MBE Advance Access published online on May 23, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm101
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Research Article |
Plastid Genome Sequence of the Cryptophyte Alga Rhodomonas salina CCMP1319: Lateral Transfer of Putative DNA Replication Machinery and a Test of Chromist Plastid Phylogeny
1 Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia CANADA
2 The Atlantic Genome Centre, Halifax, Nova Scotia CANADA
* To whom correspondence should be addressed. Tel: +1 902 494-2536; Fax: +1 902 494-1355; Email: jmarchib{at}dal.ca
Correspondence may also be addressed to Hameed Khan. Tel: +1 902 494-2536; Fax: +1 902 494-1355; Email: khanh{at}dal.ca
Received for publication March 9, 2007. Revision received May 11, 2007. Accepted for publication May 17, 2007.
Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red-algal plastids independent of those in heterokont, haptophyte and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a non-cyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte and cryptophyte (i.e., chromist) plastids were monophyletic and heterokonts and haptophytes were each other's closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.
Key Words: Cryptophytes • Plastid • Chromists • Chromalveolates • Secondary Endosymbiosis
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