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Separate introns gained within short and long soluble peridinin-chlorophyll a-protein genes during radiation of Symbiodinium (Dinophyceae) clade A and B lineages - PLoS One
Citation:
Reichman, J. AND P. Vize. Separate introns gained within short and long soluble peridinin-chlorophyll a-protein genes during radiation of Symbiodinium (Dinophyceae) clade A and B lineages - PLoS One. PLOS ONE . Public Library of Science, San Francisco, CA, 9(10):15, (2014).
Impact/Purpose:
This study is an extension of my previous dissertation research into the molecular evolution of gene families within peridinin-containing dinoflagellates in the genus Symbiodinium. Introns are present in all known eukaryotic genomes. However, there has been disagreement among evolutionary biologists for over 20 years as to whether introns are ancient features that have been lost in certain lineages (introns early hypothesis) or whether introns are evolutionary novelties (introns late hypothesis). The emerging consensus is that introns can be dynamically gained and lost. Our paper presents multiple lines of evidence for intron gain events that occurred in Symbiodinium, since the divergence of that genus from other peridinin-containing dinoflagellate lineages. The results will be of interest to scientists in the fields of microalgal evolution and genome evolution.
Description:
Here we document introns in two Symbiodinium clades that were most likely gained following divergence of this genus from other peridinin-containing dinoflagellate lineages. Soluble peridinin-chlorophyll a-proteins (sPCP) occur in short and long forms in different species, and all short and long sPCP genes characterized to date are intronless. However, we observed that long sPCP genes from two Caribbean Symbiodinium clade B isolates each contained two introns. To test the hypothesis that introns were gained during radiation of clade B, we compared sPCP genomic and cDNA sequences from 13 additional distinct Caribbean and Pacific Symbiodinium clade A, B, and F isolates. Long sPCP genes from all clade B/B1and B/B19 descendants contain orthologs of both introns. Short sPCP genes from S. pilosum (A/A2) and S. muscatinei (B/B4) plus long sPCP genes from S. microadriaticum (A/A1) and S. kawagutii (F/F1) are intronless. Short sPCP genes of S. microadriaticum have a third unique intron. Symbiodinium clade B long sPCP sequences are useful for assessing divergence among B1 and B19 descendants. Phylogenetic analyses of coding sequences from four dinoflagellate orders indicate that introns were gained independently during radiation of Symbiodinium clades A and B. Long sPCP introns were present in the most recent common ancestor of Symbiodinium clade B core types B1 and B19 and predate Caribbean expansion of clade B. Timing of short sPCP intron gain in Symbiodinium clade A is less certain. All sPCP introns were gained after fusion of ancestral short sPCP genes, which we confirm as occurring once in dinoflagellate evolution.