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.
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Data Availability
All data generated or analyzed during this study are included in this published article [and its Additional files].
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
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Acknowledgments
We would like to thank the reviewers for their helpful comments on the original 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.
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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.
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Communicated by: Yuval Cohen
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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)
Figure S2
Detail phylogenetic tree of all 1929 VQ genes clustered into ten groups. Different colors represent different subgroups. (PNG 5349 kb)
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)
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)
Figure S5
Consensus sequences of the motifs detected in the VQ genes using MEME. (PNG 1102 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)
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)
Table S1
VQ sequences in different varieties (XLSX 269 kb)
Table S2
Characteristics of VQ genes. (XLSX 138 kb)
Table S3
Number of VQ genes in different subgroups (XLSX 15 kb)
Table S4
Distribution of the conserved motifs. (XLSX 14 kb)
Table S5
Functions of VQ proteins in different species. (XLSX 11 kb)
Table S6
Gene duplication pairs. (XLSX 24 kb)
Table S7
Primers for RT-qPCR. (XLSX 10 kb)
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Cai, H., Zhang, M., Liu, Y. et al. Genome-Wide Classification and Evolutionary and Functional Analyses of the VQ Family. Tropical Plant Biol. 12, 117–131 (2019). https://doi.org/10.1007/s12042-019-09224-4
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DOI: https://doi.org/10.1007/s12042-019-09224-4