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Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

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dc.contributor.author Cattolico, Rose Ann en_US
dc.contributor.author Jacobs, Michael A. en_US
dc.contributor.author Zhou, Yang en_US
dc.contributor.author Chang, Jean en_US
dc.contributor.author Duplessis, Melinda en_US
dc.contributor.author Lybrand, Terry en_US
dc.contributor.author McKay, John en_US
dc.contributor.author Ong, Han Chuan en_US
dc.contributor.author Sims, Elizabeth en_US
dc.contributor.author Rocap, Gabrielle en_US
dc.date.accessioned 2010-04-21T15:48:29Z
dc.date.available 2010-04-21T15:48:29Z
dc.date.issued 2008 en_US
dc.identifier.citation Cattolico R, Jacobs M, Zhou Y, et al. Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains. BMC Genomics. 2008;9(1):211. en_US
dc.identifier.other 10.1186/1471-2164-9-211 en_US
dc.identifier.uri http://www.biomedcentral.com/1471-2164/9/211 en_US
dc.identifier.uri http://hdl.handle.net/1773/15716
dc.description.abstract Background: Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution. Results: H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid protein, which we hypothesize serves as a G-protein-coupled receptor. The H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date. Conclusion: The fosmid cloning technique eliminates chloroplast isolation, does not require chloroplast DNA purification, and reduces sequencing processing time. Application of this method has provided new insights into chloroplast genome architecture, gene content and evolution within the stramenopile cluster. en_US
dc.language.iso en_US en_US
dc.title Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains en_US
dc.type Article en_US


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