Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses

BMC Plant Biology

Research Article

Xiaoyang Ge¹  Qian Gong¹  Yuan Cheng¹  Zuoren Yang¹  Zhixia Wu¹  Chaojun Zhang¹  Lili Lu¹  Zhaoen Yang²  Fuguang Li²  Wenqiang Qin² 

[1] Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, 830052, Urumqi, China;Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;

关键词: Gossypium hirsutum;    WUSCHEL-related homeobox;    Segmental duplication;    Transcript factor;    Embryogenesis;   

DOI  :  10.1186/s12870-017-1065-8

 received in 2016-12-20, accepted in 2017-06-25,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundWUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton.ResultsIn this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, (AD)t), respectively. Sequence logos showed that homeobox domains were significantly conserved among the WOX genes in cotton, Arabidopsis, and rice. A total of 168 genes from three typical monocots and six dicots were naturally divided into three clades, which were further classified into nine sub-clades. A good collinearity was observed in the synteny analysis of the orthologs from At and Dt (t represents tetraploid) sub-genomes. Whole genome duplication (WGD) and segmental duplication within At and Dt sub-genomes played significant roles in the expansion of WOX genes, and segmental duplication mainly generated the WUS clade. Copia and Gypsy were the two major types of transposable elements distributed upstream or downstream of WOX genes. Furthermore, through comparison, we found that the exon/intron pattern was highly conserved between Arabidopsis and cotton, and the homeobox domain loci were also conserved between them. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of WOX genes under different stress treatments showed that the different genes were induced by different stresses.ConclusionIn present work, WOX genes, classified into three clades, were identified in the upland cotton genome. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. Moreover, the expression patterns suggested that the duplicated genes might have experienced a functional divergence. Together, these results shed light on the evolution of the WOX gene family, and would be helpful in future research.

【 授权许可】

CC BY   
© The Author(s). 2017