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.

Mantle Branch-Specific RNA Sequences of Moon Scallop Amusium pleuronectes to Identify Shell Color-Associated Genes

“…Finally, signal pathways related to mineralization, especially growth factors (GFs) and their receptors, despite the limitations of studies on invertebrate species, were studied in this project. Limited information about these cellular regulators during mineralization has been obtained from sequence analysis, [ 68 ] genomic survey, [ 69 ] and in vivo and in vitro studies. [ 70 ] However, these analogues were hypothesized to have a potential use in the regeneration of living bone for potential clinical use.…”

Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster,Pinctada fucata, Based on Transcriptome Analysis

“…We identified two Hox genes, Hox5 and Hox3 (Figure 9), which are highly expressed in D-shaped veliger, indicating that they are involved in the growth of D-shaped larvae. We also found early developmentally relevant signaling molecules such as Hedghog, TGF β , and Wnt family, which are known to play important roles in axis formation, muscle differentiation, and nervous system development [26]. Recent evidence has suggested that classic morphogens, such as Wnts, TGF β /BMP family members, and Hedgehogs, may all serve as axon guidance cues for a variety of axons in different organisms [44].…”

“…For P. fucata , the draft genome [19] and tissue transcriptomes [20–23] have been recently reported. Based on the transcriptomic sequences from a mixture of nine developmental stages of P. fucata [19], biomineralization-related gene expression profiles during larval development have been investigated [24, 25] and genes involved in body patterning [26], transcription factors [27], and homeobox genes [28] have been identified. Nonetheless, developmentally important genes and their expression patterns during the larval stages of developing P. fucata have not been systematically studied at the transcript level to date.…”

Conservative route to genome compaction in a miniature annelid

“…C. teleta embryos were fixed and WMISH was performed as previously described 152 . Capitella teleta orthologs Ct-fgf8/17/18/24 153 (Protein ID: 218971), Ct-pvf1 154 (Protein ID: 153454) and Ct-pvf2 154 (Protein ID: 220370) were mined from the publicly available genome 50 . WMISH samples were imaged on a Leica DMRA2 compound microscope coupled with a QIClick camera.…”