| Prunus mume is one of the most important ornamental species in the world landscape,flower color is one of the main embodiment of its ornamental value.We found many colors of plum,including red,purple,pink,white,green,yellow and so on,but our exploration has never been stopped.The publication of the plum genome sequence provides important information for identifying the fine ornamental characters and improving the color at the genomic level.Although there are reports about WD40 transcription factor in many plants,but not including plum.Therefore,it is very important to study the bioinformatics function of WD40 transcription factor in plum.The WD40 gene family in plum genome was identified by bioinformatics analysis,and the evolution and function of PmWD40 gene family were predicted through phylogenetic analysis,chromosomal location analysis,conserved motif analysis,gene structure analysis and other bioinformatics analysis methods.The expression of PmWD40 genes were studied under different light illumination and light quality by Real-Time PCR,and the gene of anthocyanin biosynthesis was cloned.Firstly,we used BLASTP searches against the plum genome database using known Arabidopsis thaliana full-length WD40 proteinse quences as queries.All potential candidates were subjected to SMART and Pfam analyses to ensure that the predicted proteins contained WD40 motifs.Through an extensive search for WD40 genes,77 nonredundant WD40 genes(named PmWD4001 to PmWD4077)were identified.The amino acid length of these genes is distributed between 269 and 3612,with an average length of712 amino acids,and more than half of the proteins are in an unstable state.Secondly,we constructed a phylogenetic tree of the WD40 protein families from Arabidopsis and plum,and it was found that the evolution of plum and Arabidopsis were similar and their sequences were not conserved.This is also confirmed by the exon-intron analysis,and it is found that the PmWD40 cluster are more near to the same structure.Thirdly,by analyzing the distribution of PmWD40 in chromosome location,it was found that the WD40 genes distribution were very comprehensive but uneven,the number of genes distributed on each chromosome were different,and the distribution of genes on the same chromosome were not uniform,and no specific regularity were shown.Fourthly,the motif analysis of the PmWD40 proteins are carried out by MEME online website.The results of the analysis show that there are several motifs in the PmWD40 genes,and the WD40 genes show some similarity in the sequence and the number of sequences in the same type.Meanwhile,motif 1,2,3,5 and 9 were identified as core sequences of PmWD40 proteins,which were widely distributed in the PmWD40 gene family.Fifthly,the PmWD40 genes expressed different results under different light illumination and light quality treatment.There are 27 WD40 genes in accordance with the rule of high light expression > normal light expression > low light expression,and there are 2 genes completely contrary to the law,and there are 41 genes in total failure to follow the rule.Under the treatment of different light quality,there are 9 WD40 genes that conform to the rule of the white light expression > blue light expression > yellw light expression > red light expression,and the remaining 68 genes do not follow this rule.It is found that this gene family plays an important role in anthocyanin biosynthetic pathway of Prunus mume by combining with the results of anthocyanin content determination in leaves.Sixthly,through bioinformatics analysis and expression analysis,the PmWD4048 anthocyanin biosynthesis gene was cloned from Prunus mume.The total CDS length of PmWD4048 gene is 1,029 bp,and the encoded amino acid is 342.This provides a preliminary basis for further study of PmWD4048 gene function. |
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