title: Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey.
abstract: BACKGROUND
  Lampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates.
  
  
  RESULTS
  We conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed.
  
  
  CONCLUSIONS
  Thirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC gene subfamilies in chordates have undergone obvious expansion or contraction. The ABCA subfamily showed the highest gene expansion rate during chordate evolution. The evolution of ABC transporters in lampreys requires further evaluation because the present results are based on a draft genome.
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China. jfren@shou.edu.cn.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Ren
authors.affiliation: Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA. chungyuw@msu.edu.
authors.forename: Yu-Wen
authors.initials: YW
authors.lastname: Chung-Davidson
authors.affiliation: Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA. yehchuyi@gmail.com.
authors.forename: Chu-Yin
authors.initials: CY
authors.lastname: Yeh
authors.affiliation: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. camille.scott.w@gmail.com.
authors.forename: Camille
authors.initials: C
authors.lastname: Scott
authors.affiliation: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. ctb@msu.edu.|Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. ctb@msu.edu.
authors.forename: Titus
authors.initials: T
authors.lastname: Brown
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China. liweim@msu.edu.|Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA. liweim@msu.edu.
authors.forename: Weiming
authors.initials: W
authors.lastname: Li
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D007798:Lampreys / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny
chemical_list: D018528:ATP-Binding Cassette Transporters