title: Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae.
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.
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work. Present address: International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines. fujiwara@toyaku.ac.jp kyano@isc.meiji.ac.jp.
authors.forename: Naoki
authors.initials: N
authors.lastname: Yamamoto
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work. fujiwara@toyaku.ac.jp kyano@isc.meiji.ac.jp.
authors.forename: Toru
authors.initials: T
authors.lastname: Kudo
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan These authors contributed equally to this work. fujiwara@toyaku.ac.jp kyano@isc.meiji.ac.jp.
authors.forename: Shoko
authors.initials: S
authors.lastname: Fujiwara
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Takatsuka
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan.
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Hirokawa
authors.affiliation: School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan.
authors.forename: Mikio
authors.initials: M
authors.lastname: Tsuzuki
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Takano
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Suda
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
authors.forename: Erika
authors.initials: E
authors.lastname: Asamizu
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yokoyama
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shibata
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan fujiwara@toyaku.ac.jp kyano@isc.meiji.ac.jp.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
mesh_terms: D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D063990:Gene Ontology; D058087:Haptophyta / Q000235:genetics*; D058977:Molecular Sequence Annotation; D059467:Transcriptome
keywords: Coccolithophorids; Expressed sequence tag; Haptophyta; Integrated database; Ortholog; Pleurochrysis