A comprehensive analysis of cotton VQ gene superfamily reveals their potential and extensive roles in regulating cotton abiotic stress

- However, little is known about the origin, evolution, and functions (and underlying mechanisms) of the VQ family genes in cotton..
- The expansion of the VQ gene was mainly through segmental duplication, followed by.
- Conclusions: The results in this study broaden our understanding of the VQ gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the VQs provide a solid foundation for exploring their specific functions in cotton responding to abiotic stresses.
- 1 State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China Full list of author information is available at the end of the article Chen et al.
- annotations of four Gossypium genomes, we identified the VQs of these Gossypium species, performed the ana- lyses of phylogeny, conserved structural motifs, whole- genome duplication (WGD) and functional interaction networks of the VQs, and predicted the microRNA tar- get profiles of the VQs.
- The comprehensive analysis of the VQ gene family in Gossypium will contribute to identify new key candidate genes for diverse stress resist- ance in cotton breeding..
- Identification and comparative analysis of VQs in plants To identify VQ family in G.
- arboretum, the AtVQ proteins were used as query sequences to search against the protein databases of the four Gossypium species, and the VQ- domain Pfam (PF05678) was also applied.
- The CDS lengths of these Gossypium VQs ranged from 279 bp (GhVQ89 and GbVQ89) to 1443 bp (GbVQ15), the average GC content of the transcripts was 46.01, their exon numbers varied from 1 to 9, and only a small percentage of VQs contained introns (3.37%.
- The evolutionary relationships of the species and the number of their VQ genes are shown in Fig.
- The data revealed that the numbers of VQs in A.
- cacao were less than those in the four Gossypium species (Additional File 3, Supplemental Table S2).
- We speculated that the WGD events that occurred during the evolution of angiosperms in- creased the numbers of the Gossypium VQs, and these events helped the VQs to gain new functions through neofunctionalization.
- Phylogenetic analysis of VQs.
- To explore the relationships among VQs in Gossy- pium, we conducted a phylogenetic analysis of the VQs from the 15 plant species (Fig.
- These proteins were divided into 10 clades based on the nomencla- ture of the Arabidopsis VQs.
- The VQs with rarer amino acids of the Gossypium species were also scattered in Group I to Group X, and the clusters of VQs were similar to those in angiosperms [3]..
- Cis-regulation elements and structural composition of the VQs.
- The cis-regulation elements in the promoters (from 2000 bp to − 1 bp) of the four Gossypium VQs were analyzed using the PlantCARE tool.
- The diversity of the cis-regulation elements in the pro- moters of VQs indicated that VQs might participate in regulating the Gossypium response to endogenous hormones and diverse environmental stimuli..
- Motif compositions and exon-intron structures of the VQs were shown in Fig.
- Combining the phylo- genetic data groups of the four Gossypium VQs, we.
- 1 The VQ gene family evolutionary relationship and the number details of the 15 plant species.
- The left of this figure shows the evolutionary relationships of the species.
- the right of this figure shows the number details of the VQ family of each group.
- Not sur- prisingly, Motif 1 existed in almost all of the VQs, suggesting that it was the most conservative motif..
- Most of the VQs had no intron, including of GhVQs of GbVQs of GrVQs, and of GaVQs.
- In general, VQs in the same clades would share similar motif elements and structural compositions, indicating that the VQ members in the same sub- group could have similar functions..
- 2 The VQ gene family phylogenetic relationship of the 15 plant species.
- Maximum likelihood (ML) bootstrap values are shown in the major nodes.
- Most VQs in the four Gossypium species were distributed at both ends of the chromo- somes, which corresponded to the position of the telomere..
- As previously described, duplication contributed to the expansion of genes in the polyploid events in plants [36]..
- The percentages of VQs derived from WGD were 60.47% in the At-subgenome of G.
- hirsutum, 63.04% in the Dt-subgenome of G.
- hirsu- tum, 69.04% in the At-subgenome of G.
- barbadense, 59.57% in the Dt-subgenome of G.
- 3 Potential cis-elements in promoters of VQs in Gossypium .
- in two allotetraploid species of Gossypium, we predicted the target sites of miRNAs in the coding (CDS) regions of the GhVQs and GbVQs.
- Of these, six VQ genes (GhVQ02, GhVQ40, GhVQ86, GbVQ02, GbVQ40 and GbVQ86) were pre- dicted to be targeted by Ghr-miR172 in the CDS regions;.
- 4 The converted motif and gene structure of VQs in Gossypium .
- Expression pattern analysis and function verification Expression profiles of the VQs in the two allotetraploid kinds of Gossypium were analyzed with available tran- scriptome data (Additional Files 11 and 12,.
- 5 Distribution of the VQs on chromosomes.
- VQs were widely identified in the abiotic stress re- sponses in angiosperms [3, 32].
- In this study, the expres- sion patterns of VQs in the allotetraploid Gossypium types under salt, drought, cold and heat stresses were analyzed using the published data.
- Upon PEG treatment, most of the GhVQs and GbVQs were highly expressed at 12 h (Fig.
- Most of the GhVQs and GbVQs under the hot treatment were highly expressed at 1 h (Fig.
- To validate of the expression results of GhVQs in response to salt and drought stresses, we con- ducted qRT-PCR analyses of 12 GhVQs after treatments with PEG and salt treatment.
- 6 Ortholog and paralog pairs of VQs in G.
- The functional regulation networks of the GhVQs were con- structed using the website of STRING11.0 with the module reference of Arabidopsis association, and the re- sults revealed that the GhVQs participated in plant defense interaction networks, including WRKYs, MYB15, MPK4, AR781, CSN5B and SIGAs (Fig.
- a The expression of the selected VQs in G.
- b The expression of the selected VQs in G.
- Here, we complete a comprehensive analysis of the VQ family genes and explore their evolutional mechanism in Gossy- pium species..
- The expansion, duplication and structural characteristics of VQs in Gossypium.
- arboretum and another 11 plant species, and found that the number of VQs in the genomes of 15 species was inconsistent with related to the size of their genomes.
- Through the analysis of the phylogenetic and structural features of the 15 plants VQ domains, the VQs could be divided into 10 clades.
- Ten conserved motifs were also identified in the four Gossypium VQs.
- Additionally, the motif compositions and intron contents of the Gos- sypium VQ proteins/genes in our study were consistent with the results of the phylogenetic analysis and the type.
- The colors varied from blue to red represent the scales of the relative expression levels.
- A proportion of the GmVQs [25], PeVQs [44], VvVQs [48], CsVQs [29], HaVQs [31], and NtVQs [19] also function in regulating the growth of different tissues at different developmental stages.
- our work, we assessed the expression levels of the GhVQs and GbVQs under salt, drought, cold, and heat stresses, and found that the majority of the VQs were up-regulated under drought, salt, and cold stress, or down-regulated under heat stress.
- Also, the pro- moters of the Gossypium VQs, many cis-elements that were reported to exist in other abiotic stresses respon- sive genes were detected (Fig.
- Moreover, we predicted some putative target sites of microRNAs in the Gossypium VQs.
- Our data showed that the gene structure and motif coding regions were con- served across plants, and segmental, dispersed, and tan- dem duplications were the main reason for the expansion of the VQs.
- Our study could serve as a foundation for future exploration of the specific functions of Gossypium VQs in the abiotic stress responses and the interactions with WRKYs or microRNAs..
- Identification and classification of VQs in plants.
- motif-containing sequences were confirmed in the NCBI Conserved Domain Database (https://www.ncbi.nlm.nih..
- Then, the phys- ical and chemical properties of the VQ family members, including amino acid length, mRNA length, MW, and pI, were analyzed using the online tools of the web site of softberry website (https://linux1.softberry.com/berry..
- Phylogenetic and synteny analysis of the VQs in plants All the VQ motif-containing proteins from the four Gos- sypium and other 11 plant species were aligned using MAFFT (Multiple Alignment using Fast Fourier Trans- form, v 7.4.0.7) (L-INS-algorithms) [57] with default pa- rameters, and conserved site sequences were selected by the Gblock (v 0.91b) software (https://molevol.cmima..
- barbadense using the modified MCScan algorithm of the MCScanX package (default parameters) (https://chibba.pgml.uga.edu/.
- The chromosomal positions of all VQ members were de- termined using the gene transfer (gtf) format files of the reference genomes.
- Then, the MEME tool (http://meme-suite.org/) (the motif with 10 amino acids in length and E-value less than 1e was used to detect the additional motifs of the proteins.
- Approximately 2000 bp genomic sequences locating upstream (from − 2000 to − 1) of the VQs from start co- dons were extracted from the cotton genome, which was.
- Moreover, the miRNA targets of the VQ members were predicted using the coding se- quences (CDS) regions for complementary sequences by the psRNATarget server (http://plantgrn.noble.org/.
- To determine the expression patterns of VQs in the two allotetraploid kinds of Gossypium, RNA-Seq data were obtained from the SRA database (PRJNA including those in 10 tissues (the petal, pistil, root, sepal, stem, torus, filament, leaf, anther, and bract), during ovule development.
- Total RNAs of the above samples were isolated using the RNA prep Pure Plant Kit (Polysaccharides &.
- The concentrations and integrities of the extracted RNA samples were measured and verified using a NanoDrop machine and 1% agarose gel electrophoresis, and the RNA samples were reversed transcribed into comple- mentary DNA (cDNA) using the Mir-X TM MIRNA First-Strand Synthesis Kit (TaKaRa, Dalian, China).
- The physical and chemical properties of VQs in Gossypium spp .
- a, b, c, d, e, f are the lengths of the transcripts, GC contents, exon numbers, protein lengths, PI values and MW values, respectively..
- The number of VQ genes in the 15 plant genomes..
- The phylogenetic tree of VQs in Gossypium spp.
- b The phylogenetic tree of VQs in G..
- c The phylogenetic tree of VQs in G..
- d The phylogenetic tree of VQs in G.
- The conserved motifs of VQs.
- The paralogs of VQs between G.
- The paralogs of VQs between G..
- The duplicated type of VQs in Gossypium spp.
- Information regarding the Co-expression and STRING search results of the interaction networks of the GhVQs .
- Genome-wide classification and evolutionary and functional analyses of the VQ family.
- Arabidopsis sigma factor binding proteins are activators of the WRKY33 transcription factor in plant defense.
- Genome-wide analysis of the WRKY gene family in cotton.
- Genome-Wide Identification of the VQ Protein Gene Family of Tobacco ( Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses..
- Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max).
- Genome-wide identification and analysis of the VQ motif-containing protein family in Chinese cabbage (Brassica rapa L.
- Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis).
- Genome- wide analysis of the plant-specific VQ motif-containing proteins in tomato (Solanum lycopersicum) and characterization of SlVQ6 in thermotolerance..
- Genome-wide identification and expression analysis of the VQ gene family in sunflower (Helianthus annuus L.
- Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula.
- Banana fruit VQ motif-containing protein5 represses cold-responsive transcription factor MaWRKY26 involved in the regulation of JA biosynthetic genes.
- A comprehensive survey of the grapevine VQ gene family and its transcriptional correlation with WRKY proteins

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