Building near-complete plant genomes

Michael TP, VanBuren R.

Curr Opin Plant Biol. 2020 Jan 22;54:26-33. doi: 10.1016/j.pbi.2019.12.009. [Epub ahead of print]

Abstract

Plant genomes span several orders of magnitude in size, vary in levels of ploidy and heterozygosity, and contain old and recent bursts of transposable elements, which render them challenging but interesting to assemble. Recent advances in single molecule sequencing and physical mapping technologies have enabled high-quality, chromosome scale assemblies of plant species with increasing complexity and size. Single molecule reads can now exceed megabases in length, providing unprecedented opportunities to untangle genomic regions missed by short read technologies. However, polyploid and heterozygous plant genomes are still difficult to assemble but provide opportunities for new tools and approaches. Haplotype phasing, structural variant analysis and de novo pan-genomics are the emerging frontiers in plant genome assembly.

See: https://www.ncbi.nlm.nih.gov/pubmed/31981929

Figure 3: Assembly approaches for sequencing and phasing heterozygous genomes. Long read assemblies allow assembly of multiple haplotypes from homologous chromosomes in heterozygous regions. The primary and alternative haplotypes can be collapsed into a single, non-redundant but chimeric pseudomolecule for simplicity of downstream analyses (top). Raw reads can be mapped to the contigs to resolve missing haplotype regions to create a phased, diploid assembly (middle). Partial haplotypes can be retained and labeled in a graph-based assembly (bottom).