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Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut.
BMC Genomics. 2019 Jan 16; 20(1):51.BG

Abstract

BACKGROUND

Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in peanut are lacking in spite of the availability of the peanut genome sequence.

RESULTS

In this study, we identified 50 and 45 bZIP genes from Arachis duranensis and A. ipaensis genomes, respectively. Phylogenetic analysis showed that Arachis bZIP genes were classified into nine groups, and these clusters were supported by several group-specific features, including exon/intron structure, intron phases, MEME motifs, and predicted binding site structure. We also identified possible variations in DNA-binding-site specificity and dimerization properties among different Arachis bZIPs by inspecting the amino acid residues at some key sites. Our analysis of the evolutionary history analysis indicated that segmental duplication, rather than tandem duplication, contributed greatly to the expansion of this gene family, and that most Arachis bZIPs underwent strong purifying selection. Through RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the co-expressed, differentially expressed and several well-studied homologous bZIPs were identified during seed development stages in peanut. We also used qRT-PCR to explore changes in bZIP gene expression in response to salt-treatment, and many candidate bZIPs in groups A, B, and S were proven to be associated with the salt-stress response.

CONCLUSIONS

This study have conducted a genome-wide identification, characterization and expression analysis of bZIP genes in Arachis genomes. Our results provide insights into the evolutionary history of the bZIP gene family in peanut and the funcntion of Arachis bZIP genes during seed development and in response to salt stress.

Authors+Show Affiliations

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.Industrial Crops Research Institute, Henan Academy of Agricultural Sciences Henan Province, Zhengzhou, 450002, China.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China. leiyong@caas.cn.Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China. lboshou@hotmail.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30651065

Citation

Wang, Zhihui, et al. "Genome-wide Systematic Characterization of bZIP Transcription Factors and Their Expression Profiles During Seed Development and in Response to Salt Stress in Peanut." BMC Genomics, vol. 20, no. 1, 2019, p. 51.
Wang Z, Yan L, Wan L, et al. Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut. BMC Genomics. 2019;20(1):51.
Wang, Z., Yan, L., Wan, L., Huai, D., Kang, Y., Shi, L., Jiang, H., Lei, Y., & Liao, B. (2019). Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut. BMC Genomics, 20(1), 51. https://doi.org/10.1186/s12864-019-5434-6
Wang Z, et al. Genome-wide Systematic Characterization of bZIP Transcription Factors and Their Expression Profiles During Seed Development and in Response to Salt Stress in Peanut. BMC Genomics. 2019 Jan 16;20(1):51. PubMed PMID: 30651065.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut. AU - Wang,Zhihui, AU - Yan,Liying, AU - Wan,Liyun, AU - Huai,Dongxin, AU - Kang,Yanping, AU - Shi,Lei, AU - Jiang,Huifang, AU - Lei,Yong, AU - Liao,Boshou, Y1 - 2019/01/16/ PY - 2018/10/03/received PY - 2019/01/07/accepted PY - 2019/1/18/entrez PY - 2019/1/18/pubmed PY - 2019/4/30/medline KW - Evolution KW - Expression analysis KW - Peanut KW - bZIP gene family SP - 51 EP - 51 JF - BMC genomics JO - BMC Genomics VL - 20 IS - 1 N2 - BACKGROUND: Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in peanut are lacking in spite of the availability of the peanut genome sequence. RESULTS: In this study, we identified 50 and 45 bZIP genes from Arachis duranensis and A. ipaensis genomes, respectively. Phylogenetic analysis showed that Arachis bZIP genes were classified into nine groups, and these clusters were supported by several group-specific features, including exon/intron structure, intron phases, MEME motifs, and predicted binding site structure. We also identified possible variations in DNA-binding-site specificity and dimerization properties among different Arachis bZIPs by inspecting the amino acid residues at some key sites. Our analysis of the evolutionary history analysis indicated that segmental duplication, rather than tandem duplication, contributed greatly to the expansion of this gene family, and that most Arachis bZIPs underwent strong purifying selection. Through RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the co-expressed, differentially expressed and several well-studied homologous bZIPs were identified during seed development stages in peanut. We also used qRT-PCR to explore changes in bZIP gene expression in response to salt-treatment, and many candidate bZIPs in groups A, B, and S were proven to be associated with the salt-stress response. CONCLUSIONS: This study have conducted a genome-wide identification, characterization and expression analysis of bZIP genes in Arachis genomes. Our results provide insights into the evolutionary history of the bZIP gene family in peanut and the funcntion of Arachis bZIP genes during seed development and in response to salt stress. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/30651065/Genome_wide_systematic_characterization_of_bZIP_transcription_factors_and_their_expression_profiles_during_seed_development_and_in_response_to_salt_stress_in_peanut_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5434-6 DB - PRIME DP - Unbound Medicine ER -