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Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass.
Mol Biol Rep. 2020 Jun; 47(6):4439-4454.MB

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.

Authors+Show Affiliations

College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. flsun@nwsuaf.edu.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32476099

Citation

Wang, Weiwei, et al. "Genome-wide Analysis of the Abiotic Stress-related bZIP Family in Switchgrass." Molecular Biology Reports, vol. 47, no. 6, 2020, pp. 4439-4454.
Wang W, Wang Y, Zhang S, et al. Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass. Mol Biol Rep. 2020;47(6):4439-4454.
Wang, W., Wang, Y., Zhang, S., Xie, K., Zhang, C., Xi, Y., & Sun, F. (2020). Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass. Molecular Biology Reports, 47(6), 4439-4454. https://doi.org/10.1007/s11033-020-05561-w
Wang W, et al. Genome-wide Analysis of the Abiotic Stress-related bZIP Family in Switchgrass. Mol Biol Rep. 2020;47(6):4439-4454. PubMed PMID: 32476099.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of the abiotic stress-related bZIP family in switchgrass. AU - Wang,Weiwei, AU - Wang,Yongfeng, AU - Zhang,Shumeng, AU - Xie,Kunliang, AU - Zhang,Chao, AU - Xi,Yajun, AU - Sun,Fengli, Y1 - 2020/05/31/ PY - 2020/01/23/received PY - 2020/05/27/accepted PY - 2020/6/2/pubmed PY - 2020/6/2/medline PY - 2020/6/2/entrez KW - Abiotic stress KW - Basic leucine zipper KW - Switchgrass KW - Synteny KW - Transcription factor SP - 4439 EP - 4454 JF - Molecular biology reports JO - Mol Biol Rep VL - 47 IS - 6 N2 - 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. SN - 1573-4978 UR - https://www.unboundmedicine.com/medline/citation/32476099/Genome_wide_analysis_of_the_abiotic_stress_related_bZIP_family_in_switchgrass_ L2 - https://doi.org/10.1007/s11033-020-05561-w DB - PRIME DP - Unbound Medicine ER -