The raw RNA-Seq reads were processed to remove adapters as well as low quality bases using Trimmomatic, and the trimmed reads shorter than 80% of their original length were discarded. The remaining high-quality reads were aligned to the SILVA rRNA database to remove rRNA sequences using Bowtie allowing up to three mismatches. The resulting reads/read pairs were aligned to the corresponding genome using HISAT allowing up to two mismatches. Raw counts for each predicted gene were derived based on the alignments and then normalized to FPKM (fragments per kilobase of exon per million mapped fragments).
The kiwifruit genome database contains the following projects