Genome assembly and S haplotype reconstruction in citrus

The sequencing of PN02 and DB02 was performed on the PacBio Sequel II platform (Pacific Biosciences, USA) by Beijing Biomarker Technologies Co. Ltd. (Beijing, China). A SMRTbell library with a size of 30 kb was constructed for genomic sequencing following the standard protocol provided by Pacific Biosciences. Two 300 bp libraries were constructed to survey the genome information using the BGISEQ-500 platform (BGI-Shenzhen, China).The CLR reads were assembled using Canu and polished iteratively using two rounds of Pilon (v. 1.24) with ~12 Gb of WGS BGISEQ data to generate the draft genome (PN02gv1 contig, DB02gv1 contig, and AZMgv1 contig).