An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata

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 MatsunoKazuyoshi Endo

Research output: Contribution to journalReview article

5 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)877-888
Number of pages12
JournalZoological Science
Volume30
Issue number10
DOIs
Publication statusPublished - 2013 Oct 1

Fingerprint

Pinctada fucata
oysters
early development
genomics
Biological Sciences
aquaculture
genes
pearls
shell (molluscs)
Erinaceidae
major genes
bioinformatics
embryo (animal)
complement
genome
larvae
phylogeny
organisms
methodology

Keywords

  • Ancestral protostome
  • Early development
  • Lophotrochozoans
  • Pearl oyster
  • Signaling molecules

ASJC Scopus subject areas

  • Animal Science and Zoology

Cite this

An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata. / Setiamarga, Davin H.E.; Shimizu, Keisuke; Kuroda, Junpei; Inamura, Kengo; Sato, Kei; Isowa, Yukinobu; Ishikawa, Makiko; Maeda, Reo; Nakano, Tomoyuki; Yamakawa, Tomoko; Hatori, Ryo; Ishio, Akira; Kaneko, Kayo; Matsumoto, Kenjiroo; Sarashina, Isao; Teruya, Shinnosuke; Zhao, Ran; Satoh, Nori; Sasaki, Takenori; Matsuno, Kenji; Endo, Kazuyoshi.

In: Zoological Science, Vol. 30, No. 10, 01.10.2013, p. 877-888.

Research output: Contribution to journalReview article

Setiamarga, DHE, Shimizu, K, Kuroda, J, Inamura, K, Sato, K, Isowa, Y, Ishikawa, M, Maeda, R, Nakano, T, Yamakawa, T, Hatori, R, Ishio, A, Kaneko, K, Matsumoto, K, Sarashina, I, Teruya, S, Zhao, R, Satoh, N, Sasaki, T, Matsuno, K & Endo, K 2013, 'An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata', Zoological Science, vol. 30, no. 10, pp. 877-888. https://doi.org/10.2108/zsj.30.877
Setiamarga, Davin H.E. ; Shimizu, Keisuke ; Kuroda, Junpei ; Inamura, Kengo ; Sato, Kei ; Isowa, Yukinobu ; Ishikawa, Makiko ; Maeda, Reo ; Nakano, Tomoyuki ; Yamakawa, Tomoko ; Hatori, Ryo ; Ishio, Akira ; Kaneko, Kayo ; Matsumoto, Kenjiroo ; Sarashina, Isao ; Teruya, Shinnosuke ; Zhao, Ran ; Satoh, Nori ; Sasaki, Takenori ; Matsuno, Kenji ; Endo, Kazuyoshi. / An in-silico genomic survey to annotate genes coding for early development-relevant signaling molecules in the pearl oyster, Pinctada fucata. In: Zoological Science. 2013 ; Vol. 30, No. 10. pp. 877-888.
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AU - Inamura, Kengo

AU - Sato, Kei

AU - Isowa, Yukinobu

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AU - Maeda, Reo

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AU - Ishio, Akira

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AU - Matsumoto, Kenjiroo

AU - Sarashina, Isao

AU - Teruya, Shinnosuke

AU - Zhao, Ran

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AU - Endo, Kazuyoshi

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