Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage

Abstract

The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi, and the cryptophyte Guillardia theta. All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127-130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.

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.…”

Protein targeting into complex diatom plastids: functional characterisation of a specific targeting motif

“…The plastid genomes of the diatom Phaeodactylum tricornutum and the cryptophyte Guillardia theta contain only 162 and 177 genes (Douglas and Penny 1999;Oudot-Le Secq et al 2007), however, a plastid proteome size similar to that of higher plants must be assumed because photosynthesis is a rather complex process. Plastid protein import is therefore an important process for diatoms and cryptophytes, but the mode of protein translocation into these complex plastids derived from red algae is still mysterious (Kilian and Kroth 2003).…”

High Light Acclimation in the Secondary Plastids Containing Diatom Phaeodactylum tricornutum is Triggered by the Redox State of the Plastoquinone Pool

“…After each endosymbiotic event, gene transfer from the endosymbiont to the nucleus occurred, permanently modifying the genome composition of the host cell. Still, the diatom chloroplast genome retained a small amount of approximately 130 protein-encoding genes (Oudot-Le Secq et al, 2007). As a further consequence of secondary endosymbiosis, diatom plastids are surrounded by an envelope of four membranes reflecting the endosymbiotic origin of these organelles (Green, 2011).…”