Dataset Information

Complete mitochondrial genome of Rhizosolenia setigera (Coscinodiscophyceae, Bacillariophyta).

ABSTRACT: Rhizosolenia is a species-rich genus with 144 described species, many of which are harmful algal species (HABs) with significant negative ecological impact. Despite their significance in primary production and their potential to induce HABs, genome data of these species remain extremely limited. In this study, the complete mitochondrial genome (mtDNA) of Rhizosolenia setigera Brightwell 1858 was determined for the first time, which also represented the first mtDNA of the order Rhizosoleniales. The circular mtDNA was 34,792 bp in length with GC content of 23.28%. It encoded 63 genes including 35 protein-coding genes (PCGs), 24 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 conserved open reading frames (orfs). Phylogenetic analysis using concatenated PCGs revealed that R. setigera and Melosira undulate, which also belongs to the class Coscinodiscophyceae, clustered together as expected. However, comparison of these two mtDNAs revealed extensive genome rearrangement events, suggesting large evolutionary distance. The complete mtDNA of R. setigera will facilitate research on the phylogenetic relationship among Rhizosolenia species, which will in turn facilitate exploration of the evolutionary relationships in the class of Coscinodiscophyceae.

SUBMITTER: Yao Y

PROVIDER: S-EPMC8279148 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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

Complete mitochondrial genome of Rhizosolenia setigera (Coscinodiscophyceae, Bacillariophyta).

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