A telomere-to-telomere genome of mango exclusively from long-read sequence data

Abstract

Abstract Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin mapping (Hi-C). We report here a telomere-to-telomere chromosome-level mango genome using only PacBio HiFi long reads. HiFi reads at high coverage (204X) resulted in the assembly of 17 chromosomes each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs with telomeres at one end and ribosomal repeats at the other end. Analysing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere. The assembled genome was 365 Mb with 100% completeness as assessed by BUSCO analysis. The haplotypes assembled demonstrated extensive structural differences. This approach may be useful for assembling telomere-to-telomere and haplotype-resolved genomes for many other plants.