Dataset Information

Complete mitochondrial genomes of the Laotian Rock Rat (Laonastes aenigmamus) confirm deep divergence within the species.

ABSTRACT: Mitochondrial genomes of five Laotian Rock Rat (Laonastes aenigmamus) samples from Vietnam and Laos were sequenced using an Illumina platform. After de novo assembly, 13 protein-coding genes and two rRNA (12S and 16S) of the five genomes were aligned and analyzed with those from other related species under maximum likelihood and Bayesian inferences. Both methods revealed congruent tree topologies, which support two independently evolving clades of L. aenigmamus from Laos and Vietnam. The relaxed time calibration analysis showed that the two major lineages of the Laotian Rock Rat split about 8 million years ago, which was consistent with the results from previous studies using only cytochrome b sequences. Such a deep divergence time suggests the recognition of two rock rat species, but further nuclear DNA and morphological data are needed to solve the taxonomy of this taxon.

SUBMITTER: Le M

PROVIDER: S-EPMC7800421 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Complete mitochondrial genomes of the Laotian Rock Rat (Laonastes aenigmamus) confirm deep divergence within the species.

Le Minh M Penaloza Fernando F Martins Renata R Nguyen Thanh V TV Nguyen Ha M HM Nguyen Dang X DX Nguyen Luong D LD Wilting Andreas A

Mitochondrial DNA. Part B, Resources 20161122 1

Mitochondrial genomes of five Laotian Rock Rat (Laonastes aenigmamus) samples from Vietnam and Laos were sequenced using an Illumina platform. After de novo assembly, 13 protein-coding genes and two rRNA (12S and 16S) of the five genomes were aligned and analyzed with those from other related species under maximum likelihood and Bayesian inferences. Both methods revealed congruent tree topologies, which support two independently evolving clades of L. aenigmamus from Laos and ...[more]

PMID: 33473528

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Project description:BackgroundDiplozoidae are monogenean (Monogenea: Polyopisthocotylea) fish parasites characterised by a unique life history: two larvae permanently fuse into an X-shaped "Siamese" organism. Taxonomy and phylogeny of Diplozoidae and Polyopisthocotylea remain unresolved due to the unavailability of molecular markers with sufficiently high resolution. Mitogenomes may be a suitable candidate, but there are currently only 12 available for the Polyopisthocotylea (three for Diplozoidae). The only available study of diplozoid mitogenomes found unique base composition patterns and elevated evolution rates in comparison with other Monogenean mitogenomes.MethodsTo further explore their evolution and generate molecular data for evolutionary studies, we sequenced the complete mitogenomes of two Diplozoidae species, Paradiplozoon homoion and Paradiplozoon yarkandense, and conducted a number of comparative mitogenomic analyses with other polyopisthocotyleans.ResultsWe found further evidence that mitogenomes of Diplozoidae evolve at a unique, elevated rate, which was reflected in their exceptionally long branches, large sizes, unique base composition, skews, and very low gene sequence similarity levels between the two newly sequenced species. They also exhibited remarkably large overlaps between some genes. Phylogenetic analysis of Polyopisthocotylea resolved all major taxa as monophyletic, and Mazocraeidea was split into two major clades: (Diplozoidae) + (all four remaining families: Diclidophoridae, Chauhaneidae, Mazocraeidae and Microcotylidae). It also provided further confirmation that the genus Paradiplozoon is paraphyletic and requires a taxonomic revision, so the two species may have to be renamed Indodiplozoon homoion and Diplozoon yarkandense comb. nov.ConclusionsAlthough our findings indicate that mitogenomes may be a promising tool for resolving the phylogeny of Polyopisthocotylea, elevated evolutionary rates of Diplozoidae may cause phylogenetic artefacts, so future studies should pay caution to this problem. Furthermore, as the reason for their elevated evolution remains unknown, Diplozoidae are a remarkably interesting lineage for other types of evolutionary mitogenomic studies.

Dataset Information

Complete mitochondrial genomes of the Laotian Rock Rat (Laonastes aenigmamus) confirm deep divergence within the species.

Publications

Complete mitochondrial genomes of the Laotian Rock Rat (<i>Laonastes aenigmamus</i>) confirm deep divergence within the species.

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