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1 October 2013 An In-silico Genomic Survey to Annotate Genes Coding for Early Development-Relevant Signaling Molecules in the Pearl Oyster, Pinctada fucata
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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.

© 2013 Zoological Society of Japan
Davin H. E. Setiamarga, Keisuke Shimizu, Junpei Kuroda, Kengo Inamura, Kei Sato, Yukinobu Isowa, Makiko Ishikawa, Reo Maeda, Tomoyuki Nakano, Tomoko Yamakawa, Ryo Hatori, Akira Ishio, Kayo Kaneko, Kenjiroo Matsumoto, Isao Sarashina, Shinnosuke Teruya, Ran Zhao, Nori Satoh, Takenori Sasaki, Kenji Matsuno, and Kazuyoshi Endo "An In-silico Genomic Survey to Annotate Genes Coding for Early Development-Relevant Signaling Molecules in the Pearl Oyster, Pinctada fucata," Zoological Science 30(10), 877-888, (1 October 2013). https://doi.org/10.2108/zsj.30.877
Received: 23 October 2012; Accepted: 1 March 2013; Published: 1 October 2013
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