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Open Access Research article

Genome-wide identification of whole ATP-binding cassette (ABC) transporters in the intertidal copepod Tigriopus japonicus

Chang-Bum Jeong1, Bo-Mi Kim2, Jae-Seong Lee2* and Jae-Sung Rhee3*

Author Affiliations

1 Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea

2 Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea

3 Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 406-772, South Korea

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BMC Genomics 2014, 15:651  doi:10.1186/1471-2164-15-651

Published: 5 August 2014

Abstract

Backgrounds

The ATP-binding cassette (ABC) transporter superfamily is one of the largest transporter gene families and is observed in all animal taxa. Although a large set of transcriptomic data was recently assembled for several species of crustaceans, identification and annotation of the large ABC transporter gene family have been very challenging.

Results

In the intertidal copepod Tigriopus japonicus, 46 putative ABC transporters were identified using in silico analysis, and their full-length cDNA sequences were characterized. Phylogenetic analysis revealed that the 46‚ÄČT. japonicus ABC transporters are classified into eight subfamilies (A-H) that include all the members of all ABC subfamilies, consisting of five ABCA, five ABCB, 17 ABCC, three ABCD, one ABCE, three ABCF, seven ABCG, and five ABCH subfamilies. Of them, unique isotypic expansion of two clades of ABCC1 proteins was observed. Real-time RT-PCR-based heatmap analysis revealed that most T. japonicus ABC genes showed temporal transcriptional expression during copepod development. The overall transcriptional profile demonstrated that half of all T. japonicus ABC genes were strongly associated with at least one developmental stage. Of them, transcripts TJ-ABCH_88708 and TJ-ABCE1 were highly expressed during all developmental stages.

Conclusions

The whole set of T. japonicus ABC genes and their phylogenetic relationships will provide a better understanding of the comparative evolution of essential gene family resources in arthropods, including the crustacean copepods.

Keywords:
ATP-binding cassette transporter; Copepod; Tigriopus japonicus; Genome; Development