The impact of third generation genomic technologies on plant genome assembly

•Plant genomes are more repetitive and complicate to assemble than vertebrates.•Long-read assembly contigs outperform short-read assembly scaffolds.•Long-range scaffolding can advance assembly contiguity up to chromosomal levels.•Reconstruction of haplotypes allows assembly of heterozygous and polyploid genomes.

Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies.