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Yamamoto N, Kudo T, Fujiwara S, et al. Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. Plant Cell Physiol. 2016;57(1):e6doi: 10.1093/pcp/pcv195.
Yamamoto, N., Kudo, T., Fujiwara, S., Takatsuka, Y., Hirokawa, Y., Tsuzuki, M., Takano, T., Kobayashi, M., Suda, K., Asamizu, E., Yokoyama, K., Shibata, D., Tabata, S., & Yano, K. (2016). Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. Plant & cell physiology, 57(1), e6. https://doi.org/10.1093/pcp/pcv195
Yamamoto, Naoki, et al. "Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae." Plant & cell physiology vol. 57,1 (2016): e6. doi: https://doi.org/10.1093/pcp/pcv195
Yamamoto N, Kudo T, Fujiwara S, Takatsuka Y, Hirokawa Y, Tsuzuki M, Takano T, Kobayashi M, Suda K, Asamizu E, Yokoyama K, Shibata D, Tabata S, Yano K. Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. Plant Cell Physiol. 2016 Jan;57(1):e6. doi: 10.1093/pcp/pcv195. Epub 2016 Jan 07. PMID: 26746174; PMCID: PMC4722176.
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Plant Cell Physiol. 2016 Jan;57(1):e6. doi: 10.1093/pcp/pcv195. Epub 2016 Jan 07.

Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae.

Plant & cell physiology

Naoki Yamamoto, Toru Kudo, Shoko Fujiwara, Yukiko Takatsuka, Yasutaka Hirokawa, Mikio Tsuzuki, Tomoyuki Takano, Masaaki Kobayashi, Kunihiro Suda, Erika Asamizu, Koji Yokoyama, Daisuke Shibata, Satoshi Tabata, Kentaro Yano

Affiliations

  1. 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. [email protected] [email protected].
  2. 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. [email protected] [email protected].
  3. 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. [email protected] [email protected].
  4. School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan.
  5. Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan.
  6. Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
  7. Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan [email protected] [email protected].

PMID: 26746174 PMCID: PMC4722176 DOI: 10.1093/pcp/pcv195

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.

© The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Keywords: Coccolithophorids; Expressed sequence tag; Haptophyta; Integrated database; Ortholog; Pleurochrysis

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