De novo transcriptome sequencing and comparative analysis of differentially expressed genes in kiwifruit under waterlogging stress

Kiwifruit plants are particularly sensitive to soil waterlogging. Enhancement of waterlogging tolerance in kiwifruit can potentially considerably increase its fruit production and extend the shelf life of the fruit. We generated 95,945,496 bases of high-quality sequence from kiwifruit roots after 4-day waterlogging treatment using Illumina sequencing technology, and demonstrated de novo assembly and annotation of genes. These reads were assembled into 140,187 unigenes (mean length 556 bp). Based on a similarity search with known proteins in the non-redundant (nr) protein database, 56,912 unigenes (40.60 %) were functionally annotated with a cutoff E-value of 10(-5). Using the RPKM method, we investigated differentially expressed genes by applying the Benjamini and Hochberg correction. Overall, 14,843 transcripts were identified as differentially expressed unigenes (DEG) in two samples. Among these unigenes, 5697 DEGs (about 38.5 %) were found to be induced by waterlogging, and 9146 DEGs (about 61.5 %) decreased in abundance. To identify the most important pathways represented by DEGs, we compared these genes to those in the KEGG database. The categories "ribosome,'' "plant hormone signal ;transduction,'' and "starch and sucrose metabolism'' pathways contained the three highest numbers of differentially expressed unigenes and, thus, appear to play important roles in waterlogging perception. We identified many transcription factors, belonging to AP2/ERF, WRKY, TGA, MYB, bZIP families, implicating a potential function for them in waterlogging responses in kiwifruit. Our results provide a transcriptome profile that is associated with waterlogging stress induction in kiwifruit plants. The potential waterlogging stress-related transcripts identified in this study represent candidate genes and molecular resources to further understand the molecular mechanisms of the waterlogging response in kiwifruit.