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The complete mitochondrial genome of Panopea abrupta (Myoida: Hiatellidae).

ABSTRACT: The goeduck clam Panopea abrupta (Myoida: Hiatellidae) is one of the most important freshwater aquaculture species in China. In-spite of its economic importance, however, the genomic information of this species remains unavailable. In this study, we report the complete mitochondrial genome sequence of P. abrupta along with annotated and fully characterized mitochondrial genes. The genome was found to be 15,381?bp in length with a total of 38 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs). The presence of a gene coding for ATPase subunit 8 was also noted. However, as expected in bivalves, the gene arrangements showed variations with that of the related species. This study adds to the repository of available mitogenomes of various Heterodonta and will greatly aid in future phylogenetic studies and species identification.

SUBMITTER: Yu M

PROVIDER: S-EPMC7800156 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of Panopea abrupta (Myoida: Hiatellidae).

Yu Mingjia M Zhong Shengping S Yang Shanjun S Chen Jianming J Saha Tusar T TT

Mitochondrial DNA. Part B, Resources 20161122 1

The goeduck clam Panopea abrupta (Myoida: Hiatellidae) is one of the most important freshwater aquaculture species in China. In-spite of its economic importance, however, the genomic information of this species remains unavailable. In this study, we report the complete mitochondrial genome sequence of P. abrupta along with annotated and fully characterized mitochondrial genes. The genome was found to be 15,381 bp in length with a total of 38 genes (13 protein-coding, 22 transfer RN ...[more]

PMID: 33473665

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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 Panopea abrupta (Myoida: Hiatellidae).

Publications

The complete mitochondrial genome of <i>Panopea abrupta</i> (Myoida: Hiatellidae).

Similar Datasets

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