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Dynamics of Actin Evolution in Dinoflagellates

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dc.contributor.author Kim, Sunju en
dc.contributor.author Bachvaroff, Tsvetan R. en
dc.contributor.author Handy, Sara M. en
dc.contributor.author Delwiche, Charles F. en
dc.date.accessioned 2011-09-29T13:37:30Z
dc.date.available 2011-09-29T13:37:30Z
dc.date.issued 2011
dc.identifier.citation Kim, Sunju, Bachvaroff, Tsvetan R., Handy, Sara M., and Delwiche, Charles F. 2011. "<a href="https%3A%2F%2Frepository.si.edu%2Fhandle%2F10088%2F17125">Dynamics of Actin Evolution in Dinoflagellates</a>." <em>Molecular Biology and Evolution</em>. 28 (4):1469&ndash;1480. <a href="https://doi.org/10.1093/molbev/msq332">https://doi.org/10.1093/molbev/msq332</a> en
dc.identifier.issn 0737-4038
dc.identifier.uri http://hdl.handle.net/10088/17125
dc.description.abstract Dinoflagellates have unique nuclei and intriguing genome characteristics with very high DNA content making complete genome sequencing difficult. In dinoflagellates, many genes are found in multicopy gene families, but the processes involved in the establishment and maintenance of these gene families are poorly understood. Understanding the dynamics of gene family evolution in dinoflagellates requires comparisons at different evolutionary scales. Studies of closely related species provide fine scale information relative to species divergence, while comparisons of more distantly related species provides broad context. We selected the actin gene family as a highly expressed, conserved gene previously studied in dinoflagellates. Of the 142 sequences determined in this study, 103 were from the two closely related species, Dinophysis acuminata and D. caudata, including full length and partial cDNA sequences as well as partial genomic amplicons. For these two Dinophysis species at least three types of sequences could be identified. Most copies (79%) were relatively similar and in nucleotide trees the sequences formed two bushy clades corresponding to the two species. In comparisons within species only 8-10 nucleotide differences were found between these copies. The two remaining types formed clades containing sequences from both species. One type included the most similar sequences in between species comparisons with as few as 12 nucleotide differences between species. The second type included the most divergent sequences in comparisons between and within species with up to 93 nucleotide differences between sequences. In all the sequences, most variation occurred in synonymous sites or the 5' UTR, although there was still limited amino acid variation between most sequences. Several potential pseudogenes were found (~10% of all sequences depending on species) with incomplete open reading frames due to frameshifts or early stop codons. Overall, variation in the actin gene family fits best with the 'birth and death' model of evolution based on recent duplications, pseudogenes, and incomplete lineage sorting. Divergence between species was similar to variation within species, so that actin may be too conserved to be useful for phylogenetic estimation of closely related species. en
dc.relation.ispartof Molecular Biology and Evolution en
dc.title Dynamics of Actin Evolution in Dinoflagellates en
dc.type Journal Article en
dc.identifier.srbnumber 101245
dc.identifier.doi 10.1093/molbev/msq332
rft.jtitle Molecular Biology and Evolution
rft.volume 28
rft.issue 4
rft.spage 1469
rft.epage 1480
dc.description.SIUnit SERC en
dc.description.SIUnit Peer-reviewed en
dc.citation.spage 1469
dc.citation.epage 1480

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