Spatiotemporal Gene Expressions And Regulation During Early Fruit Development In Cucumber

Cucumber(Cucumis sativus L.)is one of the top ten most valuable vegetables in the world and has extremely high economic and nutritional value.Young pepo is the consume organ of cucumber,however,the related genes and regulatory mechanism of cucumber fruit development are few studied.Therefore,we first improved the accuracy and continuity of cucumber reference genome.Additionally,we carried out dynamic expression analysis of genes and microRNAs at key time nodes(-3,0,1,3,5,8,16 dpa)and tissue sites(head placenta,head pericarp,middle placenta,middle pericarp,fruit stalk)of early cucumber fruit.Furthermore,this study explored the changes of gene expression during fruit morphogenesis,and identified a series of important functionally candidate genes,and analysis the relationship between gene expression and microRNA regulation.The main results are as follows:1)This study got a high continuous and complete reference genome(V3.0).A total of 174 contigs were obtained with a total length of 226.2 Mb and an N50 length of 8.9 Mb.V3.0 provides an extra of 29.0 Mb sequences and has an approximately 234.8-fold improvement in contiguity compared with the previous assembly.What's more,a total of 1,374 FL-LTRs were predicted in V3.0,five times more than that(267)in V2.0.2)New genome provides a more complete gene sets for functional genomic studies.A total of 24,317 protein-coding genes in V3.0 were predicted,and 96.7%of them located in the chromosome sequences.The new assembly contains 1,078 novel genes including 239 tandemly duplicated genes.3)Revealing the gene expression pattern during the early development of cucumber fruit.According to the results of PCA and WGCNA,the gene expression exhibited a space-time specificity during the early fruit development in cucumber,with a more significant difference among tissues than among developmental stages.However,the difference in gene expression patterns among tissues was decreasing with the fruit ripening.4)A series of candidate genes related to cucumber fruit development were identified.A total of 235 cell division-,1,020 cell elongation-and 2,320 fruit-special different expression transcripts were identified.What's more,53 stalk-,59 pericarp-,and 113 placenta-special different expression transcripts were found.In addition,this study found that the genes in NAC or GRAS gene families(CsaNAC90,CsGS40)play a crucial role in fruit development and have a very obvious spatiotemporal expression trend.5)The regulatory role of microRNAs in cucumber fruit development.We predicted 58 microRNAs including 21 novel microRNAs in cucumber fruit.These microRNAs have a dynamic change during the development of cucumber fruit,but they are highly conservative in the fruit stalk.941 transcripts were targeted by microRNAs,and the novel predicted microRNA(cst-miR-17)regulates a gene clusters which may affect the phloem development.In summary,this study assembled a more complete and accurate cucumber genome,providing a solid foundation for biological research of cucumber.In addition,this study explored the spatiotemporal expression of genes during cucumber fruit early development and the regulation of microRNA on genes.These elaborate results provide a strong data support and an effective reference for subsequent fruit development studies.