title: An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata.
abstract: The pearl oyster Pinctada fucata has great potential as a model system for lophotrochozoan developmental biology research. Pinctada fucata is an important commercial resource, and a significant body of primary research on this species has emphasized its basic aquaculture biology such as larval biology and growth, aquaculture, pearl formation and quality improvement, shell formation, and biomineralization. Recently, a draft genome sequence of this species was published, and many experimental resources are currently being developed, such as bioinformatics tools, embryo and larva manipulation methods, gene knockdown technique, etc. In this paper, we report the results from our genomic survey pertaining to gene families that encode developmental signaling ligands (Fgf, Hedgehog, PDGF/VEGF, TGFβ, and Wnt families). We found most of the representative genes of major signaling pathways involved in axial patterning, as well as copies of the signaling molecule paralogs. Phylogenetic character mapping was used to infer a possible evolutionary scenario of the signaling molecules in the protostomes, and to reconstruct possible copy numbers of signaling molecule-coding genes for the ancestral protostome. Our reconstruction suggests that P. fucata retains the ancestral protostome gene complement, providing further justifications for the use of this taxon as a model organism for developmental genomics research.
authors.affiliation: 1 Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Davin H E
authors.initials: DH
authors.lastname: Setiamarga
authors.forename: Keisuke
authors.initials: K
authors.lastname: Shimizu
authors.forename: Junpei
authors.initials: J
authors.lastname: Kuroda
authors.forename: Kengo
authors.initials: K
authors.lastname: Inamura
authors.forename: Kei
authors.initials: K
authors.lastname: Sato
authors.forename: Yukinobu
authors.initials: Y
authors.lastname: Isowa
authors.forename: Makiko
authors.initials: M
authors.lastname: Ishikawa
authors.forename: Reo
authors.initials: R
authors.lastname: Maeda
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Nakano
authors.forename: Tomoko
authors.initials: T
authors.lastname: Yamakawa
authors.forename: Ryo
authors.initials: R
authors.lastname: Hatori
authors.forename: Akira
authors.initials: A
authors.lastname: Ishio
authors.forename: Kayo
authors.initials: K
authors.lastname: Kaneko
authors.forename: Kenjiroo
authors.initials: K
authors.lastname: Matsumoto
authors.forename: Isao
authors.initials: I
authors.lastname: Sarashina
authors.forename: Shinnosuke
authors.initials: S
authors.lastname: Teruya
authors.forename: Ran
authors.initials: R
authors.lastname: Zhao
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
authors.forename: Takenori
authors.initials: T
authors.lastname: Sasaki
authors.forename: Kenji
authors.initials: K
authors.lastname: Matsuno
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Endo
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D003198:Computer Simulation; D005346:Fibroblast Growth Factors / Q000235:genetics / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D016678:Genome; D023281:Genomics; D053823:Hedgehog Proteins / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D049911:Pinctada / Q000196:embryology / Q000235:genetics* / Q000378:metabolism*; D010982:Platelet-Derived Growth Factor / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D015398:Signal Transduction / Q000502:physiology*; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics / Q000378:metabolism
chemical_list: D053823:Hedgehog Proteins; D010982:Platelet-Derived Growth Factor; D016212:Transforming Growth Factor beta; D042461:Vascular Endothelial Growth Factor A; D005346:Fibroblast Growth Factors