Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes.

ABSTRACT: Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Eyach15-2 to HiFi assemblies of the same sample. The use of five different assemblers starti

SUBMITTER: Rabanal FA 

PROVIDER: S-EPMC9757041 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature