Comparing transcriptome analysis between the persisting and abscising nuts at the stage of nut sizing in pecan

RNA-seq analysis was performed to identify differentially expression genes (DEGs) in abscising nuts comparing with persisting nuts at 53 DAP. 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 in Supplemental Table S3. StringTie was applied to transcript assembly based on the read alignments. A total of 33, 312 genes were identified with 954 new genes after optimal gene structure prediction and alternative splicing analysis .A total of 5, 964 DEGs were identified between two groups with 2, 505 upregulated DEGs were and 3, 459 downregulated DEG. Gene Ontology (GO) functional classification included three GO trees (cellular components, molecular functions, and biological processes) and 62 functional groups. 2, 940 DEGs were matched and assigned to 134 KEGG pathways.