Phylogenetic relationships of twenty Gymnothorax species based on cytochrome b sequence data

Du, Meizhu; Yin, Shaowu; Niu, Baozhen

doi:10.4238/gmr.15028157

Cited by 5 publications

(3 citation statements)

References 28 publications

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“…The normal phenol-chloroform method described previously [ 24 ] was used to extract genomic DNA from the caudal fin tissues of the 40 wild B . yarrelli individuals.…”

Section: Methodsmentioning

confidence: 99%

De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq

Niu

et al. 2018

PLoS ONE

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BackgroundThe yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited.Methodology and principal findingsIllumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp. A total of 9093 unigenes showed significant similarities to known proteins in public databases: 4477 and 6391 of B. yarrelli unigenes were mapped to the Gene Ontology (GO) and Clusters of Orthologous Groups (COG) databases, respectively. Moreover, 9635 unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, 8568 microsatellites (simple sequence repeats, SSRs) were detected, and 31 pairs of polymorphic primers were characterized using wild populations of B. yarrelli from the Nujiang River, Yunnan Province, China.Conclusion/SignificanceThese sequences enrich the genomic resources for B. yarrelli and will benefit future investigations into the evolutionary and biological processes of this and related Bagarius species. The SSR markers developed in this study will facilitate construction of genetic maps, investigations of genetic structures and germplasm polymorphism assessments in B. yarrelli.

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“…The normal phenol-chloroform method described previously [ 24 ] was used to extract genomic DNA from the caudal fin tissues of the 40 wild B . yarrelli individuals.…”

Section: Methodsmentioning

confidence: 99%

De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq

Niu

et al. 2018

PLoS ONE

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“…These studies included very small number of the Gymnothorax taxa, one involving three species -G. minor, G. albimarginatus and G. reevesii (Reece et al 2010) and the other involving two species -G. minor and G. tile (Chen et al 2014). Three other studies on Gymnothorax -24 species based on rrnS and rrnL genes (Tang & Fielitz 2013), 20 species based on the complete cob gene (Du et al 2016) and 7 species based on the cox1 gene (Peninal et al 2017) -did not include G. minor. Based on concatenated datasets of partial cox1, cob, rag1 and rag2 genes, the subfamily Muraeninae as well as the subfamily Uropterygiinae of Muraenidae are monophyletic (Reece et al 2010).…”

Section: G Minor Occurs In Northwestern and Southwestern Pacificmentioning

confidence: 99%

Mitogenome of Gymnothorax minor and Phylogenetic Relationship with Its Congeners and Related Genera (Anguilliformes: Muraenidae)

Song¹,

Yong²,

Loh³

et al. 2018

JSM

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Gymnothorax minor is a moray eel of the family Muraenidae found in the Western Pacific Ocean. We report here its complete mitogenome as determined by Illumina next-generation sequencing and the phylogenetic relationship with its congeners and other taxa of the family Muraenidae. The whole mitogenome of G. minor had a total length of 16,574 bp, comprising 37 genes-13 protein-coding genes (PCGs), two ribosomal ribonucleic acid (rRNA) and 22 transfer ribonucleic acid (tRNA) genes-and a control region. Excepting cox1 with GTG, the other 12 PCGs had ATG start codon. Seven of its PCGs had incomplete stop codon-five (nad2; cox1; cox2; nad3 and nad4) with T and two (atp6 and cox3) with TA. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs and 2 rRNA genes). The subfamily Muraeninae as well as the subfamily Uropterygiinae were monophyletic. However, the genus Gymnothorax was paraphyletic, with G. minor forming a sister group with Rhinomuraena quaesita in the lineage containing also G. kidako and G. formosus forming a sister group with Enchelynassa canina. The phylogenetic relationship of the genus Gymnothorax and related taxa of the family Muraenidae, based on the mitochondrial cob gene, was in general similar to that based on 15 mt-genes. The mitogenome is useful for future studies on phylogenetics and systematics of eels of the family Muraenidae and other taxa of the order Anguilliformes.

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“…Despite their abundance and important ecological role, the morays are generally difficult to study and to collect, due to their elusive nature; they are nocturnal, with cryptic behaviour. The taxonomy of the genera is still controversial, and their phylogenetic relationships have not been well established [10][11][12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation

Coluccia

Deidda

Lobina

et al. 2020

Genes

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The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyology of this fish group, the chromosomal mapping of the 5S ribosomal gene family was performed on seven species belonging to the genera Muraena and Gymnothorax from both the Atlantic and Pacific oceans. Fluorescence in situ hybridisation (FISH) experiments were realized using species-specific 5S rDNA probes; in addition, two-colour FISH was performed to investigate the possible association with the 45S ribosomal gene family. Multiple 5S rDNA clusters, located either in species-specific or in possibly homoeologous chromosomes, were found. Either a syntenic or different chromosomal location of the two ribosomal genes was detected. Our results revealed variability in the number and location of 5S rDNA clusters and confirmed a substantial conservation of the number and location of the 45S rDNA.

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Phylogenetic relationships of twenty Gymnothorax species based on cytochrome b sequence data

Cited by 5 publications

References 28 publications

De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq

De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq

Mitogenome of Gymnothorax minor and Phylogenetic Relationship with Its Congeners and Related Genera (Anguilliformes: Muraenidae)

Chromosome Mapping of 5S Ribosomal Genes in Indo-Pacific and Atlantic Muraenidae: Comparative Analysis by Dual Colour Fluorescence In Situ Hybridisation

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