A chromosome-level genome of mango exclusively from long-read sequence data

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 conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (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. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants. High genome coverage and high-fidelity (HiFi) sequencing method alone facilitated high-quality mango genome assembly. The assembled mango genome reported the highest possible completeness (100%) and contiguity (contig N50: 15 Mb). Phased haplotypes showed extensive structural variations. A mango genome was sequenced and assembled from sequence data alone. Chromosome-level assembly of other plant genomes has required other evidence, such as genetic or chromatin maps. Very high sequence coverage allowed assembly of a complete genome sequence, with each chromosome represented by a single sequence telomere to telomere. The two haplotypes were assembled separately and showed substantial structural differences.