Genome-Wide Identification, Characterization and Phylogenetic Analysis of ATP-Binding Cassette (ABC) Transporter Genes in Common Carp (Cyprinus carpio).

Xiang Liu,Shuaisheng Feng,Jianxin Feng,Shahid Mahboob,Shangqi Li,Khalid A Al-Ghanim,Wenzhu Peng,Peng Xu,Anthony M George

doi:10.1371/journal.pone.0153246

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.

Highlights

The ATP-binding cassette (ABC) transporters are integral membrane proteins and are one of the largest superfamilies ubiquitously present in all phyla [1]
Identification and phylogenetic analysis of ABC transporter genes in common carp We identified a total of 61 ABC transporter genes in the common carp genome that we classified as follows: 11 ABCAs, six ABCBs, 19 ABCCs, eight ABCDs, two ABCEs, four ABCFs, and
We found that the common carp ABCA1, ABCA5, ABCB5, ABCC2, ABCC4, ABCC5, ABCC9, ABCC12, ABCD4, ABCE1, and ABCG8 genes had undergone significant numbers of duplications compared with their orthologs in the closely related zebrafish genome, which suggested that they these genes may be derived from the 4R whole genome duplication (WGD) (Table 2)

Summary

Introduction

The ATP-binding cassette (ABC) transporters are integral membrane proteins and are one of the largest superfamilies ubiquitously present in all phyla [1]. ABC Gene Family in Common Carp Genome (201602). The authors would like to extend their sincere appreciation to the Deanship of Scientific.

Methods

Results

Conclusion