Combining bioinformatics and conventional PCR optimization strategy for one-time design of high-specificity primers for WRKY gene family using unigene database

Kumar, Avinash; Sreedharan, Simmi P.; Giridhar, P.

doi:10.1007/s11033-018-04577-7

Cited by 2 publications

(2 citation statements)

References 32 publications

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“…Following phylogenetic analysis with AtWRKY genes, the 59 SsWRKYs were divided into three main groups, 11 SsWRKY proteins belonging to Group I, 40 SsWRKY proteins classified into Group II, accounting for the largest proportion (68%), indicating that this group may have experienced gene duplication events during its evolution, and the remaining eight SsWRKY proteins belonged to Group III. Similar results have been reported from Zea mays [ 43 ], C. sativus [ 26 ], Coffea canephora [ 44 ]. Furthermore, variation of the conserved WRKY domain (WRKYGKK) was observed in the SsWRKY10 protein sequence from the subgroup IIc.…”

Section: Discussionsupporting

confidence: 90%

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Chen

Shao

et al. 2023

Plants

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WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family.

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Section: Discussionsupporting

confidence: 90%

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Chen

Shao

et al. 2023

Plants

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“…Superfamilies generally originate from gene/genome duplication and follow different evolutionary process, which leave an evolutionary imprint [54]. It is believed that the emergence of the duplicated genes not only is a way of genomic rearrangement and expansion, but also diversifies gene function to ensure optimal adaptability during evolution processes [55,56].…”

Section: The Colinearity and Duplication Of B3 Superfamily Reflected mentioning

confidence: 99%

Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

Liu

Wu³

et al. 2019

Preprint

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Combining bioinformatics and conventional PCR optimization strategy for one-time design of high-specificity primers for WRKY gene family using unigene database

Cited by 2 publications

References 32 publications

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis

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