title: Molecular diversity and evolution of defensins in the manila clam Ruditapes philippinarum.
abstract: Four types of defensins were identified in Manila clam and designated as Rpdef1, Rpdef2, Rpdef3 and Rpdef4, which encoded a polypeptide of 49, 46, 45 and 42 amino acids, respectively. Sequence alignments indicated that Rpdef1 shared 46.9% identity with Rpdef2, 40.8% with Rpdef3, and 34.7% with Rpdef4. Analysis of transcript polymorphism showed that Rpdef3 accounted for about 60% frequency of Rpdefs occurrence in clams from three geographic origins (Dalian, Qingdao and Hangzhou). By quantitative real-time RT-PCR (qRT-PCR) analysis, the transcripts of Rpdefs were mainly detected in hemocytes and they responded sensitively to bacterial challenge in hemocytes. Evolutionary analysis indicated that all Rpdefs were under positive selection with positively selected basic amino acid residues detected in the C-terminal regions, which perhaps have a functional relevance by modifying the charge distribution of Rpdefs. The results also showed some lineages with dN/dS > 1, suggesting positive selection pressures existed in some lineages of phylogeny tree constructed by mollusk defensins. Overall, our results suggest that Rpdefs perhaps played important roles in host defense and positive selection is the major driving force in generating high diversity of defensins in the Manila clam.
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Wang
authors.affiliation: South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China.
authors.forename: Linbao
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
authors.forename: Dinglong
authors.initials: D
authors.lastname: Yang
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Yu
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China.
authors.forename: Ming
authors.initials: M
authors.lastname: Cong
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China.
authors.forename: Chenglong
authors.initials: C
authors.lastname: Ji
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China.
authors.forename: Huifeng
authors.initials: H
authors.lastname: Wu
authors.affiliation: Key Laboratory of Coastal Environmental Processes and Ecological Remediation, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China. Electronic address: jmzhao@yic.ac.cn.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Zhao
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D049872:Bivalvia / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D023082:Defensins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D023082:Defensins; D020033:Protein Isoforms
keywords: Defensin; Diversity; Manila clam; Positive selection