Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

Juanjuan Li,Chong Yang,Ling Xu,Jian Wang,Weijun Zhou,Qian Huang,Faisal Islam,Basharat Ali

doi:10.1371/journal.pone.0241965

Abstract

WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.

Highlights

MethodsThe genome of H. annuus (HA412.v1.1.bronze) was downloaded from Sunflower Genome Database (https://www.sunflowergenome.org/)
In comparison to the results of Guo et al [20] and Liu et al [21], one gene (HaWRKY51) in our study was found not included in the previous works, whereas the rest had their corresponding genes. The length of these genes ranged from 388 bp (HaWRKY5) to 8445 bp (HaWRKY49), with molecular weight (MW) from 10.48 to 74.25 kDa
The common sunflower WRKY domains were divided into four large groups (Figs 1 and 2), corresponding to group I, II and III in Arabidopsis [2] and an extra WKKY group

Summary

Methods

The genome of H. annuus (HA412.v1.1.bronze) was downloaded from Sunflower Genome Database (https://www.sunflowergenome.org/). The protein sequences of the WRKY family of A. thaliana were obtained from Plant Transcription Factor Database Edu.cn/index.php) [22], which were used to search the WRKY genes from H. annuus genome via BlastP and tBlastN (E-value 1e-20). Pfam database (http://pfam.xfam.org/) and SMART database (http://smart.embl-heidelberg.de/) were used for verification of the WRKY domains [23, 24]. These potential sequences were further queried in the NCBI Conserved Domains Database (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) and InterProScan Database (http://www.ebi.ac.uk/interpro/search/sequence-search) to validate the conserved domain [25, 26]. The molecular weight (Mw) and isoelectric point (pI) of the full-length proteins were predicted using the pI/Mw tool (https://web.expasy.org/compute_pi/) in ExPASy [27].

Results

Discussion

Conclusion