Whole Genome Assembly and Annotation of Piper nigrum

The errors in the PacBio single-molecule real-time (SMRT) sequences were initially corrected using Canu46 with the default parameters. Because of heterozygosity and repeated sequences, FALCON12 was subsequently employed for de novo assembly using the corrected reads to produce primary contigs (p-Contigs). Then, FALCON-Unzip used the p-Contigs to perform phasing and directional classification of the heterozygosity from the initial assembly into updated primary Contigs (p-Contigs) and haplotigs (h-Contigs). Finally, the postprocessing step was used to polish using Arrow47 based on corrected PacBio long reads. The 10X Genomics Linked-reads were mapped to the consensus assembly described above using BWA-MEM48 with a default parameter. Then, fragScaff13 was used to extend contigs into initiatory scaffolds (Piper_nigrum_v1) according to the recommended scripts and processes of the fragScaff software.