Ccomparing transcriptome analysis between the pecan persisting and abscising nuts

RNA-seq analysis was performed to identify differentially expression genes (DEGs) in abscising nuts (A2) comparing with persisting nuts (P2) at 53 DAA. Illumina platform generated 486, 954,046 raw reads. After filtering, 323,264,216 clean reads containing a total of 44.66 Gb clean nucleotides were obtained through stringent quality assessment and data filtering. The clean reads were mapped to the pecan genome using the HISAT2 tool, and the total mapped reads, uniquely mapped reads and multiply mapped reads were summarized. StringTie was applied to transcript assembly based on the read alignments. A total of 33312 genes were identified with 954 new genes after optimal gene structure prediction and alternative splicing analysis.