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Two complete mitochondrial genomes of the black-spotted stout newt (Pachytriton brevipes) and their relative phylogenetics relationship with other Salamandridae.

ABSTRACT: The black-spotted stout newt (Pachytriton brevipes) is widely distributed in the mountains of southeastern China. In this study, we sequenced and determined the complete mitochondrial genome (mitogenomes) of two P. brevipes samples collected in Mount Wuyi. The assembled mitogenomes were 16,298 bp and 16,301 bp in length, and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, one non-coding region, and one control region. The phylogenetic analysis indicated the two samples of black-spotted stout newt grouped together and are the sister group of P. feii.

SUBMITTER: Hu HL

PROVIDER: S-EPMC7872577 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Two complete mitochondrial genomes of the black-spotted stout newt (Pachytriton brevipes) and their relative phylogenetics relationship with other Salamandridae.

Hu Hua-Li HL Zhong Jun-Jie JJ Ma Li L Lin Zhi-Hua ZH Ding Guo-Hua GH

Mitochondrial DNA. Part B, Resources 20210202 1

The black-spotted stout newt (Pachytriton brevipes) is widely distributed in the mountains of southeastern China. In this study, we sequenced and determined the complete mitochondrial genome (mitogenomes) of two P. brevipes samples collected in Mount Wuyi. The assembled mitogenomes were 16,298 bp and 16,301 bp in length, and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, one non-coding region, and one control region. The phylogenetic analy ...[more]

PMID: 33659645

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Project description:BackgroundMajority of the species within Senecioneae are classified in Senecio, making it the tribe's largest genus. Certain intergeneric relationships within the tribe are vaguely defined, with the genus Senecio being partly linked to this ambiguity. Infrageneric relationships within Senecio remain largely unknown and consequently, the genus has undergone continuous expansion and contraction over the recent past due to addition and removal of taxa. Dendrosenecio, an endemic genus in Africa, is one of its segregate genera. To heighten the understanding of species divergence and phylogeny within the tribe, the complete chloroplast genomes of the first five Senecio and six Dendrosenecio species were sequenced and analyzed in this study.ResultsThe entire length of the complete chloroplast genomes was ~ 150 kb and ~ 151 kb in Dendrosenecio and Senecio respectively. Characterization of the 11 chloroplast genomes revealed a significant degree of similarity particularly in their organization, gene content, repetitive sequence composition and patterns of codon usage. The chloroplast genomes encoded an equal number of unique genes out of which 80 were protein-coding genes, 30 transfer ribonucleic acid, and four ribosomal ribonucleic acid genes. Based on comparative sequence analyses, the level of divergence was lower in Dendrosenecio. A total of 331 and 340 microsatellites were detected in Senecio and Dendrosenecio, respectively. Out of which, 25 and five chloroplast microsatellites (cpSSR) were identified as potentially valuable molecular markers. Also, through whole chloroplast genome comparisons and DNA polymorphism tests, ten divergent hotspots were identified. Potential primers were designed creating genomic tools to further molecular studies within the tribe. Intergeneric relationships within the tribe were firmly resolved using genome-scale dataset in partitioned and unpartitioned schemes. Two main clades, corresponding to two subtribes within the Senecioneae, were formed with the genus Ligularia forming a single clade while the other had Dendrosenecio, Pericallis, Senecio and Jacobaea. A sister relationship was revealed between Dendrosenecio and Pericallis whereas Senecio, and Jacobaea were closely placed in a different clade.ConclusionBesides emphasizing on the potential of chloroplast genome data in resolving intergeneric relationships within Senecioneae, this study provides genomic resources to facilitate species identification and phylogenetic reconstructions within the respective genera.

Project description:BackgroundHeterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the "lower heterobranchs". Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia.ResultsTo assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of "lower heterobranchs". Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.ConclusionsAnalysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT + GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.

Dataset Information

Two complete mitochondrial genomes of the black-spotted stout newt (Pachytriton brevipes) and their relative phylogenetics relationship with other Salamandridae.

Publications

Two complete mitochondrial genomes of the black-spotted stout newt (<i>Pachytriton brevipes</i>) and their relative phylogenetics relationship with other Salamandridae.

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