title: Diversification of the duplicated Rab1a genes in a hypoxia-tolerant fish, common carp (Cyprinus carpio).
abstract: Common carp is a widely cultivated fish with longer than 2,000 years domestication history, due to its strong environmental adaptabilities, especially hypoxia tolerance. The common carp genome has experienced a very recent whole genome duplication (WGD) event. Among a large number of highly similar duplicated genes, a pair of Ras-associated binding-GTPase 1a (Rab1a) genes were found fast diverging. Four analogous Rab1a genes were identified in the common carp genome. Comparisons of gene structures and sequences indicated Rab1a-1 and Rab1a-2 was a pair of fast diverging duplicates, while Rab1a-3 and Rab1a-4 was a pair of less diverged duplicates. All putative Rab1a proteins shared conserved GTPase domain, which enabled the proteins serve as molecular switches for vesicular trafficking. Rab1a-1 and Rab1a-2 proteins varied in their C-terminal sequences, which were generally considered to encode the membrane localization signals. Differential expression patterns were observed between Rab1a-1 and Rab1a-2 genes. In blood, muscle, spleen, and heart, the mRNA level of Rab1a-1 was higher than that of Rab1a-2. In liver and intestine, the mRNA level of Rab1a-2 was higher. Expression of Rab1a-1 and Rab1a-2 showed distinct hypoxia responses. Under severe hypoxia, Rab1a-1 expression was down-regulated in blood, while Rab1a-2 expression was up-regulated in liver. Compared with the less diverged Rab1a-3/4 gene pair, common carp Rab1a-1/2 gene pair exhibited strong characteristics of sub-functionalization, which might contribute to a sophisticated and efficient Ras-dependent regulating network for the hypoxia-tolerant fish.
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. Electronic address: zhaozx@cafs.ac.cn.
authors.forename: Zi-Xia
authors.initials: ZX
authors.lastname: Zhao
authors.affiliation: Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China.
authors.forename: Ding-Chen
authors.initials: DC
authors.lastname: Cao
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Ru
authors.initials: R
authors.lastname: Xu
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China; Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China. Electronic address: sunxw2002@163.com.
authors.forename: Xiao-Wen
authors.initials: XW
authors.lastname: Sun
mesh_terms: D000818:Animals; D002347:Carps / Q000235:genetics / Q000378:metabolism*; D005393:Fish Diseases / Q000235:genetics / Q000378:metabolism; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism*; D020131:Genes, Duplicate; D000860:Hypoxia / Q000235:genetics / Q000378:metabolism / Q000662:veterinary*; D009928:Organ Specificity; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D020761:rab1 GTP-Binding Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D029941:Fish Proteins; D020761:rab1 GTP-Binding Proteins
keywords: Common carp; Divergence; Duplication; Hypoxia; Rab1a