Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Peona V, Blom MPK, Xu L, Burri R, Sullivan S, Bunikis I, Liachko I, Haryoko T, Jønsson KA, Zhou Q, Irestedt M, Suh A

Mol Ecol Resour 21 (1) 263-286 [2020-10-10; online 2020-10-10]

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic "dark matter") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.

Bioinformatics Compute and Storage [Service]

Bioinformatics Long-term Support WABI [Service]

Bioinformatics Support, Infrastructure and Training [Service]

NGI Stockholm (Genomics Applications) [Service]

NGI Stockholm (Genomics Production) [Service]

NGI Uppsala (Uppsala Genome Center) [Collaborative]

National Genomics Infrastructure [Collaborative]

QC bibliography QC xrefs

PubMed 32937018

DOI 10.1111/1755-0998.13252

Crossref 10.1111/1755-0998.13252