title: Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster.
abstract: Alternative splicing (AS) is thought to enhance transcriptome diversity dramatically and play an important role in stress adaptation. While well studied in vertebrates, AS remains poorly understood in invertebrates. Here, we used high-throughput RNA-sequencing data to perform a genome-wide survey of AS in the Pacific oyster (Crassostrea gigas), an economically important mollusk that is cultivated worldwide. This analysis identified 8223 AS events corresponding to 4480 genes in the Pacific oyster, suggesting that about 16 % of oyster multiexonic genes undergo AS. We observed that a majority of the identified AS events were related to skipped exons (37.8 %). Then Gene Ontology analysis was conducted to analyze the function of the genes that undergo AS and the genes that produce more than five AS isoforms. After that, the expression of AS isoforms facing temperature, salinity, and air exposure challenge were examined. To validate our bioinformatic-predicted results and examine whether AS affects stress adaptation, we selected heat-shock protein 60 (HSP60) and HSP90 genes, both of which experience AS, for reverse transcription PCR (RT-PCR). We also performed quantitative real-time PCR (qRT-PCR) to determine the relative expression of each AS isoform among different stress adapted populations. Our study indicates that AS events are likely complex in the Pacific oyster and may be related to stress adaptation. These results will complement the predicted gene database of C. gigas and provide an invaluable resource for future functional genomic studies on molluscs.
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7th Nanhai Rd, Qingdao, China.|Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.|National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors: Baoyu
authors: B
authors: Huang
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7th Nanhai Rd, Qingdao, China.|National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
authors: Linlin
authors: L
authors: Zhang
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7th Nanhai Rd, Qingdao, China.|National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.|Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors: Xueying
authors: X
authors: Tang
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7th Nanhai Rd, Qingdao, China.|National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.|Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
authors: Guofan
authors: G
authors: Zhang
authors: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7th Nanhai Rd, Qingdao, China. lili@qdio.ac.cn.|Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. lili@qdio.ac.cn.|National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. lili@qdio.ac.cn.
authors: Li
authors: L
authors: Li
mesh_terms: D000222:Adaptation, Physiological; D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D018834:Chaperonin 60 / Q000235:genetics* / Q000378:metabolism; D049896:Crassostrea / Q000235:genetics* / Q000378:metabolism; D005091:Exons; D063990:Gene Ontology; D016678:Genome; D018841:HSP90 Heat-Shock Proteins / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D058977:Molecular Sequence Annotation; D054712:Salinity; D013312:Stress, Physiological; D013696:Temperature; D059467:Transcriptome
chemical_list: D018834:Chaperonin 60; D018841:HSP90 Heat-Shock Proteins
keywords: Alternative splicing; Crassostrea gigas; HSP60; HSP90; RNA-seq