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

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 T. 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.

Figure 1

Phylogenetic analysis of 46  T. japonicus ABC transporters using the Bayesian method. Numbers at branch nodes represent the confidence level of posterior probability.

Figure 2

Conserved domain analysis of 46  T. japonicus ABC transporters. ABC in an ellipse means ATP-binding cassette (referred to as nucleotide binding domains; NBDs), and TM in a rectangle represents transmembrane domains (TMDs). Numbers in brackets refer to the number of ABC proteins in each subfamily.

Figure 3

Comparison of the number of genes in each subfamily of ABC transporters between T. japonicus and other animals.

Figure 4

Temporal transcriptional expressions of 46  T. japonicus ABC transporters in different developmental stages (N, nauplius; C, copepodid; M, male; F, female).