Genome-Wide Analysis of WRKY Genes and Their Response to Hormone and Mechanic Stresses in Carrot

Nan, Hong; Gao, Li‐Zhi

doi:10.3389/fgene.2019.00363

Cited by 45 publications

(25 citation statements)

References 85 publications

(114 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some motifs were located nearby the WRKY domain, for instance, motifs 6, 9, and 17. Just as phylogenetic analysis divided Sb WRKY genes into groups I-III and subgroups IIa-e, the presence or absence of shared motifs between Sb WRKY proteins followed the same general separation into groups, consistent with previous studies [ 76 – 79 ]. Indeed, each of these motifs occurs in most subgroups, and each subgroup can be distinguished based on the motifs they present.…”

Section: Discussionsupporting

confidence: 89%

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

et al. 2020

View full text Add to dashboard Cite

WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum ( Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors ( Sb WRKYs). The Sb WRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa–IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis ( Arabidopsis thaliana ) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all Sb WRKYs contained either one or two WRKY domains and that Sb WRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0–7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis -element analysis showed that all SbWRKYs contain at least one stress response-related cis -element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.

show abstract

Section: Discussionsupporting

confidence: 89%

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

et al. 2020

View full text Add to dashboard Cite

show abstract

“…In the present study, 490 WRKY gene family members were identified from six species of the superorder Asteranae. We identified 65 WRKY genes in carrot, which compares with 67 in a previous study of the same variety [29]. This difference may be due to the fact that the E values were set differently when the domains were screened.…”

Section: Discussionmentioning

confidence: 96%

“…sativus L.; Daucus carota L. cv. Kuroda) [25,26,27,28,29,30]. Within superorder the Asteranae, genomes of six species of the Asterales and the Apiales have been sequenced.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of WRKY Transcription Factors in the Asteranae

Guo

Zhang

Wang

et al. 2019

Plants

View full text Add to dashboard Cite

The WRKY transcription factors family, which participates in many physiological processes in plants, constitutes one of the largest transcription factor families. The Asterales and the Apiales are two orders of flowering plants in the superorder Asteranae. Among the members of the Asterales, globe artichoke (Cynara cardunculus var. scolymus L.), sunflower (Helianthus annuus L.), and lettuce (Lactuca sativa L.) are important economic crops worldwide. Within the Apiales, ginseng (Panax ginseng C. A. Meyer) and Panax notoginseng (Burk.) F.H. Chen are important medicinal plants, while carrot (Daucus carota subsp. carota L.) has significant economic value. Research involving genome-wide identification of WRKY transcription factors in the Asterales and the Apiales has been limited. In this study, 490 WRKY genes, 244 from three species of the Apiales and 246 from three species of the Asterales, were identified and categorized into three groups. Within each group, WRKY motif characteristics and gene structures were similar. WRKY gene promoter sequences contained light responsive elements, core regulatory elements, and 12 abiotic stress cis-acting elements. WRKY genes were evenly distributed on each chromosome. Evidence of segmental and tandem duplication events was found in all six species in the Asterales and the Apiales, with segmental duplication inferred to play a major role in WRKY gene evolution. Among the six species, we uncovered 54 syntenic gene pairs between globe artichoke and lettuce. The six species are thus relatively closely related, consistent with their traditional taxonomic placement in the Asterales. This study, based on traditional species classifications, was the first to identify WRKY transcription factors in six species from the Asteranae. Our results lay a foundation for further understanding of the role of WRKY transcription factors in species evolution and functional differentiation.

show abstract

“…Evolutionary alterations have helped plants adapt to abiotic and biotic stresses by controlling a network of certain genes through modulation of specific transcription factors (Nan and Gao, 2019). Extensive studies of DREB in model plants, crops (Toshitsugu et al, 2006), or other economically important plants (Zhao et al, 2014;Xie et al, 2014;Shu et al, 2016) suggest that the number, gene structure, sequences, and functions of this subfamily differ markedly among species.…”

Section: Comparisons Of Dreb Family Composition Between S Spontaneummentioning

confidence: 99%

Genome-Wide Analysis of the DREB Subfamily in Saccharum spontaneum Reveals Their Functional Divergence During Cold and Drought Stresses

et al. 2020

View full text Add to dashboard Cite

Drought and cold stresses are the main environmental factors that affect the yield of sugarcane, and DREB genes play very important roles in tolerance to drought, cold, and other environmental stresses. In this study, bioinformatics analysis was performed to characterize Saccharum spontaneum SsDREB genes. RNA sequencing (RNA-seq) was used to detect the expression profiles of SsDREBs induced by cold and drought stresses. According to our results, there are 110 SsDREB subfamily proteins in S. spontaneum, which can be classified into six groups; 106 of these genes are distributed among 29 chromosomes. Inter-and intraspecies synteny analyses suggested that all DREB groups have undergone gene duplication, highlighting the polyploid events that played an important role in the expansion of the DREB subfamily. Furthermore, RNA-seq results showed that 45 SsDREBs were up-or downregulated under cold stress; 35 of them were found to be involved in responding to drought stress. According to protein-protein interaction analysis, SsDREB100, SsDREB102, and SsDREB105 play key roles during the response to cold stress. These results reveal that functional divergence exists between collinear homologous genes or among common origin genes in the DREB subfamily of S. spontaneum. This study presents a comprehensive analysis and systematic understanding of the precise mechanism of SsDREBs in response to abiotic stress and will lead to improvements in sugarcane.

show abstract

Genome-Wide Analysis of WRKY Genes and Their Response to Hormone and Mechanic Stresses in Carrot

Cited by 45 publications

References 85 publications

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

Genome-Wide Identification of WRKY Transcription Factors in the Asteranae

Genome-Wide Analysis of the DREB Subfamily in Saccharum spontaneum Reveals Their Functional Divergence During Cold and Drought Stresses

Contact Info

Product

Resources

About