Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family

Zhang, Man; Liu, Qing; Shi, Hongbo; Guo, Mingliang; Chai, Mengnan; He, Qing-Yu; Yan, Mei; Cao, Du; Zhao, Lihua; Cai, Hanyang; Qin, Yuan

doi:10.1186/s12864-018-4511-6

Cited by 77 publications

(87 citation statements)

References 59 publications

(69 reference statements)

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“…This might the reason that pineapple possesses the smaller number of CPK genes. Gene duplication events play a vital role in genomic rearrangements and expansions [48] and are defined as either tandem duplications or segmental duplications depending on duplicated genes on the same or different chromosomes [49]. In our research, chromosomal locations and duplication events implied that gene duplication, especially segmental duplication was the major evolutionary mechanism resulting in pineapple CPK expansions (Fig.3a).…”

Section: Discussionmentioning

confidence: 60%

“…A total of 5 pineapple genes and 11 Arabidopsis genes were identified as syntenic orthologs between pineapple and Arabidopsis, 8 pineapple genes and 12 rice genes were identified as syntenic orthologs between pineapple and rice and the diversity of gene combinations reveals complex regulatory relationships. Some CPK genes present in these species, including pineapple, Arabidopsis and rice, could not be mapped into any syntenic gene pairs, it might due to multiple rounds of important chromosomal rearrangement and fusions happened in their genomes since the speciation of pineapple and Arabidopsis or rice, followed by selective gene loss, which can obscure the identification of chromosomal syntenies [49,52].…”

Section: Discussionmentioning

confidence: 99%

“…When response to S. sclerotiorum, several marker genes related to ET, JA and ABA were suppressed indicating that phytohormone signaling pathway might be involved in the resistance response process. Genes with the same function are often closely related [49], indicating that AcoCPK1, AcoCPK3 and AcoCPK6 play important roles in different signal transduction pathways and in the adaption of pineapple to changeable environments and stresses. The distinct roles of pineapple and Arabidopsis CPK genes might be caused by the divergence of monocotyledones and dicotyledones during evolutionary.…”

Section: Discussionmentioning

confidence: 99%

“…The syntenic blocks used for constructing a synteny analysis map within the pineapple genome and between the pineapple and Arabidopsis or rice genomes, were obtained by using BLASTP with the reference E < 1e-5 and top 3 matches [49]. All data used to analyze the expansion patterns of the AcoCPK family were shown in Additional file 6: Tables S3, Additional file 7: Table S4 and Table Additional file 8: S5.…”

Section: Synteny Analysis and Chromosome Localizationmentioning

confidence: 99%

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Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress

Zhang

Liu

et al. 2020

BMC Genomics

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Background: Calcium-dependent protein kinase (CPK) is one of the main Ca 2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CPK genes in pineapple. Results: Herein, we identified and characterized 17 AcoCPK genes from pineapple genome, which were unevenly distributed across eight chromosomes. Based on the gene structure and phylogenetic tree analyses, AcoCPKs were divided into four groups with conserved domain. Synteny analysis identified 7 segmental duplication events of AcoCPKs and 5 syntenic blocks of CPK genes between pineapple and Arabidopsis, and 8 between pineapple and rice. Expression pattern of different tissues and development stages suggested that several genes are involved in the functional development of plants. Different expression levels under various abiotic stresses also indicated that the CPK family underwent functional divergence during long-term evolution. AcoCPK1, AcoCPK3 and AcoCPK6, which were repressed by the abiotic stresses, were shown to be function in regulating pathogen resistance. Conclusions: 17 AcoCPK genes from pineapple genome were identified. Our analyses provide an important foundation for understanding the potential roles of AcoCPKs in regulating pineapple response to biotic and abiotic stresses

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Section: Discussionmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Synteny Analysis and Chromosome Localizationmentioning

confidence: 99%

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Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress

Zhang

Liu

et al. 2020

BMC Genomics

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“…They exist in high numbers in different species-53 bZIP family members have been found in human beings [31], 136 in soybean [27], 78 in Arabidopsis [32] and 247 in rapeseed [33]. In previous works, bZIP family members were classified into 12 groups in Arabidopsis and soybean according to their conserved DNA-binding domains (DBDs) [27,32,34]. However, here we re-divided the bZIP family members of Arabidopsis and soybean into six groups according to their conserved amino acid sequences.…”

Section: Discussionmentioning

confidence: 99%

The Soybean bZIP Transcription Factor Gene GmbZIP2 Confers Drought and Salt Resistances in Transgenic Plants

Yang

et al. 2020

IJMS

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Abiotic stresses, such as drought and salt, are major environmental stresses, affecting plant growth and crop productivity. Plant bZIP transcription factors (bZIPs) confer stress resistances in harsh environments and play important roles in each phase of plant growth processes. In this research, 15 soybean bZIP family members were identified from drought-induced de novo transcriptomic sequences of soybean, which were unevenly distributed across 12 soybean chromosomes. Promoter analysis showed that these 15 genes were rich in ABRE, MYB and MYC cis-acting elements which were reported to be involved in abiotic stress responses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that 15 GmbZIP genes could be induced by drought and salt stress. GmbZIP2 was significantly upregulated under stress conditions and thus was selected for further study. Subcellular localization analysis revealed that the GmbZIP2 protein was located in the cell nucleus. qRT-PCR results show that GmbZIP2 can be induced by multiple stresses. The overexpression of GmbZIP2 in Arabidopsis and soybean hairy roots could improve plant resistance to drought and salt stresses. The result of differential expression gene analysis shows that the overexpression of GmbZIP2 in soybean hairy roots could enhance the expression of the stress responsive genes GmMYB48, GmWD40, GmDHN15, GmGST1 and GmLEA. These results indicate that soybean bZIPs played pivotal roles in plant resistance to abiotic stresses.

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Genome-Wide Identification Reveals the Potential Functions of the bZIP Gene Family in Common Bean (Phaseolus vulgaris) in Response to Salt Stress During the Sprouting Stage

Zhang

Yin

et al. 2021

J Plant Growth Regul

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Basic leucine zipper (bZIP) is a diverse transcription factor in plants that is involved in many stress responses, especially salt stress. However, the roles of bZIP genes in the common bean have not been elucidated. 84 proteins in common bean were identified here. Through phylogenetic analysis, the PvbZIPs were classified into five subfamilies, and these clusters were supported by several group-specific features, including gene structure, motifs, and cis-regulatory elements. Collinearity analysis revealed the connection between PvbZIPs and bZIPs from two other dicotyledonous species, namely Arabidopsis and Soybean (Glycine max). Expression patterns of the PvbZIPs genes indicated that they exhibit a tissue-specific manner at the sprouting stage. RNA-seq and qRT-PCR analyses indicated that PvbZIPs exhibit different expression patterns under salt stress in salt tolerance and salt-sensitive varieties. According to KEGG analysis of PvbZIPs-enriched pathways, PvbZIPs appear to target the abscisic acid (ABA) signaling pathway which might result in enhanced salt tolerance. Our findings elucidate on functional characterization of PvbZIP in Phaseolus vulgaris and its role in salt stress regulation through ABA.

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Evolutionary and expression analyses of soybean basic Leucine zipper transcription factor family

Cited by 77 publications

References 59 publications

Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress

Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress

The Soybean bZIP Transcription Factor Gene GmbZIP2 Confers Drought and Salt Resistances in Transgenic Plants

Genome-Wide Identification Reveals the Potential Functions of the bZIP Gene Family in Common Bean (Phaseolus vulgaris) in Response to Salt Stress During the Sprouting Stage

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