Genome-Wide Analysis of the WRKY Transcription Factor Gene Family and Their Response to Salt Stress in Rubber Tree
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Genome-Wide Analysis of the WRKY Transcription Factor Gene Family and Their Response to Salt Stress in Rubber Tree Hong Nan 1 & Yang-Lei Lin 2,3 & Jin Liu 4 & Hui Huang 2 & Wei Li 1 & Li-zhi Gao 1,2 Received: 27 May 2020 / Accepted: 25 August 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract The multigene family WRKY is plant-specific transcription factors, which is involved in numerous aspects of plant growth and development. Here, we report a genome-wide search for the rubber tree WRKY (HbWRKY) genes and their expression profiles at various tissues including latexes. We also present a comprehensive overview of whole HbWRKY gene family, including gene structure, chromosomal locations, conserved protein domains, gene duplications and phylogenetic inferences. We identify a total of 108 full-length HbWRKY genes, which were classified into the three major subgroups. The genome-scale syntenic analysis showed that WGDs might have played a major role in the evolution of the HbWRKY gene family. Our further real-time reverse transcription-PCR (qRT-PCR) experiments validated that the HbWRKY genes are divergently expressed and gene expression divergence seemingly existed among the duplicated WRKY genes, suggesting a fundamentally functional divergence of the duplicated WRKY paralogs in rubber tree. We also investigated the gene expression profiling of the HbWRKYs under salt stress, to which the majority of genes differentially responded. This study acquires a new insight into the evolution of the HbWRKYs, which will help further functional characterization of theses candidate genes in rubber tree. Keywords WRKY transcription factor . Rubber tree . Phylogenetic analysis . Expression divergence . Genomic synteny
Introduction Plants have developed diverse molecular mechanisms to cope with various types of biotic and abiotic stresses. Numerous transcription factors (TFs), which confer tolerance to different types of stresses, have been identified in plants. They are important regulators to determine gene expression by binding
Communicated by: Ray Ming Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12042-020-09268-x) contains supplementary material, which is available to authorized users. * Li-zhi Gao [email protected] 1
Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
2
Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
3
University of the Chinese Academy of Sciences, Beijing 100039, China
4
Yunnan Institute of Tropical Crops, Jinghong 666100, China
to specific cis-acting elements in the promoter regions (Todaka et al. 2012). The WRKY gene family is one of the largest TF families and widespread in higher plants. Since the first WRKY gene (SPF1) was identified in potato (Ipomoea batatas) (Ishiguro and Nakamura 1994), numerous WRKY genes have been well studied in many
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