Identification, bioinformatics analysis of LEA (Late embryogenesis abundant) genes in cucumber genome and analysis of gene expression profiles under drought stress condition

LEA (late embryogenesis abundant) proteins are firstly discovered in seeds and then identified in vegetative tissues of different plant species. Although genome wide studies of different gene family members have been performed in cucumber, there is no such a study for LEA genes. We have identified 79 LEA genes in the cucumber genome and they were located in cucumber chromosomes. Based on gene locations on chromosomes, CsLEA genes have been named as CsLEA-01 to CsLEA-79. It was found that 44 CsLEA genes contain no introns. Based on phylogenetic analysis, CsLEA genes could be classified into 7 groups. The most abundant tandem duplication ratio was observed in chromosome 3 and this event was observed about %70 of total CsLEA genes. The maximum orthologous relationship of CsLEA genes was determined with LEA genes found in the poplar genome with 81% ratio. The in silico micro-RNA (miRNA) target analyses indicated that 37 CsLEA genes were targeted by different miRNAs, especially mir854 and mir414 are the most abundant identified ones. Public available RNA-seq data were analyzed for expression analysis of CsLEA genes in different tissues of cucumber. The expression profiles of 10 CsLEA genes in the root and leaf tissues of drought-stressed cucumber were examined using qRT-PCR. Among them, CsLEA-54 induced after stress application in leaf and root tissues. CsLEA-09, CsLEA-32 and CsLEA-57 genes responded to drought after 3 h later and might be considered as early response genes to water limitation. It is thought that this research could help us to understanding of contribution of CsLEAs to drought tolerance mechanisms in cucumber and to create different insights for new studies.