The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia

Transcriptional response of four C1q domain containing protein (C1qDC) genes from Venerupis philippinarum exposed to the water soluble fraction of No.0 diesel oil

“…Remarkably, the multiple alignments of the 14 C1qDC proteins made evident the high sequence variability of C1q domains (Fig. 3), which was in line with previous report (Gerdol et al, 2015). In addition, the eight highly conserved residues in human gC1q domains were clearly identified, but the third and sixth conserved residues in VpC1qDC1 were replaced by Asp and Phe, respectively (Fig.…”

“…In addition, VpC1qDC1 and VpC1qDC2 show coiled-coil regions N-terminal to the C1q domain (Fig. 2), which is the largest subclass (sC1q-like type 2) of C1qDC proteins in C. gigas (Gerdol et al, 2015). Conversely, VpC1qDC3 instead showed a low complexity domain before the globular C1q domain (Fig.…”

“…Hitherto a large number of C1q domain containing protein (C1qDC) genes have been documented from numerous phylogenetically diverse organisms, such as 52 C1qDC gene models in zebrafish (Mei and Gui, 2008), 32 in humans (Tang et al, 2005), 29 in mice (Yuzaki, 2008), 75 in Branchiostoma floridae (Huang et al, 2008), and 7 in the Strongylocentrotus purpuratus (Hibino et al, 2006). Recently, the massive expansion of C1qDC in many mollusks have been reported, such as 524 in Mytilus edulis (Philipp et al, 2012), 232 in M. galloprovincialis (Gerdol et al, 2011), and in 337 in Crassostrea gigas (Gerdol et al, 2015). The increased expression of C1qDC transcripts were linked to the infections of Gram-positive, Gram-negative bacteria and cell wall components (lipopolysaccharide, glucan and peptidoglycan) (Adema et al, 2010;H.H.…”

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

“…This method can be further improved by incorporating expression data of a larger population (smaller time interval between larval collection points), more treatments or better annotations of transcripts, like in Gerdol et al (2015) or tested in Zhao and Zhang (2015). Overall, this work provided an association between genes and mechanisms that are essential for larval development, provided they perform crucial roles in growth or mortality.…”

“…Despite their ecological and economical importance, bivalves functional genomics started to get more attention only in recent years, e.g., tissue-specific expression (Craft et al, 2010), RNAimediated gene-targeting (You et al, 2012), de novo genome annotation (Zhang et al, 2012;Gerdol et al, 2015), innate immune system discovery (Philipp et al, 2012), whole transcriptome genetic regulatory network inferences (Bassim et al, 2014b), and exploration of bivalve shell layers (Liao et al, 2015). Here we developed a statistical learning pipeline to regularize (reduce) the number of differentially expressed genes between stages of both dietary conditions.…”