Identification and expression analysis of phytochrome interacting factors in cucumber

【Objective】Identification and expression analysis of cucumber phytochrome-interacting factor（PIF）family genes would lay a foundation for further exploration to clarify their functions in cucumber growth，development，and biotic and abiotic stress response.【Method】Cucumber PIF family genes were identified at the whole cucumber genome level by bioinformatics methods，and the exon-intron structure，chromosome location，gene duplication，phylogenetic relationships，conserved motifs，tissue and stress-associated expression profiles were also analyzed.【Result】A total of 6 PIF family genes were identified in cucumber genome，which were unevenly distributed on six chromosomes. Gene duplication analysis showed that these cucumber PIF genes made up a segmental duplication event（CsPIF1a and CsPIF1b）. Phylogenetic analysis showed that PIF proteins from cucumber，Arabidopsis，pepper，maize and rice could be divided into four different groups（PIF1，PIF2/3/6，PIF4/5，and PIF7/8）. Conservative motif analysis revealed the existence of many conserved motifs，which was consistent with the classification of PIF proteins. Gene structure analysis showed that CsPIF genes had 5 or 6 introns，which was relatively stable when compared to other plants. CsPIF genes expressed in all tissues of cucumber，and its expression were greatly different in various tissues. For example，CsPIF1a，CsPIF1b，and CsPIF7 showed the highest expression of transcripts infemale flower，leaf，and tendril，respectively，CsPIF4 displayed higher expression levels in stem and leaf than in other tissues，CsPIF8 was highly expressed in stem，female flower，and tendril，while CsPIF3 showed constitutive expression in different tissues. In addition，some of them were down-regulated and up-regulated by heat and salt stress treatments，respectively. Most CsPIF genes hadgreatly altered expression in response to downy mildew（DM）inoculation，and the expression levels of CsPIF4 and CsPIF8 were observably increased after root-knot nematode（RKN）treatment.【Conclusion】The expression levels of some CsPIF genesare greatly altered under various abiotic and biotic stress treatments，suggesting that they might play vital roles in response to adverse conditions of cucumber.