| Rosaceae species possess important economic value,including many important fruit trees and ornamental plants,such as strawberry,black raspberry,apple,pear,peach,and rose.However,the cultivation of fruit trees often suffers from a variety of stresses,such as drought,low temperature and disease,which seriously affects the growth,development and fruit quality of fruit trees.Studies have shown that VQ proteins are a highly conserved protein family,which can interact with WRKY proteins to regulate the growth and development of plants and responding to biotic and abiotic stresses,regulate the expression of corresponding functional genes,and improve plant stress resistance.In the Rosaceae species,systematic studies about VQ gene family are limited so far.Since the genome sequencing of black raspberry,apple,pear,peach,Chinese plum and strawberry were completed,it represents a possible to analyze their VQ gene family.The main contents and research results are as follows:1.The VQ genes in six Rosaceae species(black raspberry,woodland strawberry,plum,peach,pear and apple)were identified by bioinformatics method.The gene duplication events and the selection pressure of the VQ genes in these Rosaceae species were analyzed in the evolutionary process.Our results showed that a total of 192 VQ genes were identified,including 23 VQ genes in black raspberry,23 in woodland strawberry,25 in Chinese plum,26 in peach,46 in pear,and 49 in apple.Based on the phylogenetic tree,we divided these VQ genes into 14 clades,indicating that there were at least 14 ancestral genes before the divergence of the six species.In the evolutionary process,89 gene duplication events were found in the VQ genes of the six Rosaceae species.In addition,the Ka/Ks values of most VQ gene pairs were less than 1,indicating that these VQ genes in the six Rosaceae species underwent mainly purifying selection during evolution.2.The VQ genes in five Fragaria species(F.nipponica,F.iinumae,F.orientalis,F.nubicola and F.x ananassa)were identified by bioinformatics method.We analyzed the evolutionary relationship,domain organization,genomic structure and cis-element in VQ genes in six Fragaria species,and the expression levels of VQ genes in F.vesca.The results showed that a total of 111 VQ genes were identified,including 19 VQ genes in F.nipponica,21 in F.iinumae,23 in F.orientalis,23 in F.nubicola,and 25 in F.x ananassa.By analyzing the phylogenetic tree,we divided these VQ genes into 15 clades,indicating that at least 15 ancestral genes existed before the differentiation of the six Fragaria species,and we found a total of 28 gene duplication events.The VQ proteins in the six Fragaria species contained a conserved VQ domain.Most of the VQ genes lacked introns,and the VQ proteins in each clade showed a similar motif composition.The Ka/Ks values for most gene pairs were less than 1,which illustrated that most of the VQ genes also underwent purifying selection in six Fragaria species.Four types of cis-elements in the promoter regions of VQ genes were detected,which is an important basis for further investigation about plant stress response.Furthermore,the expression analysis of FvVQ genes indicated that these genes showed different expression patterns in the examined organs and tissues.3.First,we identified 58 WRKY genes in the whole genome of F.vesca.Then,based on the WRKY-VQ protein interactions results in Arabidopsis and using orthologous relations method,9 pairs of WRKY-VQ interacting proteins were predicted in F.vesca.By analyzing the expression data of WRKY-VQ interacting proteins in different tissues and organs during different development stages,we found that most of the interacting proteins showed similar expression patterns.Moreover,we calculated the pearson correlation coefficient and found that the expression levels of FvVQ 17/FvWRKY8,FvVQl/FvWRKY36 and FvVQ1/FvWRKY8 were significantly correlated,indicating that the three pairs of interacting proteins were more conserved in function. |
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