The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis

Zhang, Renyi; Zhu, Tingting; Luo, Qiquan

doi:10.3390/genes14061227

Cited by 9 publications

(4 citation statements)

References 32 publications

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“…The overlapping of nucleotides between adjacent genes is a common characteristic found in teleost mitogenomes, which aids in compacting the mitogenomes [30,36]. The overlapping regions between ND4L/ND4 and ATP8/ATP6 were identi ed as common features found in Melanotaenia species [6,21,[26][27][28][29] and other teleosts [37][38][39][40]. In addition, in this study showed that greater diversity in both location and intergenic nucleotide lengths compared to the overlaps.…”

Section: Discussionmentioning

confidence: 59%

Insights into structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis)

Marnis,

Syahputra,

Kadarusman

et al. 2024

Preprint

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The Fasin Rainbow fish, scientifically known as Melanotaenia fasinensis, is highly sought after by aquarium enthusiasts due to its vibrant colors and adaptability to artificial aquatic environments. This species is endemic to the karst landscape of the Bird’s Head region in Papua, Indonesia, and belongs to the Melanotaeniidae family. Discovered relatively recently in 2010, it has been designated as endangered by the International Union for Conservation of Nature (IUCN) in 2021. However, there is currently insufficient data regarding its phylogenetic positioning. To address this gap, our study employed next-generation sequencing to analyze the entire mitochondrial genome of M. fasinensis. The mitochondrial genome consists of 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a total length of 16,731 base pairs. The base composition of the mitogenome revealed percentages of 27.76% adenine (A), 27.34% thymine (T), 16.15% guanine (G), and 28.75% cytosine (C). Our phylogenetic analysis, based on nucleotide sequences mitogenome, indicated that M. fasinensis occupies a relatively basal position within the Melanotaenia genus. This study provides valuable molecular insights for further exploration of phylogeography and evolutionary history, not only for M. fasinensis but also for other members of the Melanotaenia genus.

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Section: Discussionmentioning

confidence: 59%

Insights into structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis)

Marnis,

Syahputra,

Kadarusman

et al. 2024

Preprint

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“…Interestingly, nad5 and nad6 genes of O. pama exhibited a Ka/Ks value greater than 1, indicating that they might have undergone positive selection where non-synonymous substitutions were prevalent over synonymous substitutions. Whereas in most other fishes, all the PCGs exhibited Ka/Ks value less than one including nad5 and nad6 76 , 77 . The remarkable findings within the Sciaenidae family suggest that examining the link between nad genes and adaptation to different environments and ecological niches could provide valuable insights.…”

Section: Discussionmentioning

confidence: 80%

Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama

Siddika,

Ahmed,

Alam

et al. 2024

Sci Rep

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The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.

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“…We found that only tRNA Ser(AGY) lacked the dihydrouridine (DHU) arm, and the remaining tRNA genes all formed a typical cloverleaf secondary structure. This loss was reported in many fishes [30]. The tRNA genes were distributed throughout the mitogenome and ranged in length from 67 bp (tRNA Cys ) to 76 bp (tRNA Leu(UUR) and tRNA Lys ).…”

Section: Ribosomal and Transfer Rna Genesmentioning

confidence: 85%

“…The minimum overlapped region was 1 bp, and the maximum overlapped region was 7 bp. The mitochondrial gene overlap and the gene spacer have long been known throughout teleost species [29,30].…”

Section: Genome Organization and Base Compositionmentioning

confidence: 99%

The Mitochondrial Genome of Linichthys laticeps (Cypriniformes: Cyprinidae): Characterization and Phylogeny

Zhang,

Zhu,

et al. 2023

Genes

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Mitochondrial genomes (mitogenomes) have been widely used in phylogenetic analysis and evolutionary biology. The Labeoninae is the largest subfamily of Cypriniformes and has great economic importance and ecological value. In this study, we sequenced, annotated, and characterized the complete mitogenome of Linichthys laticeps and then constructed the phylogenetic tree with previously published Labeoninae mitogenomes. The mitogenome of L. laticeps was 16,593 bp in length, with an A + T content of 57.1%. The mitogenome contained a standard set of 37 genes and a control region with the same order and orientation of genes as most fish mitogenomes. Each protein-coding gene (PCG) was initiated by an initial ATG codon, excluding COI, that began with a GTG codon. Furthermore, most of the PCGs were terminated by a conventional stop codon (TAA/TAG), while an incomplete termination codon (TA/T) was detected in 7 of the 13 PCGs. Most tRNA genes in L. laticeps were predicted to fold into the typical cloverleaf secondary structures. The Ka/Ks (ω) values for all PCGs were below one. The phylogenetic relationships of 96 Labeoninae mitogenomes indicated that Labeoninae was not a monophyletic group and L. laticeps was closely related to the genera Discogobio and Discocheilus. Overall, our study provided the first complete annotated mitogenome of L. laticeps, which filled a knowledge gap in Labeoninae and extended the understanding of the taxonomy and mitogenomic phylogeny of the subfamily Labeoninae.

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The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis

Cited by 9 publications

References 32 publications

Insights into structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis)

Insights into structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis)

Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama

The Mitochondrial Genome of Linichthys laticeps (Cypriniformes: Cyprinidae): Characterization and Phylogeny

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