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Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa.
BMC Plant Biol. 2020 Sep 01; 20(1):405.BP

Abstract

BACKGROUND

Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa.

RESULTS

We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.

CONCLUSIONS

The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa's resistance to salt stress.

Authors+Show Affiliations

College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China. Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China.College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China.College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China.College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China. Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China.College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China. Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China.Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou, 034000, People's Republic of China. lingchenhaifeng@163.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32873228

Citation

Li, Feng, et al. "Genome-wide Survey, Characterization, and Expression Analysis of bZIP Transcription Factors in Chenopodium Quinoa." BMC Plant Biology, vol. 20, no. 1, 2020, p. 405.
Li F, Liu J, Guo X, et al. Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa. BMC Plant Biol. 2020;20(1):405.
Li, F., Liu, J., Guo, X., Yin, L., Zhang, H., & Wen, R. (2020). Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa. BMC Plant Biology, 20(1), 405. https://doi.org/10.1186/s12870-020-02620-z
Li F, et al. Genome-wide Survey, Characterization, and Expression Analysis of bZIP Transcription Factors in Chenopodium Quinoa. BMC Plant Biol. 2020 Sep 1;20(1):405. PubMed PMID: 32873228.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa. AU - Li,Feng, AU - Liu,Jianxia, AU - Guo,Xuhu, AU - Yin,Lili, AU - Zhang,Hongli, AU - Wen,Riyu, Y1 - 2020/09/01/ PY - 2019/10/06/received PY - 2020/08/25/accepted PY - 2020/9/3/entrez PY - 2020/9/3/pubmed PY - 2020/9/3/medline KW - Evolutionary analysis KW - Gene expression patterns KW - Phylogenetic classification KW - Quinoa (Chenopodium quinoa) KW - bZIP transcription factor family SP - 405 EP - 405 JF - BMC plant biology JO - BMC Plant Biol VL - 20 IS - 1 N2 - BACKGROUND: Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa. RESULTS: We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. CONCLUSIONS: The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa's resistance to salt stress. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/32873228/Genome_wide_survey_characterization_and_expression_analysis_of_bZIP_transcription_factors_in_Chenopodium_quinoa_ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-020-02620-z DB - PRIME DP - Unbound Medicine ER -