Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass

Abstract

The large basic leucine zipper (bZIP) transcription factor family is conserved in plants. These proteins regulate growth, development, and stress response. Here, we conducted a genome-wide analysis to identify the bZIP genes associated with stress resistance in switchgrass (Panicum virgatum L.). We identified 178 PvbZIPs unevenly distributed on 18 switchgrass chromosomes. An evolutionary analysis segregated them into 10 subfamilies. Gene structure and conserved motif analyses indicated that the same subfamily members shared similar intron-exon modes and motif compositions. This finding corroborated the proposed PvbZIP family grouping. A promoter analysis showed that PvbZIP genes participate in various stress responses. Phylogenetic and synteny analyses characterized 111 switchgrass bZIPs as orthologs of 70 rice bZIPs. A protein interaction network analysis revealed that 22 proteins are involved in salt and drought tolerance. An expression atlas disclosed that the expression patterns of several PvbZIPs differ among various tissues and developmental stages. Online data demonstrated that 16 PvbZIPs were significantly downregulated and five were significantly upregulated in response to heat stress. Other PvbZIPs participated in responses to abiotic stress such as salt, drought, cold, and heat. Our genome-wide analysis and identification of the switchgrass bZIP family characterized multiple candidate PvbZIPs that regulate growth and stress response. This study lays theoretical and empirical foundations for future functional investigations into other transcription factors.

Plant Transcription Factors Involved in Drought and Associated Stresses

“…However, despite the fact that this was the largest MYB TF group, no structures of plant R2R3-MYB proteins are known. Although many studies highlighted the biological function of R2R3-MYB TFs in plants, only recently, Wang et al [ 175 ] elucidated the structure of R2R3-type MYB in Arabidopsis WER (AtMYB66). This analysis showed that the key residues in all R2R3-MYB proteins responsible for DNA recognition were highly conserved and that nearly half of R2R3-MYB members utilized the 5′-ACC-3′ sequence for DNA recognition, suggesting that these R2R3-MYB members may undergo subtle conformational changes or have other features that favor DNA binding.…”

Genome-wide identification, phylogeny and expression analysis of the bZIP gene family in Alfalfa (Medicago sativa)

“…The bZIP gene family members exhibited specific expression levels in 7 tissues of Carthamus tinctorius L [41]. StbZIPs (bZIP members in Solanum tuberosum) were found to be differently expressed in tissues [45], bZIP transcription factor members in sweet potato (Ipomoea trifida) were expressed in a tissue-specific manner [39], while bZIP members in grapevine (Vitis vinifera) [46], pepper (Capsicum annuum L.) [37] and switchgrass [47] were differently expressed in different tissues. IbABF4, as an ABF gene encoding bZIP domain, is specifically expressed in leaves, petioles, stems and roots, with the highest expression in roots [48].…”

Regulation Mechanisms of Plant Basic Leucine Zippers to Various Abiotic Stresses

“…To date, a large number of bZIP transcription factors have been identified in almost all eukaryotes. There are 57,77,62,96,85,87,89,262,92,89,178,103,65,69,125,64,55,114 bZIP transcription factors been found in Ananas comosus, Arabidopsis thaliana, Citrullus lanatus, Fagopyum talaricum, Gossypium raimondii, Gossypium arboreum, Oryza sativa, Glycine max, Sorghum bicolor, Hordeum vulgare L, Panicum virgatum L, Olea europaea L, Solanum tuberosum L., Solanum lycopersicum, Zea mays, Cucumis sativus, Vitis vinifera and Malus domestica, respectively (Correâ et al, 2008;Nijhawan et al, 2008;Wang et al, 2011;Wei et al, 2012;Baloglu et al, 2014;Li et al, 2015;Pourabed et al, 2015;Li et al, 2016;Zhang et al, 2018;Yang W. et al, 2019;Azeem et al, 2020;Liu et al, 2020;Rong et al, 2020;Wang et al, 2020;Zhao et al, 2020). Only 25, 21, and 21 bZIP transcription factors were found in yeast, nematode, and fruit fly, respectively (Riechmann et al, 2000).…”

“…Hence, the classification of bZIP transcription factors has become more and more sophisticated. Due to the advancement of bioinformatics, there are increasing researches provide preliminary analyses on globally identifying bZIP members from the fresh released genomic database of many plants, such as potato, switchgrass, olive, pineapple, cotton, watermelon, and tartaty buckwheat, laying the foundation for subsequent research (Yang W. et al, 2019;Azeem et al, 2020;Liu et al, 2020;Rong et al, 2020;Wang et al, 2020;Zhao et al, 2020). Recent years, there are increasing reports on regulation mechanism of various bZIPs on different stress responses (Liu et al, 2012;Ji et al, 2013;Hwang et al, 2014;van Leene et al, 2016;Tsugama et al, 2016;Zhang L. N. et al, 2017;Wang et al, 2019).…”