Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes

Zhang, Kun; Liu, Yifan; Chen, Jian; Zhang, Hua; Gong, Li; Jiang, Lihua; Liu, Liqin; Lü, Zhen-Ming; Liu, Bingjian

doi:10.1007/s11033-020-06120-z

Cited by 7 publications

(4 citation statements)

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“…The top utilized amino acids are Leu, Ile, and Ala, and the few top utilized amino acids are Asp, Arg, and Cys (Figure S1). This phenomenon is also commonly seen in the mitochondrial genomes of other fish ( Su et al, 2015 ; Zhang et al, 2021b ). We measured the RSCU of the three Garra species mitogenomes ( Figure 1 ) and the results showed that the usage of NNA and NNC (N for A, T, C, G) was more frequent than NNT and NNG in the G. dengba , G. tibetana, and G. yajiangensis .…”

Section: Resultsmentioning

confidence: 58%

“…Like the typical mitochondrial genome of vertebrates ( Zhang et al, 2021b ; Liu et al, 2019b ), the 13 PCGs consist of one cytochrome b ( Cyt b ), two ATPases ( ATP6 and ATP8 ), and three cytochrome c oxidases ( COI-COIII ), and seven NADH dehydrogenases ( ND1-ND6 and ND4L ). Twelve PCGs ( ND1 , ND2 , COI , COII , ATP8 , ATP6 , COIII , ND3 , ND4L , ND4 , ND5 , and Cytb ) were coded on the heavy strand (H-strand) and the remaining ND6 gene was coded on the light strand (L-strand) ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

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Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

Zhang

Peng

et al. 2022

Front. Genet.

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Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.

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Section: Resultsmentioning

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

Zhang

Peng

et al. 2022

Front. Genet.

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“…The mitochondrial genome has been widely used in molecular evolution, phylogeny, and population genetics because of its maternal inheritance, stable genetic composition, fast evolutionary rate, low recombination frequency, and highly conserved gene content (Ballard and Whitlock 2004;Oliveria et al 2008;Galtier et al 2009;Simon and Hadrys 2013;Hao et al 2021;Zhao et al 2021). Complete mitochondrial genomes can provide much more reliable phylogenetic information than smaller parts of the mitochondrial DNA (Huang et al 2017;Hou et al 2020) and have been considered reliable markers for constructing fish phylogenies in recent studies of the taxonomy and phylogeny of cyprinids (Wang et al 2008;Tang et al 2010;Muniyangdi et al 2015;Huang et al 2017;Chung et al 2020;Zhang et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

Li¹,

Qiu²,

Du³

2022

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Rhodeus cyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R. cyanorostris. The mitogenome of R. cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R. cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R. cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeus cyanorostris exhibits the closest phylogenetic relationship with R. pseudosericeus, R. amarus, and R. sericeus. This study discloses the complete mitochondrial genome sequence of R. cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.

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“… 2021 ; Zhang et al. 2021 ). Except for COI, which started with GTG, all protein-coding genes utilized ATG as a start codon.…”

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The Complete Mitochondrial Genome of Plectorhinchus Chaetodonoides (Perciformes: Haemulidae)

Zhang

Chen

et al. 2022

Mitochondrial DNA Part B

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Plectorhinchus chaetodonoides Lacepède, 1801 is a widespread multicolored sweetlips fish found in the Indo-West Pacific Ocean where its appearance and color patterns drastically change during growth. In this study, the whole mitochondrial genome of P. chaetodonoides was sequenced which revealed it is 16,546 bp long and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one noncoding regulatory region. The GC content of the whole genome was 47.5% and 48.2%, 46.3%, 46.8%, 42.5% in the protein coding genes, tRNAs, rRNAs, and control regions, respectively. Molecular phylogenetic analysis resolved P. chaetodonoides as closely associated with Diagramma pictum and nested within a clade of Haemulidae that is allied with species from the Lutjanidae, Kyphosidae, Teraponidae, and Sciaenidae families. These results provide an essential genomic resource for future evolutionary and conservation studies of P. chaetodonoides as well as the Haemulidae family.

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Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes

Cited by 7 publications

References 47 publications

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

The Complete Mitochondrial Genome of Plectorhinchus Chaetodonoides (Perciformes: Haemulidae)

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Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes

Cited by 7 publications

References 47 publications

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

﻿Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

The Complete Mitochondrial Genome of Plectorhinchus Chaetodonoides (Perciformes: Haemulidae)

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Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis