In silico genome-wide identification and phylogenetic analysis of the WRKY transcription factor family in sweet orange (Citrus sinensis)

Abstract

WRKY transcription factors (TFs) play important roles in several biological processes, especially in defense against different biotic and abiotic stresses. An extensive in silico characterization of the CitsWRKY gene family was performed. In this study, 77 WRKY genes from the Citrus sinensis genome were identified. Based on sequence alignment and phylogenetic analysis, these 77 proteins were classified into three main groups, with most WRKY proteins placed in group I (36 CitsWRKY), group II (35 CitsWRKY), and group III (6 CitsWRKY). Analysis of conserved motifs showed that most identified CitsWRKY proteins carry a conserved WRKY domain. Structural analysis of the genes showed that the number of introns in CitsWRKY genes varied from zero to five. CitsWRKY genes were found to be randomly distributed on all nine chromosomes. The expansion of this gene family may have resulted from 14 tandem and five segmental duplication events. Evaluation of synteny events suggested that some WRKY genes emerged before the divergence of C. sinensis and Arabidopsis. Expression analysis demonstrated that these genes frequently occur in developing tissues such as fruit, flowers, ovaries, meristem, and phloem (65%, 66%, and 85% in groups I, II , and III, respectively), and are stimulated by biotic or abiotic stresses (15%, 16%, and 10% in groups I, II, and III, respectively). The characterization and analysis of these genes will aid in the selection of candidate genes for future functional analyses of the WRKY family in citrus, which will expand our understanding of genetic determinants of stress tolerance.

Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata

“…Recent studies have proposed that gene duplication is considered to be one of the primary driving forces in the expansion of gene families and genome evolution, and the major duplication patterns are tandem duplication and segmental duplication ( Cannon et al, 2004 ). Tandem duplications have been reported to play major roles in the expansion of the WRKY family in Solanum tuberosum ( Shi et al, 2017 ) and Citrus sinensis ( Silva et al, 2017 ); however, segmental duplications seem to be more common than tandem duplications are in the expansion of the WRKY family, such as in O. rufipogon ( Nan et al, 2020 ), Cicer arietinum ( Waqas et al, 2019 ), and Ananas comosus ( Xie et al, 2018 ). These findings are consistent with research in Camelina sativa ( Song et al, 2020 ).…”

Genome-wide identification and molecular characterization of Citrusunshiu WRKY transcription factors in Satsuma mandarin: clues for putative involvement in cell growth, fruit ripening, and stress response

“…Regarding the members of the CiuWRKY family, we have updated our previous results obtained by Ayadi et al (2016), who identified 51, 48, and only one WRKY TF in Citrus sinensis, C. clementina, and Citrus unshiu, respectively. On the other hand, da Silva et al (2017) found 77 WRKY genes from the Citrus sinensis genome, most of them classified in group I (36 CitsWRKYs), group II ( 35CitsWRKYs), and group III (6 CitsWRKYs). The number of WRKY TFs found in Satsuma mandarin (51) was close to that in other fleshy fruit type species like Citrus clementina (48), cucumber (55), melon (56), watermelon (57), and grapevine (59) (Ling et al, 2011;Wang et al, 2014;Ayadi et al, 2016;Jiao et al, 2018;Li et al, 2018).…”

“…The genomic organization diversity (exon/intron distribution, number, size) of CiuWRKY genes provides additional evidence of phylogenetic groupings (Wang et al, 2014;da Silva et al, 2017). Remarkably, almost half (25) of the 51 CiuWRKY genes contain three exons, similarly to C. sinensis, O. sativa, and H. brasiliensis, in which 37 of 77, 42 of 92, and 40 of 81 WRKY genes contain three exons, respectively (Xie et al, 2005;Li et al, 2014;da Silva et al, 2017). Therefore, in terms of genomic structure, through this exon number conservation between different species, there is significant similarity among C.…”