Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (19): 4048-4060.doi: 10.3864/j.issn.0578-1752.2021.19.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Identification of VQ Gene Family in Fagopyrum tataricum and Its Expression Profiles in Response to Leaf Spot Pathogens

ZHENG FengSheng1(),WANG HaiHua1,2(),WU QingTao1,SHEN Quan1,2,TIAN JianHong1,PENG XiXu1,3,TANG XinKe1,3()   

  1. 1School of Life Science, Hunan University of Science and Technology, Xiangtan 411201, Hunan
    2Key Laboratory of Genetic Improvement and Multiple Utilization of Economic Crops in Hunan Province, Xiangtan 411201, Hunan
    3Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, College of Hunan Province, Xiangtan 411201, Hunan
  • Received:2021-02-25 Accepted:2021-06-07 Online:2021-10-01 Published:2021-10-12
  • Contact: HaiHua WANG,XinKe TANG E-mail:13647321087@163.com;hhwang@hnust.edu.cn;xinketang@126.com

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Abstract:

【Objective】VQ gene family plays important roles in plant growth, development and responses to biotic or abiotic stress. The aim of this study is to comprehensively identify Fagopyrum tataricum L. Gaertn. VQ (FtVQ) gene family on genome-wide scale and analyze its expression profiles under challenge of leaf spot pathogens Alternaria. alternata and Nigrospora osmanthi, and treatment of defense-related hormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), thus providing a solid foundation not only for further elucidation possible roles of members of the VQ genes in defense response to leaf spot pathogens and underlying mechanisms in tartary buckwheat, but also for mining gene resources of breeding for crop disease resistance. 【Method】Based on the Hidden Markov Model profile of the conserved VQ domain (PF05678), HMMER 3.0 software was used to identify FtVQ genes from F. tataricum cv. Pinku1 genome database. Bioinformatic tools such as DNAMAN, MapInspect, MEGA, MEME, OrthoFinder and PLACE were used to analyze gene structure, chromosomal location of genes, cis-elements of gene promoters, physicochemical properties of proteins, conserved motifs of proteins, subcellular localization of proteins, and phylogenetic relationships. Quantitative real-time PCR (qPCR) was employed to analyze the expression profiles of leaf FtVQ genes of tartary buckwheat plants under infection of the pathogens and treatment of the hormones. 【Result】A total of 28 VQ genes were identified in the genomes of tartary buckwheat, with the gene size ranging from 566 to 1454 bp. The FtVQ genes contain no introns, and distribute unevenly on chromosomes 1-8. According to their physical locations on the chromosomes, the FtVQ genes were named from FtVQ1 to FtVQ28. Each of the FtVQ proteins has a highly conserved VQ motif FxxxVQx (L/F/I/V/A/Y) TG, where x represents any amino acid. Analysis of subcellular localization showed that 21 FtVQ proteins were predicted to the nucleus, and the others to the chloroplasts or cytoplasm. Based upon their amino acid sequence and presence of various conserved motifs, the FtVQ proteins were classified into five subfamilies (Ⅰ-Ⅴ). Each subfamily shared relatively conserved gene structures and protein motifs. The analysis of gene duplication revealed that F. tataricum genome had 8 pairs of paralogous pairs, all of which were segmental duplicated genes, suggesting that segmental duplication played major roles in FtVQ gene expansion. The ratio of nonsynonymous to synonymous substitutions (Ka/Ks) of paralogous pairs was less than 1, suggesting that they underwent purifying pressure during the evolution process. Prediction of cis-elements showed that pathogen-, SA-, JA-, or ET-responsive elements, such as BIHD1OS, CGTCA, ERELEA4, W-box and W-box-like sequences, were present within the promoters of all the FtVQ genes. Especially, FtVQ10, FtVQ14, FtVQ15, FtVQ22, FtVQ23 and FtVQ27 contained more elements in their promoter regions. 55% to 70% of the detectable FtVQ genes were differentially expressed genes (DEGs), and 72.7% to 85.7% of the DEGs were significantly induced on the level of transcription under the infection of leaf spot fungi A. alternata and N. osmanthi, or the treatment of SA, methyl jasmonate and ethephon. 【Conclusion】The tartary buckwheat genome contains 28 members of VQ gene family. Some FtVQ genes may be involved tartary buckwheat defense response to leaf spot pathogens.

Key words: tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.), VQ gene family, Alternaria leaf spot, Nigrospora leaf spot, defense-related hormones

Table 1

VQ genes identified in tartary buckwheat and their sequence characteristics"

基因名称
Gene name		 序列登录号
Sequenced ID		 染色体
Chromosome		 内含子
Introns		 正/反链 +/-
strand		 基因大小
Gene size (bp)		 编码序列
Coding sequence		 编码的蛋白质 Encoded protein
氨基酸长度
aa length (aa)		 分子量
Molecular length (kD)		 等电点
pI		 亚细胞定位
Subcellular localization
FtVQ1 FtPinG0005794900 1 0 + 772 549 182 20.00 8.71 细胞核Nucleus
FtVQ2 FtPinG0005409400 1 0 - 1059 588 195 20.90 10.11 细胞核Nucleus
FtVQ3 FtPinG0002545500 1 0 + 678 678 225 24.27 10.31 细胞核Nucleus
FtVQ4 FtPinG0002567300 1 0 - 654 651 216 23.52 7.07 细胞核Nucleus
FtVQ5 FtPinG0006482000 1 0 + 566 249 82 9.08 6.50 细胞核Nucleus
FtVQ6 FtPinG0001835400 2 0 + 688 405 134 15.21 11.09 叶绿体Chloroplast
FtVQ7 FtPinG0009771100 2 0 + 840 840 279 30.09 8.36 细胞核Nucleus
FtVQ8 FtPinG0004496500 2 0 - 938 297 98 10.54 9.83 细胞核Nucleus
FtVQ9 FtPinG0001284900 2 0 + 629 603 200 21.83 8.79 叶绿体Chloroplast
FtVQ10 FtPinG0001084300 3 0 + 895 507 168 18.02 9.82 细胞核Nucleus
FtVQ11 FtPinG0001089800 3 0 + 705 705 234 24.66 5.94 细胞核Nucleus
FtVQ12 FtPinG0002126400 3 0 + 780 729 242 25.78 10.20 细胞核Nucleus
FtVQ13 FtPinG0007726900 4 0 + 418 387 128 14.60 7.67 细胞核Nucleus
FtVQ14 FtPinG0001986300 4 0 + 357 354 116 13.24 9.52 细胞质Cytoplasm
FtVQ15 FtPinG0003123700 5 0 + 601 468 155 16.79 8.27 叶绿体Chloroplast
FtVQ16 FtPinG0007087100 5 0 + 453 429 142 15.71 10.54 细胞核Nucleus
FtVQ17 FtPinG0005585600 5 0 + 687 687 228 24.25 5.26 细胞核Nucleus
FtVQ18 FtPinG0002695900 6 0 + 850 603 200 21.09 5.20 叶绿体Chloroplast
FtVQ19 FtPinG0001480300 6 0 + 1454 1083 360 38.10 7.40 细胞核Nucleus
FtVQ20 FtPinG0006939600 6 0 + 899 477 158 17.28 5.56 细胞核Nucleus
FtVQ21 FtPinG0003079000 6 0 + 606 606 201 20.96 9.64 细胞核Nucleus
FtVQ22 FtPinG0009737600 6 0 + 797 594 197 21.25 6.08 细胞核Nucleus
FtVQ23 FtPinG0002065200 6 0 + 588 582 193 20.86 8.15 细胞核Nucleus
FtVQ24 FtPinG0002067700 6 0 + 468 444 147 16.01 4.48 细胞核Nucleus
FtVQ25 FtPinG0003595000 7 0 + 1343 882 293 30.96 10.77 细胞核Nucleus
FtVQ26 FtPinG0002292500 8 0 - 740 642 213 22.98 10.72 叶绿体Chloroplast
FtVQ27 FtPinG0003287200 8 0 + 699 630 209 22.81 6.62 细胞核Nucleus
FtVQ28 FtPinG0003376500 8 0 + 654 654 217 23.91 7.24 叶绿体Chloroplast

Fig. 1

Phylogenetic relationships of tartary buckwheat VQ proteins (left) and their gene structures (right) Black, grey rectangles indicate coding sequence (CDS) and upstream/downstream sequence in the right figure"

Fig. 2

Multiple sequence alignment of the VQ motif for tartary buckwheat VQ proteins The FxxxVQxTG motif is clearly highly conserved. According to the difference of the first amino acid before "TG" of the conserved sequence, the tartary buckwheat VQ proteins are further classified into six types, i.e., LTG, FTG, ITG, VTG, ATG and YTG"

Fig. 3

Schematic diagram of conserved motifs of tartary buckwheat VQ proteins Left panel is phylogenetic tree of FtVQ proteins, which are divided into five groups. Each group is further divided into subgroups. Right panel depicts the distribution of the 3 conserved motifs in the tartary buckwheat VQ protein family following analysis with MEME. Each specific motif is marked by a different colored box. The length of each box is not proportional to the actual size of the motif"

Fig. 4

Chromosomal locations of tartary buckwheat VQ genes The duplicated paralogous pairs of VQ genes are connected with gray-dotted lines"

Table 2

Paralogous pairs of tartary buckwheat VQ genes"

旁系同源基因对
Paralogous pairs		 Ka值
Ka value		 Ks值
Ks value		 Ka/Ks 重复年代（百万年）
Duplication date (Mya)
FtVQ2-FtVQ10 0.5833 1.9208 0.3037 105.54
FtVQ7-FtVQ19 0.7035 3.3733 0.2085 185.35
FtVQ23-FtVQ27 0.4747 2.8328 0.1680 155.65
FtVQ15-FtVQ28 0.5945 3.4488 0.1724 189.50
FtVQ1-FtVQ12 0.4369 0.8331 0.5244 45.77
FtVQ11-FtVQ17 0.2927 1.3880 0.2110 76.27
FtVQ14-FtVQ24 1.0473 1.3114 0.7986 72.05
FtVQ4-FtVQ9 0.1333 5.0748 0.0260 278.83

Fig. 5

Phylogenetic tree of VQ genes from tartary buckwheat, Arabidopsis and rice based on full-length sequence of proteins VQ proteins from rice, Arabidopsis, and rice, and Tartary buckwheat are denoted by red, green and blue"

Fig. 6

Cis-elements of promoters of tartary buckwheat VQ genes"

Fig. 7

Expression profiles of tartary buckwheat VQ genes under different treatments A: A. alternata (Aa); B: N. osmanthi (No); C: Salicylic acid (SA); D: Methyl jasmonate (MeJA); E: Ethephon (ETH). The color scale above the figures represents log2 expression values. Blue represents low expression and red indicates a high expression level"

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