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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.

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Acknowledgments

This work was supported by JST, CREST.

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Correspondence to Tsuyoshi Tanaka.

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Supplementary Table S-1

Comparative analysis of basal gene expression apparatus in the chloroplast among Fistulifera sp. JPCC DA0580 and other chromalveolates (XLSX 16 kb)

Supplementary Table S-2

Comparative analysis of basal photosynthetic apparatus in the chloroplast among Fistulifera sp. JPCC DA0580 and other chromalveolates (XLSX 18 kb)

Supplementary Table S-3

Photosynthetic component including distinctive divergence of Fistulifera sp. JPCC DA0580 among plastids derived from diatoms (XLSX 16 kb)

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Tanaka, T., Fukuda, Y., Yoshino, T. et al. High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580. Photosynth Res 109, 223–229 (2011). https://doi.org/10.1007/s11120-011-9622-8

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  • DOI: https://doi.org/10.1007/s11120-011-9622-8

Keywords

  • Diatom
  • Chloroplast genome
  • Next-generation DNA sequencing
  • Lateral gene transfer
  • Endosymbiosis