

Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae