Dataset Information

Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster.

ABSTRACT: Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster.

SUBMITTER: Gao D

PROVIDER: S-EPMC4573066 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster.

Gao Dahai D Ko Dennis C DC Tian Xinmin X Yang Guang G Wang Liuyang L

Evolutionary bioinformatics online 20150913 Suppl 1

Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whol ...[more]

PMID: 26417197

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Project description:The maintenance of cellular homeostasis is an important process for successful immune defense against pathogenic invading, in which unfolded protein response (UPR) pathway regulates endoplasmic reticulum (ER) homeostasis upon exposure to environmental changes. Protein kinase-like ER kinase (PERK) is an important ER stress sensor to be activated during the UPR to regulate cells homeostasis. In the present study, one PERK homologue was identified from Pacific oyster Crassostrea gigas (designated as CgPERK). The cDNA of CgPERK was of 4307 bp with a 3174 bp open reading frame (ORF) encoding a polypeptide of 1058 amino acids. There were two conserved protein kinases domains and two conserved autophosphorylation sites at Lys618 and Thr980 in CgPERK. The mRNA transcript of CgPERK was constitutively expressed in all the tested tissues including mantle, adductor muscle, hepatopancreas, gill, gonad and labial palp with the highest expression level in hemocytes (31.15-fold compared to mantle). The CgPERK protein was found to be located mainly in the cytoplasm of hemocytes. The mRNA expression level of CgPERK in hemocytes was significantly up-regulated and reached the highest level (5.25-fold compared to seawater group, p < 0.01) at 48 h after the oysters were stimulated with poly(I: C). Meanwhile, a significant increase of fluorescence autophagosome spots in hemocytes was also observed at 36 h post stimulation. After the mRNA expression of CgPERK was knocked down (0.49-fold compared to dsGFP group, p < 0.01) by injection of CgPERK dsRNA, the mRNA expression of autophagy related 12 (ATG12) in hemocytes was significantly decreased at 12 h post poly(I: C) stimulation, which was 0.53-fold (p < 0.01) compared to dsGFP-injected oysters. When the CgPERK was inhibited by its inhibitor GSK2656157 stimulation, the autophagosomes rate of hemocytes decreased significantly at 12 h post poly(I: C) stimulation, which was 0.34-fold (p < 0.01) of that of DMSO group. Collectively, these results suggested that CgPERK, as an UPR initiator, was involved in autophagosomes formation upon poly(I: C) stimulation by regulating the expression of ATG12, and ER stress stimulated the autophagosome formation on an ATG protein-dependent manner in oysters.

Dataset Information

Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster.

Publications

Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster.

Similar Datasets

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