Abstract
Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera.
Highlights
Pleurochrysis are one of the coccolithophorids, which produce calcified scales, called coccoliths, on the cell surface
Research with the two genera has revealed that the coccolith production mechanism and other morpho-physiological characteristics are very different between the two orders, e.g. the subcellular compartments where coccolith production occurs, chemical variation of coccolith acid polysaccharides and the morphology of the base plate of the coccolith
To provide a platform for similarity searches against other algae, this database stores protein sequences collected from public databases for 10 algal species, Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ectocarpus siliculosus, Emiliania huxleyi, Guillardia theta, Hemiselmis andersenii, Micromonas sp
Summary
Pleurochrysis are one of the coccolithophorids, which produce calcified scales, called coccoliths, on the cell surface. As representatives of the orders, Pleurochrysis (Coccolithales) and Emiliania (Isochrysidales) have been used for coccolithophorid research as they can be cultured in the laboratory (Berges et al 2001, Marsh 2003). A reference genome of Emiliania huxleyi, which is the predominant coccolithophorid species in the current ecosystem, has been published (Read et al 2013). On this E. huxleyi genome, 30,569 gene models were predicted (Read et al 2013) and their sequence information is available in the genome portal of the Joint Genome Institute (JGI) (Nordberg et al 2014).
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call