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Tropical Plant Biology

, Volume 12, Issue 2, pp 117–131 | Cite as

Genome-Wide Classification and Evolutionary and Functional Analyses of the VQ Family

  • Hanyang Cai
  • Man Zhang
  • Yanhui Liu
  • Qing He
  • Mengnan Chai
  • Liping Liu
  • Fangqian Chen
  • Youmei Huang
  • Maokai Yan
  • Heming Zhao
  • Jerming Hu
  • Yuan QinEmail author
Article
  • 62 Downloads

Abstract

VQ protein, contain a conserved and short FxxxVQxLTG amino acid sequence motif. Some VQ proteins play important roles in development process and abiotic/biotic stress in plants. However, there has not been a systematic study of the VQ family in plants. The results revealed that Group I genes are conserved in plant development in angiosperms; Group IV and Group X in eudicots and Group I, Group VI and Group VII in monocots are involved in drought response; Group I and Group IV are the most important groups and conservational in response to salt stress in eudicots but not in monocots; VQ genes in Group II and Group IV which responded to cold stress were overlapped in angiosperms; Group IV, Group V, Group VI and Group IX in eudicots and Group VI in monocots play key roles in response to ABA treatment; Group IV in eudicots while Group V and Group VI are irreplaceable in response to biotic stress in monocots. We propose that this study provides solid foundations for the investigation of the functions and evolution of VQ genes in angiosperms.

Keywords

VQ motif-containing proteins WRKY transcription factors Angiosperms Evolution Abiotic stress Biotic stress 

Abbreviations

PIF1

PHY-INTERACTING FACTOR 1

SIB1

SIGMA FACTOR-BINDING PROTEIN1

SIB2

SIGMA FACTOR-BINDING PROTEIN2

JA

Jasmonic acid

ABA

Abscisic acid

qRT-PCR

Quantitative real-time PCR

RNA-seq

RNA sequencing

Notes

Acknowledgments

We would like to thank the reviewers for their helpful comments on the original manuscript.

Author Contributions

H.C. designed the study and performed the experiments. M.Z. performed the molecular analyses. Y.L., M.C., and Q.H. analyzed the data. J.H. assisted with the data interpretation and manuscript writing. Y.Q. and H.C. conceived the study and wrote the manuscript.

Funding

This work was supported by the National Nature Science Foundation of China (U1605212; 31700279; 31522009), the Fujian Innovative Center for Germplasm Resources and Innovation project of the Characteristic Horticultural Crop Seed Industry (KLA15001D), the Fujian Agriculture and Forestry University International collaboration project (KXb16006A), and a Newton Advanced Fellowship to Y.Q.

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

12042_2019_9224_Fig10_ESM.png (299 kb)
Figure S1

Conserved amino acid analysis of the VQ core sequence FxxhVQxhTG motif among 1929 protein sequences. 1st-10th represents the different amino acid from FxxhVQxhTG motif. Each pie chart represents the type and proportion of amino acids. The letters on the right side of each pie chart represent abbreviations for different amino acids. (PNG 299 kb)

12042_2019_9224_MOESM1_ESM.tif (451 kb)
High Resolution Image (TIF 451 kb)
12042_2019_9224_Fig11_ESM.png (5.2 mb)
Figure S2

Detail phylogenetic tree of all 1929 VQ genes clustered into ten groups. Different colors represent different subgroups. (PNG 5349 kb)

12042_2019_9224_MOESM2_ESM.tif (6.2 mb)
High Resolution Image (TIF 6305 kb)
12042_2019_9224_Fig12_ESM.png (1.2 mb)
Figure S3

Exon/intron structures of the VQ genes of six plant species. a–f, Exon/intron structures in the VQ genes of (a) Selaginella moellendorfii, (b) Amborella, (c) Arabidopsis, (d) soybean, (e) pineapple, and (f) rice. Exons are drawn to scale and represented by boxes. Solid lines connecting two exons represent introns. (PNG 1239 kb)

12042_2019_9224_MOESM3_ESM.tif (2.4 mb)
High Resolution Image (TIF 2502 kb)
12042_2019_9224_Fig13_ESM.png (1.1 mb)
Figure S4

The motif composition within the VQ genes of six plant species. a–f, The motif composition within the VQ genes of (a) Selaginella moellendorfii, (b) Amborella, (c) Arabidopsis, (d) soybean, (e) pineapple, and (f) rice. The motifs, numbered 1–10, are displayed in different boxes. (PNG 1159 kb)

12042_2019_9224_MOESM4_ESM.tif (3.4 mb)
High Resolution Image (TIF 3476 kb)
12042_2019_9224_Fig14_ESM.png (1.1 mb)
Figure S5

Consensus sequences of the motifs detected in the VQ genes using MEME. (PNG 1102 kb)

12042_2019_9224_MOESM5_ESM.tif (3.9 mb)
High Resolution Image (TIF 4005 kb)
12042_2019_9224_Fig15_ESM.png (151 kb)
Figure S6

Chromosomal distribution and gene duplication of VQ genes, determined using respective reference genomes. a–d, Chromosomal distribution and gene duplication of the VQ genes in (a) Arabidopsis, (b) soybean, (c) pineapple, and (d) rice. (PNG 150 kb)

12042_2019_9224_MOESM6_ESM.tif (685 kb)
High Resolution Image (TIF 685 kb)
12042_2019_9224_Fig16_ESM.png (96 kb)
Figure S7

The transcriptional levels of VQ4 and VQ33 in the Arabidopsisvq4 and vq33 mutants. a, The expression levels of (a) VQ4 and (b) VQ33 in their respective T-DNA insertion mutant lines were detected using RT-qPCR. The expression level in the wild type (WT) was set as “1”. Data represent the means ± SD of three biological replicates. (PNG 95 kb)

12042_2019_9224_MOESM7_ESM.tif (105 kb)
High Resolution Image (TIF 104 kb)
12042_2019_9224_MOESM8_ESM.xlsx (270 kb)
Table S1 VQ sequences in different varieties (XLSX 269 kb)
12042_2019_9224_MOESM9_ESM.xlsx (139 kb)
Table S2 Characteristics of VQ genes. (XLSX 138 kb)
12042_2019_9224_MOESM10_ESM.xlsx (15 kb)
Table S3 Number of VQ genes in different subgroups (XLSX 15 kb)
12042_2019_9224_MOESM11_ESM.xlsx (14 kb)
Table S4 Distribution of the conserved motifs. (XLSX 14 kb)
12042_2019_9224_MOESM12_ESM.xlsx (11 kb)
Table S5 Functions of VQ proteins in different species. (XLSX 11 kb)
12042_2019_9224_MOESM13_ESM.xlsx (25 kb)
Table S6 Gene duplication pairs. (XLSX 24 kb)
12042_2019_9224_MOESM14_ESM.xlsx (11 kb)
Table S7 Primers for RT-qPCR. (XLSX 10 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Hanyang Cai
    • 1
  • Man Zhang
    • 2
  • Yanhui Liu
    • 1
  • Qing He
    • 2
  • Mengnan Chai
    • 2
  • Liping Liu
    • 1
  • Fangqian Chen
    • 1
  • Youmei Huang
    • 1
    • 2
  • Maokai Yan
    • 1
  • Heming Zhao
    • 1
  • Jerming Hu
    • 3
  • Yuan Qin
    • 1
    • 2
    Email author
  1. 1.State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
  3. 3.Institute of Ecology and Evolutionary BiologyNational Taiwan UniversityTaipeiTaiwan

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