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Analysis of the complete mitochondrial genome sequence of Palinura homarus.

ABSTRACT: The complete mitochondrial genome sequence of Palinura homarus was obtained using PCR amplification and walking sequencing (GenBank accession no. JN_542716). The complete mitochondrial genome of P. homarus was 15,665?bp long and showed significant AT bias (67% AT content, 33% GC content). The A?+?T-rich region included copy-related control information and a poly (dT) structure that related to replication and transcription. In this study, the gene arrangement was consistent with other Palinura mitochondrial genomes and the sequence was strikingly similar to Panulirus ornatus, which would be useful in species identification and natural resources conservation.

SUBMITTER: Xiao BH

PROVIDER: S-EPMC7800352 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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Analysis of the complete mitochondrial genome sequence of Palinura homarus.

Xiao Bao-Hua BH Zhang Wuchai W Yao Wei W Liu Chu-Wu CW Liu Li L

Mitochondrial DNA. Part B, Resources 20170202 1

The complete mitochondrial genome sequence of Palinura homarus was obtained using PCR amplification and walking sequencing (GenBank accession no. JN_542716). The complete mitochondrial genome of P. homarus was 15,665 bp long and showed significant AT bias (67% AT content, 33% GC content). The A + T-rich region included copy-related control information and a poly (dT) structure that related to replication and transcription. In this study, the gene arrangement was consistent with oth ...[more]

PMID: 33490437

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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.

Project description:BACKGROUND: Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes-a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. RESULTS: The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a approximately 20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22-336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages. CONCLUSION: Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.

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Analysis of the complete mitochondrial genome sequence of Palinura homarus.

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Analysis of the complete mitochondrial genome sequence of <i>Palinura homarus</i>.

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