Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses

Ling, Lei; Zhang, Wenrui; An, Yimin; Du, Binghao; Wang, Dan; Guo, Changhong

doi:10.1007/s10142-020-00733-0

Cited by 38 publications

(36 citation statements)

References 51 publications

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“…Gene duplication events usually include the segmental duplication and tandem duplication of the chromosome. This behavior can enhance the functional diversification of the gene family during plant evolution, which is necessary in order for plants to adapt to various environmental changes [ 79 , 80 ]. These two patterns of gene duplication can increase the number of members of the gene family [ 81 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula

Zhao

Zhang

Sun

et al. 2021

IJMS

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Polycomb group (PcG) proteins, which are important epigenetic regulators, play essential roles in the regulatory networks involved in plant growth, development, and environmental stress responses. Currently, as far as we know, no comprehensive and systematic study has been carried out on the PcG family in Medicago truncatula. In the present study, we identified 64 PcG genes with distinct gene structures from the M. truncatula genome. All of the PcG genes were distributed unevenly over eight chromosomes, of which 26 genes underwent gene duplication. The prediction of protein interaction network indicated that 34 M. truncatula PcG proteins exhibited protein–protein interactions, and MtMSI1;4 and MtVRN2 had the largest number of protein–protein interactions. Based on phylogenetic analysis, we divided 375 PcG proteins from 27 species into three groups and nine subgroups. Group I and Group III were composed of five components from the PRC1 complex, and Group II was composed of four components from the PRC2 complex. Additionally, we found that seven PcG proteins in M. truncatula were closely related to the corresponding proteins of Cicer arietinum. Syntenic analysis revealed that PcG proteins had evolved more conservatively in dicots than in monocots. M. truncatula had the most collinearity relationships with Glycine max (36 genes), while collinearity with three monocots was rare (eight genes). The analysis of various types of expression data suggested that PcG genes were involved in the regulation and response process of M. truncatula in multiple developmental stages, in different tissues, and for various environmental stimuli. Meanwhile, many differentially expressed genes (DEGs) were identified in the RNA-seq data, which had potential research value in further studies on gene function verification. These findings provide novel and detailed information on the M. truncatula PcG family, and in the future it would be helpful to carry out related research on the PcG family in other legumes.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula

Zhao

Zhang

Sun

et al. 2021

IJMS

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“…The putative involvement of L. japonicus Hsf genes in numerous tissues or developmental stages, and in response to several abiotic stresses was also revealed by the same authors using expression analysis. On other hand, a total of 25 proliferating cell factor (TCP) genes were identified from the genome of L. japonicus in a genome-wide analysis ( Ling et al, 2020 ). The promoter analysis revealed that cis-elements were related to stress responses, in line with results of qRT-PCR indicating that the L. japonicus TCP genes played regulatory roles in both salt and drought stresses.…”

Section: Survey Methodologymentioning

confidence: 99%

Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes

Menéndez

Ruíz

2021

PeerJ

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Although legumes are of primary economic importance for human and livestock consumption, the information regarding signalling networks during plant stress response in this group is very scarce. Lotus japonicus is a major experimental model within the Leguminosae family, whereas L. corniculatus and L. tenuis are frequent components of natural and agricultural ecosystems worldwide. These species display differences in their perception and response to diverse stresses, even at the genotype level, whereby they have been used in many studies aimed at achieving a better understanding of the plant stress-response mechanisms. However, we are far from the identification of key components of their stress-response signalling network, a previous step for implementing transgenic and editing tools to develop legume stress-resilient genotypes, with higher crop yield and quality. In this review we scope a body of literature, highlighting what is currently known on the stress-regulated signalling elements so far reported in Lotus spp. Our work includes a comprehensive review of transcription factors chaperones, redox signals and proteins of unknown function. In addition, we revised strigolactones and genes regulating phytochelatins and hormone metabolism, due to their involvement as intermediates in several physiological signalling networks. This work was intended for a broad readership in the fields of physiology, metabolism, plant nutrition, genetics and signal transduction. Our results suggest that Lotus species provide a valuable information platform for the study of specific protein-protein (PPI) interactions, as a starting point to unravel signalling networks underlying plant acclimatation to bacterial and abiotic stressors in legumes. Furthermore, some Lotus species may be a source of genes whose regulation improves stress tolerance and growth when introduced ectopically in other plant species.

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“…[5,[8][9][10][11][12]. The TCP genes have a variety of functions, participating in the regulation of numerous growth and developmental processes, such as the coordination of cell proliferation, inflorescence development, shoot branching, leaf development, phytohormone biosynthesis, and the circadian clock regulation [13][14][15][16][17][18][19][20][21][22][23][24]. Dendrobium catenatum Lindl.…”

Section: Identification Of Tcp Family Genes In D Catenatummentioning

confidence: 99%

“…For example, Arabidopsis thaliana has 24 TCP genes, Oryza sativa has 28 TCP genes, Lycopersicon esculentum has 30 TCP genes, Populus euphratica has 33 TCP genes, Populus trichocarpa has 36 TCP genes, Citrullus lanatus has 27 TCP genes, Prunus mume has 19 TCP genes, and Petunia inflata has 34 TCP genes [ 5 , 8 , 9 , 10 , 11 , 12 ]. The TCP genes have a variety of functions, participating in the regulation of numerous growth and developmental processes, such as the coordination of cell proliferation, inflorescence development, shoot branching, leaf development, phytohormone biosynthesis, and the circadian clock regulation [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl.

Zhang

Yang

et al. 2021

IJMS

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Teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family members are plant-specific transcription factors that regulate plant growth and development by controlling cell proliferation and differentiation. However, there are no reported studies on the TCP gene family in Dendrobium catenatum Lindl. Here, a genome-wide analysis of TCP genes was performed in D. catenatum, and 25 TCP genes were identified. A phylogenetic analysis classified the family into two clades: Class I and Class II. Genes in the same clade share similar conserved motifs. The GFP signals of the DcaTCP-GFPs were detected in the nuclei of tobacco leaf epidermal cells. The activity of DcaTCP4, which contains the miR319a-binding sequence, was reduced when combined with miR319a. A transient activity assay revealed antagonistic functions of Class I and Class II of the TCP proteins in controlling leaf development through the jasmonate-signaling pathway. After different phytohormone treatments, the DcaTCP genes showed varied expression patterns. In particular, DcaTCP4 and DcaTCP9 showed opposite trends after 3 h treatment with jasmonate. This comprehensive analysis provides a foundation for further studies on the roles of TCP genes in D. catenatum.

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Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses

Cited by 38 publications

References 51 publications

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula

Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes

Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl.

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