title: High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580.
abstract: The chloroplast genome of the highly neutral-lipid-producing marine pennate diatom Fistulifera sp. strain JPCC DA0580 was fully sequenced using high-throughput pyrosequencing. The general features and gene content were compared with three other complete diatom chloroplast genomes. The chloroplast genome is 134,918 bp with an inverted repeat of 13,330 bp and is slightly larger than the other diatom chloroplast genomes due to several low gene-density regions lacking similarity to the other diatom chloroplast genomes. Protein-coding genes were nearly identical to those from Phaeodactylum tricornutum. On the other hand, we found unique sequence variations in genes of photosystem II which differ from the consensus in other diatom chloroplasts. Furthermore, five functional unknown ORFs and a putative serine recombinase gene, serC2, are located in the low gene-density regions. SerC2 was also identified in the plasmids of another pennate diatom, Cylindrotheca fusiformis, and in the plastid genome of the diatom endosymbiont of Kryptoperidinium foliaceum. Exogenous plasmids might have been incorporated into the chloroplast genome of Fistulifera sp. by lateral gene transfer. Chloroplast genome sequencing analysis of this novel diatom provides many important insights into diatom evolution.
authors.affiliation: Department of Biotechnology, Faculty of Engineering, Tokyo University of Agriculture & Technology, Tokyo, Japan. tsuyo@cc.tuat.ac.jp
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.forename: Yorikane
authors.initials: Y
authors.lastname: Fukuda
authors.forename: Tomoko
authors.initials: T
authors.lastname: Yoshino
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Maeda
authors.forename: Masaki
authors.initials: M
authors.lastname: Muto
authors.forename: Mitsufumi
authors.initials: M
authors.lastname: Matsumoto
authors.forename: Shigeki
authors.initials: S
authors.lastname: Mayama
authors.forename: Tadashi
authors.initials: T
authors.lastname: Matsunaga
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics; D001483:Base Sequence; D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics; D017377:Diatoms / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D054628:Genome, Chloroplast / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D045332:Photosystem II Protein Complex / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D045332:Photosystem II Protein Complex; D004247:DNA