Gossypium hirsutum (AD1) 'TM-1' genome HAU_v2.0

About the Assembly

We assembled the TM-1 and 3-79 genomes with Canu (version 2.1.1), which included correction, trimming, and assembly in three steps. We performed these steps manually. First, ONT reads and PacBio reads from both genomes were corrected and trimmed using Canu with default parameters (correctedErrorRate = 0.045 for PacBio reads; correctedErrorRate = 0.144 for Nanopore reads). Trimmed highquality reads from ONT (~40x) and PacBio (~40x) were delivered as input to Canu using a mix of formats with default parameters. To improve base quality, we aligned Illumina paired-end reads (~50x) to contigs using BWA–MEM and polished them with Pilon (version 1.23) (–fix bases –mindepth 10 –minmq 30). High-quality paired-end Hi-C reads based on DpnII for G. hirsutum TM-1 and G. barbadense 3-79 were mapped to the two contig-scale assemblies using Juicer (version 1.6). The original contigs were organized into chromosomes with the 3D-DNA pipeline (version 180 419) (-r 2 -i 15000 –buildgapped- map). Finally, we used Juicebox Assembly Tools (v1.11.08) to manually correct and refine the connections.

 Summary of assemblies of G. hirsutum and G. barbadense genome