Hybrid Genome Assembly of Narrow-Leafed Lupin

Paired‐end Illumina gDNA libraries of 100 bp length and 170, 500 and 800 bp insert sizes were generated (82.2× coverage). This was complemented by mate‐paired libraries of 50 bp read length and 2, 4, 10, 20 and 40 Kb insert sizes generating a total of 150.41 Gb or 162.8× coverage. Illumina sequence reads were trimmed for adapter and low‐quality sequences via CutAdapt v1.1 (min length 25 bp, rounds 3, match length 5 bp) (Martin, 2011). Mate‐paired libraries were filtered for contaminating paired‐end reads by merging pairs of reads with overlapping 3′ sequences via FLASH v1.2.2 (Magoč and Salzberg, 2011). Additional RNA‐seq Illumina data used in this project to complement genome sequence data were described in a previous study (Kamphuis et al., 2015). The total genome size for narrow‐leafed lupin was estimated by performing a 17‐mer frequency analysis of genomic paired‐end libraries via Kmerfreq (Liu et al., 2013), using the following equation: total genome size = (K‐mer frequency/primary peak depth).