Dataset Information

Genome-Wide Identification and Expression Analysis of the WRKY Gene Family in Cassava.

ABSTRACT: The WRKY family, a large family of transcription factors (TFs) found in higher plants, plays central roles in many aspects of physiological processes and adaption to environment. However, little information is available regarding the WRKY family in cassava (Manihot esculenta). In the present study, 85 WRKY genes were identified from the cassava genome and classified into three groups according to conserved WRKY domains and zinc-finger structure. Conserved motif analysis showed that all of the identified MeWRKYs had the conserved WRKY domain. Gene structure analysis suggested that the number of introns in MeWRKY genes varied from 1 to 5, with the majority of MeWRKY genes containing three exons. Expression profiles of MeWRKY genes in different tissues and in response to drought stress were analyzed using the RNA-seq technique. The results showed that 72 MeWRKY genes had differential expression in their transcript abundance and 78 MeWRKY genes were differentially expressed in response to drought stresses in different accessions, indicating their contribution to plant developmental processes and drought stress resistance in cassava. Finally, the expression of 9 WRKY genes was analyzed by qRT-PCR under osmotic, salt, ABA, H2O2, and cold treatments, indicating that MeWRKYs may be involved in different signaling pathways. Taken together, this systematic analysis identifies some tissue-specific and abiotic stress-responsive candidate MeWRKY genes for further functional assays in planta, and provides a solid foundation for understanding of abiotic stress responses and signal transduction mediated by WRKYs in cassava.

SUBMITTER: Wei Y

PROVIDER: S-EPMC4742560 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Genome-Wide Identification and Expression Analysis of the WRKY Gene Family in Cassava.

Wei Yunxie Y Shi Haitao H Xia Zhiqiang Z Tie Weiwei W Ding Zehong Z Yan Yan Y Wang Wenquan W Hu Wei W Li Kaimian K

Frontiers in plant science 20160205

The WRKY family, a large family of transcription factors (TFs) found in higher plants, plays central roles in many aspects of physiological processes and adaption to environment. However, little information is available regarding the WRKY family in cassava (Manihot esculenta). In the present study, 85 WRKY genes were identified from the cassava genome and classified into three groups according to conserved WRKY domains and zinc-finger structure. Conserved motif analysis showed that all of the id ...[more]

PMID: 26904033

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Project description:Camellia oleifera Abel. is an economically important woody edible-oil species that is mainly cultivated in hilly areas of South China. The phosphorus (P) deficiency in the acidic soils poses severe challenges for the growth and productivity of C. oleifera. WRKY transcription factors (TFs) have been proven to play important roles in biological processes and plant responses to various biotic/abiotic stresses, including P deficiency tolerance. In this study, 89 WRKY proteins with conserved domain were identified from the C. oleifera diploid genome and divided into three groups, with group II further classified into five subgroups based on the phylogenetic relationships. WRKY variants and mutations were detected in the gene structure and conserved motifs of CoWRKYs. Segmental duplication events were considered as the primary driver in the expanding process of WRKY gene family in C. oleifera. Based on transcriptomic analysis of two C. oleifera varieties characterized with different P deficiency tolerances, 32 CoWRKY genes exhibited divergent expression patterns in response to P deficiency stress. qRT-PCR analysis demonstrated that CoWRKY11, -14, -20, -29 and -56 had higher positive impact on P-efficient CL40 variety compared with P-inefficient CL3 variety. Similar expression trends of these CoWRKY genes were further observed under P deficiency with longer treatment period of 120d. The result indicated the expression sensitivity of CoWRKYs on the P-efficient variety and the C. oleifera cultivar specificity on the P deficiency tolerance. Tissue expression difference showed CoWRKYs may play a crucial role in the transportation and recycling P in leaves by affecting diverse metabolic pathways. The available evidences in the study conclusively shed light on the evolution of the CoWRKY genes in C. oleifera genome and provided a valuable resource for further investigation of functional characterization of WRKY genes involved to enhance the P deficiency tolerance in C. oleifera.

Project description:NAC [no apical meristem (NAM), Arabidopsis transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins is one of the largest groups of plant specific transcription factors and plays a crucial role in plant growth, development, and adaption to the environment. Currently, no information is known about the NAC family in cassava. In this study, 96 NAC genes (MeNACs) were identified from the cassava genome. Phylogenetic analysis of the NACs from cassava and Arabidopsis showed that MeNAC proteins can be clustered into 16 subgroups. Gene structure analysis found that the number of introns of MeNAC genes varied from 0 to 5, with the majority of MeNAC genes containing two introns, indicating a small gene structure diversity of cassava NAC genes. Conserved motif analysis revealed that all of the identified MeNACs had the conserved NAC domain and/or NAM domain. Global expression analysis suggested that MeNAC genes exhibited different expression profiles in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different accessions. Transcriptome analysis demonstrated that MeNACs had a widely transcriptional response to drought stress and that they had differential expression profiles in different accessions, implying their contribution to drought stress resistance in cassava. Finally, the expression of twelve MeNAC genes was analyzed under osmotic, salt, cold, ABA, and H2O2 treatments, indicating that cassava NACs may represent convergence points of different signaling pathways. Taken together, this work found some excellent tissue-specific and abiotic stress-responsive candidate MeNAC genes, which would provide a solid foundation for functional investigation of the NAC family, crop improvement and improved understanding of signal transduction in plants. These data bring new insight on the complexity of the transcriptional control of MeNAC genes and support the hypothesis that NACs play an important role in plant growth, development, and adaption of environment.

Dataset Information

Genome-Wide Identification and Expression Analysis of the WRKY Gene Family in Cassava.

Publications

Genome-Wide Identification and Expression Analysis of the WRKY Gene Family in Cassava.

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