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.
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Acknowledgments
We appreciate the anonymous reviewers for their comments on this manuscript. This study was supported by MOST (2018YFD1000502) (to H. Huang) and Yunnan Innovation Team Project (to L. Z. Gao).
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ESM 1
Multiple sequence alignment of domains among the HbWRKY proteins. The alignment was performed using Clustal W. Dashes indicate gaps. ‘N’ and ‘C’ denote the N-terminal and C-terminal WRKY domains of a specific WRKY protein. (PNG 5171 kb)
ESM 2
Phylogenetic analysis of the 324 WRKY proteins in Arabidopsis, rice and rubber tree. A. The phylogenetic tree was constructed using Neighbor-Joining method based on WRKY domains. B. The phylogenetic tree was constructed using maximum-likelihood method based on WRKY domains. Reliability of the predicted trees was tested using bootstrapping with 1000 replicates. (PNG 1845 kb)
ESM 3
The schematic distribution of motifs within the HbWRKY proteins. (PNG 771 kb)
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Phylogenetic relationships and conserved motif compositions of the WRKY genes in the rubber tree genome. Phylogenetic tree was constructed using the maximum-likelihood method based on alignments of the predicted complete proteins. The conserved motifs were detected using MEME software and represented by colored boxes. Reliability of the predicted tree was tested using bootstrapping with 1000 replicates. The length of WRKY proteins can be estimated using the scale at the bottom and conserved motif were shown in Table S1. (PNG 626 kb)
ESM 5
The exon-intron structures of the HbWRKY genes. The exons and introns are indicated by blue rectangles and black lines, respectively. (PNG 388 kb)
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Nan, H., Lin, YL., Liu, J. et al. Genome-Wide Analysis of the WRKY Transcription Factor Gene Family and Their Response to Salt Stress in Rubber Tree. Tropical Plant Biol. 14, 22–33 (2021). https://doi.org/10.1007/s12042-020-09268-x
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DOI: https://doi.org/10.1007/s12042-020-09268-x