Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication

BMC Genomics

Zhi Zou¹  Jianghua Yang² 

[1] 0000 0000 9835 1415, grid.453499.6, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, Hainan, People’s Republic of China;0000 0000 9835 1415, grid.453499.6, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, Hainan, People’s Republic of China;

关键词: Aquaporin;    AQP;    Gene duplication;    Expansion;    Evolution;    Orthologous group;    Phylogenetic analysis;    Whole-genome duplication;   

DOI  :  10.1186/s12864-019-5780-4

来源: publisher

【 摘 要 】

BackgroundAquaporins (AQPs) are a class of integral membrane proteins that facilitate the passive transport of water and other small solutes across biological membranes. Despite their importance, little information is available in cassava (Manihot esculenta), a perennial shrub of the Euphorbiaceae family that serves the sixth major staple crop in the world.ResultsThis study presents a genome-wide analysis of the AQP gene family in cassava. The family of 42 members in this species could be divided into five subfamilies based on phylogenetic analysis, i.e., 14 plasma membrane intrinsic proteins (PIPs), 13 tonoplast intrinsic proteins (TIPs), nine NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and two small basic intrinsic proteins (SIPs). Best-reciprocal-hit-based sequence comparison and synteny analysis revealed 34 orthologous groups (OGs) present in the Euphorbiaceae ancestor, and nearly one-to-one or two-to-one orthologous relationships were observed between cassava with rubber/physic nut, reflecting the occurrence of one so-called ρ recent whole-genome duplication (WGD) in the last common ancestor of cassava and rubber. In contrast to a predominant role of the ρ WGD on family expansion in rubber, cassava AQP duplicates were derived from the WGD as well as local duplication. Species-specific gene loss was also observed in cassava, which includes the entire NIP4 group and/or six OGs. Comparison of conserved motifs and gene expression profiles revealed divergence of paralogs in cassava as observed in rubber.ConclusionsOur findings will not only improve our knowledge on family evolution in Euphorbiaceae, but also provide valuable information for further functional analysis of AQP genes in cassava and rubber.

【 授权许可】

CC BY