ECB-ART-47366
Genes (Basel)
2019 Aug 05;108:. doi: 10.3390/genes10080592.
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Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins.
Balakirev ES
.
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Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.
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???displayArticle.link??? Genes (Basel)
Species referenced: Echinodermata
Genes referenced: ago1b LOC100887844 mt-nd5 ND6
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Figure 1. The ND5 and ND6 C-terminus sequences of the sea urchins Strongylocentrotus intermedius (A,B) and Mesocentrotus nudus (C,D). Conceptual translation of the ND5 and ND6 genes is shown as three-letter abbreviations (echinoderm mitochondrial genetic code). The ND5 gene is encoded on the H-strand, and the ND6 gene is encoded on the L-strand. The strands and corresponding transcripts are denoted by horizontal arrows → (H strand) and ← (L strand). The 5’ and 3’ ends are shown on the left. For the L variant, there is an overlap (highlighted in bold) between ND5 and ND6 encoded on the opposite strand. Nucl. is nucleotides; AA is amino acid residues. The ND6 polymorphic site 488A>G is indicated by bold vertical arrows under the numeral 488; the corresponding codons (TAG and TGG) are highlighted in bold red type indicating the changes in S and L variants. The readthrough extension for the S variants is highlighted in italics. | |
Figure 2. A maximum likelihood tree constructed using complete mitochondrial genomes of sea urchins (class Echinoidea). The tree is based on the general time reversible + gamma + invariant sites (GTR + G + I) model of nucleotide substitution. The mitochondrial genome of Cucumaria miniata (AY182376; class Holothuroidea) is used as an outgroup. The numbers at the nodes are bootstrap percentage probability values based on 500 replications (values below 75% are omitted). The species above the first (on top) horizontal line belong to the superfamily Odonthophora; above the second horizontal line, to the infraorder Echinidea; above the third horizontal line, to the order Camarodonta including the infraorders Echinidea and Temnopleuridea. The ND6 L and S variants are indicated by the corresponding letters on the right: L, long (165 amino acids) ND6 variant; S, short (162 amino acids) ND6 variant; L, S, both ND6 variants detected for Strongylocentrotus intermedius and Mesocentrotus nudus. The Eucidaris tribuloides ND6 variant (indicated by asterisk) is shorter than the S variant of other sea urchins due to the deletion of seven amino acids at the C-terminus (see Figure S1). |
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