title: Genome-Wide Identification, Characterization and Phylogenetic Analysis of ATP-Binding Cassette (ABC) Transporter Genes in Common Carp (Cyprinus carpio).
abstract: The ATP-binding cassette (ABC) gene family is considered to be one of the largest gene families in all forms of prokaryotic and eukaryotic life. Although the ABC transporter genes have been annotated in some species, detailed information about the ABC superfamily and the evolutionary characterization of ABC genes in common carp (Cyprinus carpio) are still unclear. In this research, we identified 61 ABC transporter genes in the common carp genome. Phylogenetic analysis revealed that they could be classified into seven subfamilies, namely 11 ABCAs, six ABCBs, 19 ABCCs, eight ABCDs, two ABCEs, four ABCFs, and 11 ABCGs. Comparative analysis of the ABC genes in seven vertebrate species including common carp, showed that at least 10 common carp genes were retained from the third round of whole genome duplication, while 12 duplicated ABC genes may have come from the fourth round of whole genome duplication. Gene losses were also observed for 14 ABC genes. Expression profiles of the 61 ABC genes in six common carp tissues (brain, heart, spleen, kidney, intestine, and gill) revealed extensive functional divergence among the ABC genes. Different copies of some genes had tissue-specific expression patterns, which may indicate some gene function specialization. This study provides essential genomic resources for future studies in common carp.
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.|Department of Aquaculture, College of Animal Sciences, Shanxi Agriculture University, Taigu, Shanxi, China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Liu
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Shangqi
authors.initials: S
authors.lastname: Li
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Wenzhu
authors.initials: W
authors.lastname: Peng
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
authors.forename: Shuaisheng
authors.initials: S
authors.lastname: Feng
authors.affiliation: Henan Academy of Fishery Sciences, Zhengzhou, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Feng
authors.affiliation: Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.|Department of Zoology, GC University, Faisalabad, Pakistan.
authors.forename: Shahid
authors.initials: S
authors.lastname: Mahboob
authors.affiliation: Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.
authors.forename: Khalid A
authors.initials: KA
authors.lastname: Al-Ghanim
authors.affiliation: CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.|College of Ocean & Earth Science, Xiamen University, Xiamen, China.
authors.forename: Peng
authors.identifier: http://orcid.org/0000-0002-1531-5078
authors.initials: P
authors.lastname: Xu
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000145:classification / Q000235:genetics*; D000818:Animals; D002347:Carps / Q000235:genetics*; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000145:classification / Q000235:genetics*; D017353:Gene Deletion; D020440:Gene Duplication; D020869:Gene Expression Profiling; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005810:Multigene Family; D010802:Phylogeny; D026801:Synteny; D014018:Tissue Distribution
chemical_list: D018528:ATP-Binding Cassette Transporters; D029941:Fish Proteins