Genome-wide Identification And Characterization Of Zinc Finger Proteins In Cucumber

Zinc finger proteins are important transcription factors in plants,including C2H2,C3 H,C2C2?CO-LIKE,Dof,GATA,LSD and YABBY?gene families,which play an important role in development and response to external stimulation.Cucumber is a model species for studying plant sex determination,vascular bundles and fruit development.Data deposit of cucumber genomes,transcriptomes and variome are available on public databanks.The important role of individual zinc finger protein in cucumber has been reported,but the identification,evolution,characterization and functional analysis of these important gene families at the genomic level are rarely reported.In this study,seven zinc finger protein genes were identified in the cucumber genome,and the C2H2 gene family was analyzed systematically.It provided theoretical basis and information for studying the role of these genes in important agronomic traits of cucumber.The main conclusions include:?1?278 zinc finger protein genes were identified in the cucumber genome and they are distributed on 7 chromosomes.C2H2,C3 H,CO-LIKE,Dof,GATA,LSD and YABBY gene families have 120,51,26,36,26,6 and 13 members,respectively.The number of genes per gene family is different,C2H2 gene family have the biggest number,while the LSD gene family the smallest.?2?The sequence of the zinc finger structure of the C2H2 gene family is CX?1-4?CX?11-15?HX?3-8?H,according to the sequences feature of the protein domain between the second cysteine and the first histidine,we divided 120 genes to four subgroups,Q-TYPE?QALGGH sequences?,M-TYPE?change of 1-2 amino acids in QALGGH sequences?,Z-TYPE?change of more than 3 amino acids in QALGGH sequences?,C-TYPE?not conservative sequences?,where Q-TYPE type and C-TYPE type were the main types of cucumber C2H2 gene family.?3?Each subfamily of C2H2 gene contains similar gene structure and sequence.Most of the members of Group-I and Group-II are single-exon genes,which contain one Q-TYPE and multiple Q-TYPE/M-TYPE sequence.Members in Group-III have a complex structure,containing one or more C-TYPE sequence.Group-V members have 2-4 exons,containing one or more Z-TYPE sequence.?4?The orthologous genes of C2H2 in seven species?cucumber,melon,watermelon,poplar,Arabidopsis thaliana,rice and millet?were analyzed.Seventy of CsC2H2's orthologue genes could be found in at least one species of non-cucurbitaceae,indicating that these genes are more conserved in different species,Fruit gall Tu gene that has been cloned is one of them.There are 47 CsC2H2 genes only found in melon or watermelon,indicating that these genes are Cucurbitaceae unique genes,such as melon sex gene CmWIP1 and its orthologous gene.Three CsC2H2 genes did not appear in the other six species,indicating that these genes are cucumber-specific genes.?5?The promoter cis-element analysis showed that most C2H2 genes contained cis-elements that responding to plant hormones or abiotic stress.Gene expression analysis of 28 CsC2H2 after ABA treatment found that 20 genes been upregulated,especially,CsC2H2₁18 expression rises up to 11 times.The discovery of these up-regulated genes laid the foundation for the future study of their role in abiotic stress.?6?Zinc finger proteins are widely involved in various aspect of plant life process.Analysis of gene expression data found that CsYA₁2 and other four genes were highly expressed in all tissues,and CsC3H₁ was highly expressed in non-pollinated ovary,and the CsC3H₄ and other seven genes were highly expressed in roots,and the CsC2H2₅9 and other six genes were highly expressed in the leaves,three genes,such as CsCO₅,were highly expressed in the tendril tissue,CsYA₇ and other four genes were highly expressed in female flowers and male flowers.These genes may play an important role in the development of different organs.