Transcriptome sequencing of fruit and leaf of Docynia indica (Wall.) Decne.

In the current study, we used RNA-seq analysis to study early gene expression and regulation of Docynia indica fruit and leaf. Our concern was to prepare the libraries and generate adapter clean high quality data for both the samples. The high quality data were then assembled and FASTA sequence of transcript were generated. Transcripts were further processed for unigenes prediction using CD-HIT package and CDS were predicted from the unigenes sequences using Transdecoder. The protein sequences corresponding to the predicted coding regions within the unigenes were subjected to similarity search against NCBI's non-redundant (nr) database using the BLASTP algorithm. Simultaneously all protein sequences were searched for similarity against Uniprot, KOG and Pfam using BLASTP. GO mapping was carried out in order to retrieve GO terms for all the BLASTP functionally annotated proteins against NR database using Blast2GO cli 1.4.1. Ortholog assignment and mapping of the CDS to the biological pathways were performed using KEGG automatic annotation server (KAAS). SSR were identified in CDS sequences of each sample with the MISA perl script. Differential gene expression (DGE) was inferred between samples by applying the R package edgeR.