Expression Profiles of Wuschel-Related Homeobox Gene Family in Pineapple (Ananas comosus L)

Abstract

WUSCHEL-related homeobox (WOX) gene family has important role in plant developmental process and represents a class of plant specific transcription factors that are involved in early phase of embryogenesis by coordinating gene transcription. Recent available pineapple whole genome sequences provide a base for detail comprehensive phylogenetic analysis of the WOX genes in pineapple. Ten WOX genes were found in pineapple genome and were located on 6 chromosomes. On the basis of phylogenetic analysis, WOX gene family was divided into three clades and structural analysis revealed that WOX gene family is highly conserved in pineapple. Gene structure analysis revealed that five genes had two exons with only one intron. Expression profiles based on RNA-Seq of different tissues revealed seven genes showed very low expression in almost all tissues (leaf, flower, root, fruit, stamen, sepal, petal and ovule) at all developmental stages. AcoWOX13 exhibited relatively higher expression in all tissues while the highest expression was shown by AcoWUS at ovule stage 1. Expression analysis under abiotic stresses analyzed by qRT-PCR, showed a dynamic response of WOX genes to abiotic stresses. Interestingly qRT-PCR had result pattern similar to RNA-Seq data as AcoWOX13 had high expression for all abiotic stresses while other WOX genes were down-regulated. This is the first genome-wide study of the WOX genes in pineapple coupled with high throughput RNA-seq for the identification, structural and functional analysis of 10 WOX genes in pineapple. Our study provides more insight for future studies regarding the functions of WOX genes in pineapple.