Dataset Information

The complete mitochondrial genome of Metasepia tullbergi (Cephalopoda: Sepiidae).

ABSTRACT: The first complete mitochondrial genome of Metasepia tullbergi has been characterized in this study. The circular mitogenome is 16182 bp in length and comprises 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The organization of these genes is highly consistent with that of other Sepiidae. The overall base composition of mitogenome is 39.20% A, 36.07% T, 8.98% G, and 15.75% C, with 75.27% AT. Phylogenetic analysis further suggests that M. tullbergi is placed within the Sepiidae and is closely related to Sepia latimanus and S. apama.

SUBMITTER: Lee HT

PROVIDER: S-EPMC8008933 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of Metasepia tullbergi (Cephalopoda: Sepiidae).

Lee Hung-Tai HT Liao Cheng-Hsin CH Huang Chang-Wen CW Ma Chia-Huan CH Hsu Te-Hua TH

Mitochondrial DNA. Part B, Resources 20210326 3

The first complete mitochondrial genome of Metasepia tullbergi has been characterized in this study. The circular mitogenome is 16182 bp in length and comprises 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The organization of these genes is highly consistent with that of other Sepiidae. The overall base composition of mitogenome is 39.20% A, 36.07% T, 8.98% G, and 15.75% C, with 75.27% AT. Phylogenetic analysis further suggests that ...[more]

PMID: 33829084

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Project description:BackgroundMitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although complete mitochondrial genome sequences have been reported for more than 600 animals, the taxonomic sampling is highly biased toward vertebrates and arthropods, leaving much of the diversity yet uncharacterized.ResultsThe mitochondrial genome of the bellybutton nautilus, Nautilus macromphalus, a cephalopod mollusk, is 16,258 nts in length and 59.5% A+T, both values that are typical of animal mitochondrial genomes. It contains the 37 genes that are almost universally found in animal mtDNAs, with 15 on one DNA strand and 22 on the other. The arrangement of these genes can be derived from that of the distantly related Katharina tunicata (Mollusca: Polyplacophora) by a switch in position of two large blocks of genes and transpositions of four tRNA genes. There is strong skew in the distribution of nucleotides between the two strands, and analysis of this yields insight into modes of transcription and replication. There is an unusual number of non-coding regions and their function, if any, is not known; however, several of these demark abrupt shifts in nucleotide skew, and there are several identical sequence elements at these junctions, suggesting that they may play roles in transcription and/or replication. One of the non-coding regions contains multiple repeats of a tRNA-like sequence. Some of the tRNA genes appear to overlap on the same strand, but this could be resolved if the polycistron were cleaved at the beginning of the downstream gene, followed by polyadenylation of the product of the upstream gene to form a fully paired structure.ConclusionNautilus macromphalus mtDNA contains an expected gene content that has experienced few rearrangements since the evolutionary split between cephalopods and polyplacophorans. It contains an unusual number of non-coding regions, especially considering that these otherwise often are generated by the same processes that produce gene rearrangements. The skew in nucleotide composition between the two strands is strong and associated with the direction of transcription in various parts of the genomes, but a comparison with K. tunicata implies that mutational bias during replication also plays a role. This appears to be yet another case where polyadenylation of mitochondrial tRNAs restores what would otherwise be an incomplete structure.

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 Metasepia tullbergi (Cephalopoda: Sepiidae).

Publications

The complete mitochondrial genome of <i>Metasepia tullbergi</i> (Cephalopoda: Sepiidae).

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