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

Zhaoen Yang,Yuan Cheng,Zhixia Wu,Wenqiang Qin,Xiaoyang Ge,Qian Gong,Fuguang Li,Chaojun Zhang,Zuoren Yang,Lili Lu

doi:10.1186/s12870-017-1065-8

Zhaoen Yang, Yuan Cheng + Show 8 more

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https://doi.org/10.1186/s12870-017-1065-8

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Abstract

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.

Highlights

WUSCHEL-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
Thereafter, PROSITE and InterProscan 56.0 were used to search for the HB domain in the obtained sequences and 14, 12, 12, 19, 11, 21, 20, 38, and 33 genes were confirmed as WOX family members in rice, sorghum, poplar, maize, cacao, G. arboreum, G. raimondii, G. hirsutum (NAU), and G. hirsutum (BJI), respectively (Additional file 1:Table S1)
According to newly sequenced A genome database (Unpublished) by PacBio RS II [43], we found the previous annotations of Cotton_A_11936 and Cotton_A_11937 were not accurate, and the total WOX genes in G. arboreum should be 20, so we used GaWOX1 to represent them for further study

Summary

Introduction

WUSCHEL-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. Previous reports have shown that WOXs assay a wide variety of important roles in development and growth process of plants, such as in embryonic patterning, stem cell maintenance, and organ formation [2, 3]. AtWUS expressed in shoot apical meristem, ovule, and anther has been proven to play important roles in stem cell maintenance [6]. AtWOX11 directly responds to an auxin maximum, induced by wounding in and around the procambium, and like AtWOX12, it positively upregulates LATERAL ORGAN BOUNDARIES DOMAIN 16 and 29 genes, resulting in the initiation of a leaf procambium or the transition of its neighboring parenchyma cells to root founder cells [18]. AtWOX14 and WOX4, regulatory elements downstream of PHLOEM INTERCALATED WITH XYLEM (PXY), regulate vascular cell division instead of vascular organization, playing crucial roles in stem formation [20]

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