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.

Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome

“…We also identified 135 chloroplast genes and 31 mitochondrial genes (the chloroplast genes were previously reported [Tanaka et al, 2011]). No homoeologous gene pairs were found in the mitochondrial or chloroplast genomes.…”

“…The scaffolds were assembled with LASTZ and LALIGN to yield a draft genome sequence corresponding to 24.8-fold redundant sequence coverage. At this stage, a chloroplast genome (135 kb) (Tanaka et al, 2011) and a mitochondrial genome (>38.6 kb) were identified; however, we failed to determine the chromosome structures from the alignment blocks in the draft nuclear genome.…”

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

“…However, in most diatom species, existence of different rbcL variants, their inheritance and copy number, and also the number of chloroplasts per cell, is not well investigated. Chloroplast genome sequencing studies on diatoms have indicated the presence of only one rbcL copy in some centric and pennate diatoms (Kowallik et al 1995;Oudot-Le Secq et al 2007;Tanaka et al 2011), but have not been established in other diatoms.…”

Complete Chloroplast Genome Sequence of Freshwater Araphid Pennate Diatom Alga Synedra acus from Lake Baikal

“…JPCC DAO0580 (Tanaka et al 2011). Additionally, the plastid genomes of two dinoflagellates Kryptoperidinium foliaceum and Durinskia baltica, also known as dinotoms because they harbouring a diatom endosymbiont, were sequenced recently (Imanian et al 2010).…”