Bridging the gap: long reads enable more contiguous assembly of repeat-rich plant genomes
Larissa and her team used long-read nanopore sequencing + exome capture array & 3C to assemble the cultivated lentil genome, with ‘vastly improved’ contiguity compared to a previous short-read assembly.
They used the same technique to assemble Lens ervoides, a wild relative of cultivated lentil of interest as a potential source of new variation for breeding programs.
This produced ‘an even better assembly’: 4.7 Mb contig N50, 96% of sequence anchored into 7 pseudomolecules.
Long read assembly enabled analysis of repeat content, not possible using short reads, where repeats often collapsed.
SV detection: ‘even at 5 to 10-fold coverage, we were able to identify a large number of good-quality variants, from large indels to breakpoints and duplications.’