*2.1. Plant Materials, DNA Extraction, and Sequencing*

An inbred landrace of *P. vulgaris* accession G19833 derived from the Andean pool (Race Peru) was selected for sequencing. Seeds were obtained from the germplasm bank of the Embrapa Arroz e Feijão, Brazil [30]. Root tips obtained from germinated seeds were pre-treated with 2 mM 8-hydroxyquinoline

for 18 h at 10 ◦C, fixed in ethanol-acetic acid (3:1 *v*/*v*), and stored in fixative at −20 ◦C for up to several weeks. Total genomic DNA was extracted from root tips using DNAeasy Plant Mini Kits (Qiagen). To construct the shotgun library, DNA was fragmented by nebulization. The raw reads were sequenced with a combination of Roche/454 GS FLX sequencing reads, Illumina HiSeq-2500 sequencing short reads (primarily to correct 454 sequencing errors) and PacBio RS II sequencing long reads (primarily to validate the assembly of the master conformation). The raw reads of *P. vulgaris* used in this study were available in the NCBI Sequence Read Archive (SRA) under accessions SRR069592, SRR5628227, and SRR2912756.
