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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

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Abstract

The teosinte branched1, cycloidea, and proliferating cell factor family (TCP) proteins, plant-specific transcription factors, are involved in the regulation of plant development; however, the TCP gene family of legumes has been based primarily on a single crop. Here, a total of 55, 22, 26, 21, and 25 genes containing the VQ motif were identified from the genomes of Glycine max, Cicer arietinum, Phaseolus vulgaris, Medicago truncatula, and Lotus japonicus, respectively. Based on the phylogenetic analysis, we divided these TCP genes into three distinct subfamilies: PCF, CYC/TB1, and CIN. The conserved domain analysis indicated that the TCP gene family members contain the bHLH and R domains. The TCP genes from the same evolutionary branches of legumes shared similar motifs and structures. The promoter analysis revealed that cis-elements were related to stress responses, phytohormone responses, and physical and reproductive growth regulation. In addition, the TCP genes presented different expression patterns in the five legumes. Most of them showed specific expression patterns during development. The results of qRT-PCR indicated that the TCP genes played regulatory roles in both salt and drought stresses. The present study provides novel and detailed information regarding the legume TCP gene family, which aids in functional characterisation of the TCP genes in other plants.

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Funding

This work was supported by the grant from the National and Science Foundation of China (No. 31770575, 31972507), the National Major Project for Cultivation of Transgenic Crops (#2016ZX08004-002-003), the National Key Research and Development Program of China (2017YFD0101303), and the Graduate Innovation Fund of Harbin Normal University (HSDBSCX2016-4).

Author information

L.L. and C.G. conceived and designed the experiments. L.L. wrote the manuscript. L.L. conducted experiments and analysed data. W.Z., Y.A., and B.D. performed the qRT-PCR experiments. C.G. and D.W. revised the manuscript.

Correspondence to Changhong Guo.

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Electronic supplementary material

Supplemental Fig. 1

The program extracts the FPKM of the TCP genes. (JPG 87 kb)

Supplemental Fig. 2

The number of TCPs in the subfamilies PCF, CIN and CYC/TB1, different subfamily in different color. (JPG 4812 kb)

Supplemental Fig. 3

Multiple sequence alignment, gene structure and multiple motifs of five legumes. Alignment of TCP domain of 149 TCP proteins in five legumes. Amino acids that are conserved throughout are shaded in different colors. Conserved domains including Basic, Helix 1, Loop, and Helix 2. Alignment of R-domain of the CYC/TB1 subfamily members. (JPG 16925 kb)

Supplemental Fig. 4

Phylogenetic tree, conserved motifs and gene structure in TCPs. (A)Phylogenetic relationships (B) Conserved motifs of the TCPs (C)Exon/intron structures of TCP genes. (JPG 7990 kb)

Supplemental Fig. 5

Sequence logo of motifs in TCP genes. (JPG 990 kb)

Supplemental Fig. 6

Whole genome duplication (WGD)-derived legume TCP genes. The phylogenetic relationships of the five legumes based on the differentiation time of them. Two WGD events, the Glycine-lineage-specific and early-legume WGD events, are indicated on the corresponding clades. (JPG 1119 kb)

Supplemental Table 1

Details of TCP sequences (XLS 130 kb)

Supplemental Table 2

List of five legumes TCP genes information identified in the Medicago truncatula, Cicer arietinum, Glycine max, Phaseolus vulgaris and Lotus japonicus (XLS 52 kb)

Supplemental Table 3

List of primers used in qRT-PCR (XLS 38 kb)

Supplemental Table 4

List of cis-acting element of TCP genes (1.5 kb upstream of the translation start site) (XLS 439 kb)

Supplemental Table 5

List of Ka, Ks and Ka/Ks values calculated for orthologous TCP gene pairs among five legumes (XLS 42 kb)

Supplemental Table 6

The expression of TCP genes in the same stage under different abiotic stresses (XLS 12 kb)

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Ling, L., Zhang, W., An, Y. et al. Genome-wide analysis of the TCP transcription factor genes in five legume genomes and their response to salt and drought stresses. Funct Integr Genomics (2020). https://doi.org/10.1007/s10142-020-00733-0

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Keywords

  • TCP gene family
  • Legume
  • Phylogeny analysis
  • Expression analysis
  • Abiotic stress