Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 West Atlantic and NIES293 West Pacific strainsReport as inadecuate




Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 West Atlantic and NIES293 West Pacific strains - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 9:211

First Online: 08 May 2008Received: 19 October 2007Accepted: 08 May 2008

Abstract

BackgroundHeterokont 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.

ResultsH. 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 tyr 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 H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date.

ConclusionThe 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.

List of abbreviationscpDNAChloroplast DNA

IRInverted Repeat

LSCLarge Single Copy

SSCSmall Single Copy

PCRPolymerase Chain Reaction

bpbase pairs

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-9-211 contains supplementary material, which is available to authorized users.

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Author: Rose Ann Cattolico - Michael A Jacobs - Yang Zhou - Jean Chang - Melinda Duplessis - Terry Lybrand - John McKay - Han Ch

Source: https://link.springer.com/article/10.1186/1471-2164-9-211







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