Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves

Abstract

C1q-domain-containing (C1qDC) proteins are rapidly emerging as key players in the innate immune response of bivalve mollusks. Growing experimental evidence suggests that these highly abundant secretory proteins are involved in the recognition of microbe-associated molecular patterns, serving as lectin-like molecules in the bivalve proto-complement system. While a large amount of functional data concerning the binding specificity of the globular head C1q domain and on the regulation of these molecules in response to infection are quickly accumulating, the genetic mechanisms that have led to the extraordinary lineage-specific expansion of the C1qDC gene family in bivalves are still largely unknown. The analysis of the chromosome-scale genome assembly of the Eastern oyster Crassostrea virginica revealed that the 476 oyster C1qDC genes, far from being uniformly distributed along the genome, are located in large clusters of tandemly duplicated paralogs, mostly found on chromosomes 7 and 8. Our observations point out that the evolutionary process behind the development of a large arsenal of C1qDC lectin-like molecules in marine bivalves is still ongoing and likely based on an unequal crossing over.

Characterizing the Epigenetic and Transcriptomic Responses to Perkinsus marinus Infection in the Eastern Oyster Crassostrea virginica

“…For the genes identified by both our study and the previous controlled exposure (complement C1q tumor necrosis factor-related protein 7-like and multimerin-2-like) we see an approximate sixfold increase in expression between the moderate-heavy and verylight infection categories. The role of these genes in immune responses is further supported by recent assessments of the functional role of these gene families in bivalve innate immunity (Gerdol et al, 2019). We also observed two versions of a ninjurin FIGURE 4 | Violin plots of interaction between gene body methylation and gene expression for 5,295 genes with both gene body methylation and expression data.…”

“…The positive association of infection of this gene within module Pink may suggest a role of angiogenesis in healing tissues degraded by P. marinus secreted proteases (La Peyre et al, 1995). In addition, multimerin-2-like genes have been proposed to have similar domains to complement component C1q genes (Gerdol et al, 2019) that were significantly differentially expressed in the above pairwise analysis of gene expression. In addition, two genes within this module, Thymosin beta-4 and kelch-like protein, have been associated with immune defense against pathogens, Thymosin beta-4 is also involved in antibacterial activity in C. gigas (Nam et al, 2015) and was found to facilitate the clearance of Vibrio alginolyticus in C. hongkongensi (Li et al, 2017).…”

Genome-Wide Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in Cattle

“…As a result, 25 non-redundant CDK protein sequences including CDK1-10,CDK11B, CDK12-20, CDKL1-5 were identi ed in Bos taurus (Table 1). In parallel, 22,21,22,24,22,25 and 24 CDK family proteins were recognized in Bos grunniens, Hybrid-Bos Indicus, Hybrid-Bos taurus, Bos mutus, Bison bison bison, Bos indicus and Bubalus bubalis, respectively (Additional le 1) and the protein sequences of all the CDKs were provided in Additional le 2. Transcript ENSBIXT00000049337 is a newly identi ed member of CDK family in Hybrid-Bos taurus, which is named CDK20 according to the sequence similarity and collinearity.…”

“…The family genes may distribute on different chromosomes or co-locate on the same chromosome, which are generally de ned as segmental duplication events in the former and tandem duplication events in the latter [23][24][25]. Chromosomal distributions of the CDK family genes showed that they located on 13 to 16 chromosomes in six species of bovidae, indicating both segmental and tandem duplication events have occurred for the expansion of CDK genes.…”

Novel globular C1q domain-containing protein (PmC1qDC-1) participates in shell formation and responses to pathogen-associated molecular patterns stimulation in Pinctada fucata martensii

“…Related to the evolution of shells and the bivalve mollusk lifestyle 22 , 23 , the C1qDC gene of bivalve mollusks has undergone a massive expansion. The number of C1qDC genes in humans 24 , mice 25 , zebrafish 26 , and amphioxus 27 ranges from 29 to 52.…”