Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey

BMC Genomics

Weiming Li⁴  Titus Brown²  Camille Scott¹  Chu-Yin Yeh⁴  Yu-Wen Chung-Davidson⁴  Jianfeng Ren³ 

[1] Department of Computer Science and Engineering, Michigan State University, East Lansing 48824, MI, USA;Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824, MI, USA;Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China;Department of Fisheries and Wildlife, Michigan State University, East Lansing 48824, MI, USA

关键词: Gene expression;    RNA-Seq;    Lampreys;    Chordates;    Evolution;    ABC transporter;   

Others  :  1211968
DOI  :  10.1186/s12864-015-1677-z

 received in 2015-01-23, accepted in 2015-06-01,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Ren et al.

【 图 表 】

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