Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera

Abstract

BackgroundWRKY transcription factors are one of the largest families of transcriptional regulators in plants. WRKY genes are not only found to play significant roles in biotic and abiotic stress response, but also regulate growth and development. Grapevine (Vitis vinifera) production is largely limited by stressful climate conditions such as cold stress and the role of WRKY genes in the survival of grapevine under these conditions remains unknown.ResultsWe identified a total of 59 VvWRKYs from the V. vinifera genome, belonging to four subgroups according to conserved WRKY domains and zinc-finger structure. The majority of VvWRKYs were expressed in more than one tissue among the 7 tissues examined which included young leaves, mature leaves, tendril, stem apex, root, young fruits and ripe fruits. Publicly available microarray data suggested that a subset of VvWRKYs was activated in response to diverse stresses. Quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 36 VvWRKYs are changed following cold exposure. Comparative analysis was performed on data from publicly available microarray experiments, previous global transcriptome analysis studies, and qRT-PCR. We identified 15 VvWRKYs in at least two of these databases which may relate to cold stress. Among them, the transcription of three genes can be induced by exogenous ABA application, suggesting that they can be involved in an ABA-dependent signaling pathway in response to cold stress.ConclusionsWe identified 59 VvWRKYs from the V. vinifera genome and 15 of them showed cold stress-induced expression patterns. These genes represented candidate genes for future functional analysis of VvWRKYs involved in the low temperature-related signal pathways in grape.

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

“…Most SiWRKY genes were highly expressed in roots, whereas a few SiWRKY genes were expressed in developing seeds. This is consistent with observations made in other plants, including rice [18], cucumber [33], grape [42], apple [13], cassava [30], cotton [43], physic nut [41], and cabbage [44]. Our results revealed that SiWRKY genes are expressed tissuespecifically and the high expression levels observed in roots might reflect their roles in responses to abiotic and biotic stresses that first affect plants below ground.…”

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

“…As shown in Figs.2 and 3, 77 CitsWRKY proteins were classified into three main groups. This is consistent with the classification of WRKY family members in A. thaliana (Eulgem et al, 2000), O. sativa (Ross et al, 2007), Z. mays , and V. vinifera (Wang et al, 2014).…”

“…Structural diversity provides additional evidence of phylogenetic groupings, besides evolutionary information, for multigene families in which the gain or loss of an exon/intron can result from rearrangements and/or fusions of different chromosomal regions (Wang et al, 2014). The most closely related members of the same group, in general, showed the same standard exon/intron structure, such as number, position, and size of intron.…”

“…Thus, considering the fundamental role of WRKYTFs in several molecular, biochemical, and physiological processes, this gene family has been extensively characterized in different species such as Arabidopsis thaliana (Eulgem et al, 2000), Oriza sativa (Ross et al, 2007), Zea mays , Hordeum vulgare (Liu et al, 2014), Vitis vinifera (Wang et al, 2014), Manihot esculenta (Wei et al, 2016) and in trees including Populus trichocarpa (He et al, 2012) and, Hevea brasiliensis . However, few studies have identified the members of the WRKY family in oranges (Ayadi et al, 2016).…”

CARACTERIZAÇÃO IN SILICO DOS GENES ENVOLVIDOS NO METABOLISMO DO NITROGÊNIO EM MILHO (Zea mays)

“…A diversidade estrutural fornece evidências adicionais aos agrupamentos filogenéticos, além de informações evolutivas das famílias multigênicas, no qual o ganho ou perda de um exon/íntron pode ser causada por rearranjos e/ou fusões de diferentes porções dos cromossomos (WANG et al, 2014). O padrão de distribuição dos íntrons/exons dos genes que fazem parte da assimilação de N em milho é mostrado na Figura 2.…”