Transcriptome profiling of PeCRY1 transgenic Populus tomentosa

Cryptochromes, a class of blue light photoreceptors, play vital roles in regulating growth and development in higher plants. Despite their control over various important traits, there have been few studies focusing on cryptochromes in forest trees to date. In this study, the Euphrates poplar (Populus euphratica) gene PeCRY1 (cryptochrome 1 of Populus euphratica) was isolated and heterologously expressed in Populus tomentosa. Three biological replicates of each of the PeCRY1 transgenic P. tomentosa (CRY1) and wild-type (WT) plants were processed for transcriptome profiling. We found 34792 commonly expressed transcripts among the 93868 detected unigenes. Using R package DESeq, we identified 357 differentially expressed genes (DEGs), including 132 upregulated and 225 downregulated genes. Gene ontology (GO) enrichment and KEGG pathway enrichment were used to better understand the functions of detected DEGs. Biosynthetic processes, such as starch and sucrose metabolism, which are closely related to growth and development, were highly enriched. Organic cyclic compound biosynthesis was downregulated, whereas carbohydrate metabolism was upregulated. Through KEGG pathway enrichment, we observed that the pentose phosphate pathway, photosynthesis, and circadian rhythm were significantly enriched. Another method of expression analysis based on quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated our RNA sequencing (RNA-seq) results.