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

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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.

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Abbreviations

WOX:

WUSCHEL-related homeobox

RNA-Seq:

RNA sequencing

qRT-PCR:

quantitative real-time PCR

WUS:

Wuschel

NaCl:

sodium chloride

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Acknowledgments

This work was supported by NSFC (31522009; 31470284; U1605212 to Y.Q.), Fujian Innovative Center for Germplasm Resources and Innovation project of Characteristic Horticultural Crop Seed Industry (KLA15001D), FAFU international collaboration project and Natural Science Foundation of Fujian Province (2017 J01601).

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Authors and Affiliations

  1. Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Center for Genomics and Biotechnology; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, 350002, China

    Zia ur Rahman, Syed Muhammad Azam, Yanhui Liu, Cheng Yan, Hina Ali, Lihua Zhao, Piaojuan Chen, Li Yi & Qin Yuan

  2. College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    S. V. G. N. Priyadarshani & Qin Yuan

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  1. Zia ur Rahman
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  2. Syed Muhammad Azam
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  3. Yanhui Liu
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  4. Cheng Yan
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  5. Hina Ali
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Correspondence to Qin Yuan.

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Communicated by: Hongwei Cai

Syed Muhammad Azam and Yanhui Liu are co-author

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Rahman, Z.u., Azam, S.M., Liu, Y. et al. Expression Profiles of Wuschel-Related Homeobox Gene Family in Pineapple (Ananas comosus L). Tropical Plant Biol. 10, 204–215 (2017). https://doi.org/10.1007/s12042-017-9192-9

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