Dataset Information

The complete mitochondrial genome of a marine gastropod: Umbonium thomasi (Trochida, Trochidae).

ABSTRACT: The mitogenome sequence of a marine gastropod, Umbonium thomasi (Crosse, 1863) (Trochida, Trochidae), was determined first in the genus Umbonium. The assembled mitogenome, consisting of 15,998?bp in length, has 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The order and structure of the genes are similar to those of other Trochid species. The overall base composition of mitogenome is 34.8% A, 22.1% C, 14.0% G, and 29.1% T with an A?+?T bias of 64%. The complete mitogenome of U. thomasi provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis of marine gastropods.

SUBMITTER: Kim H

PROVIDER: S-EPMC7510657 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of a marine gastropod: Umbonium thomasi (Trochida, Trochidae).

Kim Hana H Yu Cheol C Kim Hyung June HJ Jung Yun-Hwan YH

Mitochondrial DNA. Part B, Resources 20181125 1

The mitogenome sequence of a marine gastropod, Umbonium thomasi (Crosse, 1863) (Trochida, Trochidae), was determined first in the genus Umbonium. The assembled mitogenome, consisting of 15,998 bp in length, has 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The order and structure of the genes are similar to those of other Trochid species. The overall base composition of mitogenome is 34.8% A, 22.1% C, 14.0% G, and 29.1% T with an A + T bias of 64%. Th ...[more]

PMID: 33365411

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Project description:BackgroundGastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (Pyramidella dolabrata, Ascobulla fragilis, Siphonaria pectinata, Onchidella celtica, and Myosotella myosotis), and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods.ResultsComparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI) arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group.ConclusionFour main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia). The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of P. dolabrata) nor Pulmonata (polyphyletic) nor Opisthobranchia (because of the inclusion S. pectinata) were recovered as monophyletic groups. The gene order of the Vetigastropoda might represent the ancestral mitochondrial gene order for Gastropoda and we propose that at least three major rearrangements have taken place in the evolution of gastropods: one in the ancestor of Caenogastropoda, another in the ancestor of Patellogastropoda, and one more in the ancestor of Heterobranchia.

Project description:The complete sequence of honeybee (Apis mellifera) mitochondrial DNA is reported being 16,343 bp long in the strain sequenced. Relative to their positions in the Drosophila map, 11 of the tRNA genes are in altered positions, but the other genes and regions are in the same relative positions. Comparisons of the predicted protein sequences indicate that the honeybee mitochondrial genetic code is the same as that for Drosophila; but the anticodons of two tRNAs differ between these two insects. The base composition shows extreme bias, being 84.9% AT (cf. 78.6% in Drosophila yakuba). In protein-encoding genes, the AT bias is strongest at the third codon positions (which in some cases lack guanines altogether), and least in second codon positions. Multiple stepwise regression analysis of the predicted products of the protein-encoding genes shows a significant association between the numbers of occurrences of amino acids and %T in codon family, but not with the number of codons per codon family or other parameters associated with codon family base composition. Differences in amino acid abundances are apparent between the predicted Apis and Drosophila proteins, with a relative abundance in the Apis proteins of lysine and a relative deficiency of alanine. Drosophila alanine residues are as often replaced by serine as conserved in Apis. The differences in abundances between Drosophila and Apis are associated with %AT in the codon families, and the degree of divergence in amino acid composition between proteins correlates with the divergence in %AT at the second codon positions. Overall, transversions are about twice as abundant as transitions when comparing Drosophila and Apis protein-encoding genes, but this ratio varies between codon positions. Marked excesses of transitions over chance expectation are seen for the third positions of protein-coding genes and for the gene for the small subunit of ribosomal RNA. For the third codon positions the excess of transitions is adequately explained as due to the restriction of observable substitutions to transitions for conserved amino acids with two-codon families; the excess of transitions over expectation for the small ribosomal subunit suggests that the conservation of nucleotide size is favored by selection.

Dataset Information

The complete mitochondrial genome of a marine gastropod: Umbonium thomasi (Trochida, Trochidae).

Publications

The complete mitochondrial genome of a marine gastropod: <i>Umbonium thomasi</i> (Trochida, Trochidae).

Similar Datasets

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