Chromium genome library gel bead kit v2

Four 10× Genomics linked-read libraries (female and male of D&B and Rio Grande strains; Supplementary Table S1) were constructed on a 10× Genomics Chromium Controller (10× Genomics, Inc., San Francisco, CA, USA) using 1.1 ng HMW gDNA input with the Chromium Genome Reagent Kit v2 and Chromium Genome Library & Gel Bead Kit v2 (10× Genomics, Inc.). Individual libraries were barcoded using the Chromium i7 Multiplex Kit (10× Genomics, Inc.). Final library quality and size distribution were determined by Agilent TapeStation 4200 (Agilent Technologies), and the concentrations were measured with Qubit 3.0 Fluorometer (Thermo Fisher Scientific). The libraries were sequenced using a 2 × 150 bp paired-end format on an Illumina NovaSeq 6000 sequencing  (Illumina NovaSeq 6000 Sequencing System, RRID:SCR_016387) at Novogene (Novogene Corporation Inc., Sacramento, CA, USA).

The gDNA was size‐selected on a BluePippin system (Sage Science Inc.) using a cutoff range of 40–80 kb. The 10× Chromium shotgun libraries were prepared following the Chromium Genome Reagent kits v2 User Guide RevB protocol, using the Chromium™ Genome Library & Gel Bead Kit v2, Chromium™ Genome Chip Kit, and Chromium™ i7 Multiplex Kit (10X Genomics Inc.) and sequenced by Illumina HiSeqX with 2 × 150 cycles (Illumina Inc.).

Stem (cladode) samples of H. undatus cultivar “David Bowie” (Fig. 1A) were collected from the USDA-ARS Tropical Agriculture Research Station in Mayaquez, Puerto Rico. Whole-genome sequencing libraries were prepared using Chromium Genome Library & Gel Bead Kit v.2 (10X Genomics, cat. no. 120258) and sequenced on a NovaSeq6000 sequencer (Illumina, San Diego, CA) with paired-end 150 bp reads.