Genome-wide characterization of the Rab gene family in Gossypium by comparative analysis

BACKGROUND: Rab protein family is the largest subfamily of small G protein family. As one of the most important families in plant, Rab family plays an important role in the process of plant growth and development. So far, the identification of 57 members of the Rab family in Arabidopsis has been completed. In cotton, the relevant family has not been reported. RESULTS: Here, we identified 87, 169, 136, 80 Rabs in the four sequenced cotton species, G. raimondii (D(5)), G. hirsutum acc. TM-1 (AD(1)), G. barbadense acc. 3-79 (AD(2)) and G. arboreum (A(2)), respectively. Biological information analysis showed that the number of amino acid is 200–300 aa among Rab family members in G. raimondii and the protein molecular weight is between 20 and 30 kDa, which is consistent with the characterization of the Rab protein itself. 87 GrRabs in G. raimondii are divided into eight groups. In each group, intron numbers and subcellular localization of Rab protein are basically the same. We mapped the distribution of GrRab genes on 13 chromosomes of G. raimondii except two genes. Among the 87 GrRabs in G. raimondii, we identified 60 pairs of GrRabs formed in whole genome duplication. Among all the gene pairs, the Ka/Ks values were less than 1. This indicates that it is the results of the purification selection and will help maintain the conservation of gene in structure and function. Further, 4 of the 87 GrRabs showed tandem duplication. They were GrRabA2a vs GrRabD1a and GrRabA2h vs GrRabD1b respectively. Expression patterns analysis of 169 GhRabs in G. hirsutum acc. TM-1 indicates that most Rab family members play a certain role in different tissues/organs and different growth stages of cotton, implying their potential function in the polar growth of pollen tube, root hair and fiber cell, as well as improving stress and disease tolerance. CONCLUSION: The systematic investigation of Rab genes in cotton will lay a foundation for understanding the functional roles of different Rab members in the polar growth and stress tolerance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40529-017-0181-y) contains supplementary material, which is available to authorized users.