Dataset Information

Particular gene order and complete mitochondrial genome of Ariosoma meeki (Congridae, Ariosoma).

ABSTRACT: Ariosoma meeki (A. meeki) is a demersal and carnivorous fish species belongs to the family Congridae. Some wild populations of A. meeki are in danger because of the overfishing and environmental pollution. In order to better understand the germplasm resources, the complete mitochondrial genome of A. meeki was firstly determined in this study. The complete mitochondrial genome is 16,404 nucleotides, comprising 12 protein-coding genes, 2 ribosomal RNA genes, 20 tRNA genes, and 2 main non-coding regions, but ND6 and two tRNA genes were not found in the A. meeki mitogenome. The A. meeki mitogenome was currently the first member of Ariosoma genus with gene and tRNA deletion. In addition, phylogenetic analysis result demonstrated that A. meeki and A. shiroanago were clustered in a clade and formed a sister relationship.

SUBMITTER: Chu Q

PROVIDER: S-EPMC7707401 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Particular gene order and complete mitochondrial genome of Ariosoma meeki (Congridae, Ariosoma).

Chu Qing Q Chen Jiong J Xu Tianjun T

Mitochondrial DNA. Part B, Resources 20191025 2

Ariosoma meeki (A. meeki) is a demersal and carnivorous fish species belongs to the family Congridae. Some wild populations of A. meeki are in danger because of the overfishing and environmental pollution. In order to better understand the germplasm resources, the complete mitochondrial genome of A. meeki was firstly determined in this study. The complete mitochondrial genome is 16,404 nucleotides, comprising 12 protein-coding genes, 2 ribosomal RNA genes, 20 tRNA gen ...[more]

PMID: 33366190

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Project description:As a result of great diversity in life histories and a large number of described species, taxonomic and phylogenetic uncertainty permeates the entire crustacean order of Isopoda. Large molecular datasets capable of providing sufficiently high phylogenetic resolution, such as mitochondrial genomes (mitogenomes), are needed to infer their evolutionary history with confidence, but isopod mitogenomes remain remarkably poorly represented in public databases. We sequenced the complete mitogenome of Cymothoa indica, a species belonging to a family from which no mitochondrial genome was sequenced yet, Cymothoidae. The mitogenome (circular, 14484 bp, A+T = 63.8%) is highly compact, appears to be missing two tRNA genes (trnI and trnE), and exhibits a unique gene order with a large number of rearrangements. High compactness and the existence of palindromes indicate that the mechanism behind these rearrangements might be associated with linearization events in its evolutionary history, similar to those proposed for isopods from the Armadillidium genus (Oniscidea). Isopods might present an important model system to study the proposed discontinuity in the dynamics of mitochondrial genomic architecture evolution. Phylogenetic analyses (Bayesian Inference and Maximum Likelihood) conducted using nucleotide sequences of all mitochondrial genes resolved Oniscidea and Cymothoida suborders as paraphyletic. Cymothoa indica was resolved as a sister group (basal) to all remaining isopods, which challenges the accepted isopod phylogeny, where Cymothoida are the most derived, and Phreatoicidea the most basal isopod group. There is growing evidence that Cymothoida suborder might be split into two evolutionary distant clades, with parasitic species being the most basal split in the Isopoda clade, but a much larger amount of molecular resources carrying a high phylogenetic resolution will be needed to infer the remarkably complex evolutionary history of this group of animals with confidence.

Project description:BackgroundSequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines.ResultsThe study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4x 10 bp and 3x 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all.ConclusionGene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.

Dataset Information

Particular gene order and complete mitochondrial genome of Ariosoma meeki (Congridae, Ariosoma).

Publications

Particular gene order and complete mitochondrial genome of <i>Ariosoma meeki</i> (Congridae, <i>Ariosoma</i>).

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