Comparative mitochondrial genomics of tetras: insights into phylogenetic relationships in Characidae

Xu, Wei; Wang, Jiachen; Xu, Runfeng; Jiang, Haoming; Ding, Jiayu; Wu, Han; Wu, Yaoyao; Liu, Hongyi

doi:10.1007/s11756-022-01195-4

Cited by 3 publications

(10 citation statements)

References 40 publications

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“…2 . The RSCUs analysis of S. grahami showed that codons tended to use more A or T at the third codon, which is consistent with some previous studies 27 , 28 . The dN/dS of the PCGs in the mitogenome of Spirobolus ( S bungii , S. grahami , and S. walkeri ) were calculated, too (Table 4 ).…”

Section: Resultssupporting

confidence: 91%

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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Section: Resultssupporting

confidence: 91%

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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“…Since molecular taxonomy usually employs mitochondrial gene sequences to infer phylogenetic relationships [8], we used the sequence of 13 PCGs to improve the understanding of Characidae phylogeny. Our results did not support four genera (Hemigrammus, Hyphessobrycon, Moenkhausia, and Psalidodon) (Figure 6), corroborating the findings of the previous studies [10] and indicating that Hyphessobrycon is not a monophyletic group.…”

Section: Discussionsupporting

confidence: 80%

“…Phylogenetic analysis was performed using the same genomes reported previously [9]. We created a concatenated set of base sequences from 35 species to examine the phylogenetic relationships of the Characidae (see Supplementary Table S1; [10,[23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]). Geneious ® software (version 9.0.5) was used to generate the alignments [38] and Lebiasina astrigata (Regan, 1903) was used as an outgroup.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…The genus Hyphessobrycon includes about 160 species [2] and is polyphyletic. Although polyphyly has been demonstrated by molecular phylogenies and total evidence approaches [7][8][9][10], others have proposed a monophyletic species group within Hyphessobrycon using morphological taxonomy [11,12] and integrative taxonomy [2]. Thus, the phylogeny of this group is still controversial.…”

Section: Introductionmentioning

confidence: 99%

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The Complete Mitogenome of Amazonian Hyphessobrycon heterorhabdus (Characiformes: Characidae) as a Valuable Resource for Phylogenetic Analyses of Characidae

Montag

Koroiva

Ribeiro-dos-Santos

et al. 2023

Fishes

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Hyphessobrycon heterorhabdus (Ulrey, 1894), popularly known as ‘Flag Tetra’ in English speaking countries, belongs to the genus Hyphessobrycon of the family Characidae, and is widely present in the eastern Amazon basin. Here, using Illumina sequencing, we report the complete mitogenome sequence of H. heterorhabdus. Overall, the mitogenome has 17,021 bp, containing 13 protein-coding, 22 tRNA, and 2 rRNA genes. Non-ambiguous nucleotide compositions of the H. heterorhabdus mitogenome are A: 29.2%, T: 29.4%, G: 15.6%, and C: 25.8%. As recently indicated, the phylogenetic analyses did not support four separate genera (Hemigrammus, Hyphessobrycon, Moenkhausia, and Psalidodon) of Characidae. Understanding the H. heterorhabdus mitogenome is important for taxonomic purposes as well as for the molecular characterization of environmental pollutants. Thus, the mitogenome described here will be a valuable resource for studies on environmental changes, evolutionary genetics, species delimitation, and phylogenetic analyses in Characidae.

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“…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 ]. The 13 PCGs are NADH dehydrogenase subunit 1 ( ND1 ), NADH dehydrogenase subunit 2 ( ND2 ), Cytochrome c oxidase subunit I ( COX1 ), Cytochrome c oxidase subunit II ( COX2 ), ATP synthase F0 subunit 8 ( ATP8 ), ATP synthase F0 subunit 6 ( ATP6 ), Cytochrome c oxidase subunit III ( COX3 ), NADH dehydrogenase subunit 3 ( ND3 ), NADH dehydrogenase subunit 4L ( ND4L ), NADH dehydrogenase subunit 4 ( ND4 ), NADH dehydrogenase subunit 5 ( ND5 ), NADH dehydrogenase subunit 6 ( ND6 ), and Cytochrome b ( Cytb ) (arranged in the common order in the mitogenome of the order Characiformes) [ 12 , 13 ]. The utilization of mitogenomes in molecular identification and phylogenetic analysis is prevalent due to their rapid evolution rate, simple structure, low molecular weight, and maternal inheritance [ 14 , 15 ].…”

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 of tetras: insights into phylogenetic relationships in Characidae

Cited by 3 publications

References 40 publications

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

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

The Complete Mitogenome of Amazonian Hyphessobrycon heterorhabdus (Characiformes: Characidae) as a Valuable Resource for Phylogenetic Analyses of Characidae

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

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