Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains
<p>Abstract</p> <p>Background</p> <p>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 gen...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-05-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/211 |
| _version_ | 1818787485837164544 |
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| author | Lybrand Terry Duplessis Melinda Chang Jean Zhou Yang Jacobs Michael A Cattolico Rose McKay John Ong Han Sims Elizabeth Rocap Gabrielle |
| author_facet | Lybrand Terry Duplessis Melinda Chang Jean Zhou Yang Jacobs Michael A Cattolico Rose McKay John Ong Han Sims Elizabeth Rocap Gabrielle |
| author_sort | Lybrand Terry |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>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 <it>Heterosigma akashiwo </it>strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution.</p> <p>Results</p> <p><it>H. akashiwo </it>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 <it>H. akashiwo</it>, not previously reported in any chloroplast genome, include <it>tyr</it>C, 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 <it>H. akashiwo </it>chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-18T14:08:32Z |
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| spelling | doaj.art-f1ffd400d2154017aa865f3f269e7eb82022-12-21T21:05:11ZengBMCBMC Genomics1471-21642008-05-019121110.1186/1471-2164-9-211Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strainsLybrand TerryDuplessis MelindaChang JeanZhou YangJacobs Michael ACattolico RoseMcKay JohnOng HanSims ElizabethRocap Gabrielle<p>Abstract</p> <p>Background</p> <p>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.</p> <p>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 <it>Heterosigma akashiwo </it>strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution.</p> <p>Results</p> <p><it>H. akashiwo </it>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 <it>H. akashiwo</it>, not previously reported in any chloroplast genome, include <it>tyr</it>C, 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 <it>H. akashiwo </it>chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/9/211 |
| spellingShingle | Lybrand Terry Duplessis Melinda Chang Jean Zhou Yang Jacobs Michael A Cattolico Rose McKay John Ong Han Sims Elizabeth Rocap Gabrielle Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains BMC Genomics |
| title | Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains |
| title_full | Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains |
| title_fullStr | Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains |
| title_full_unstemmed | Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains |
| title_short | Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains |
| title_sort | chloroplast genome sequencing analysis of it heterosigma akashiwo it ccmp452 west atlantic and nies293 west pacific strains |
| url | http://www.biomedcentral.com/1471-2164/9/211 |
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