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

Area of Science:

• Genomics
• Plant Biology
• Bioinformatics

Background:

• Long-read sequencing technologies have advanced plant genome assembly.
• Current methods often combine long reads with chromatin conformation capture for chromosome-level results.

Purpose of the Study:

• To report a chromosome-level mango genome assembly solely utilizing PacBio high-fidelity (HiFi) long reads.
• To demonstrate the utility of high-coverage long-read sequencing for plant genome analysis.

Main Methods:

• Sequencing the mango genome using PacBio HiFi long reads at 204x coverage.
• Assembling contigs into chromosome-level structures by analyzing telomeric and ribosomal repeat regions.
• Assessing genome completeness using Benchmarking Universal Single-Copy Orthologs (BUSCO).

Main Results:

• A 365 Mb chromosome-level mango genome assembly was achieved, with most chromosomes as single contigs.
• Seventeen chromosomes were fully assembled with telomeres at both ends.
• The remaining three chromosomes were completed by pairing contigs, achieving telomere-to-telomere assembly.
• Genome completeness was assessed at 100% via BUSCO analysis.
• Extensive structural differences were observed between assembled haplotypes.

Conclusions:

• High-coverage PacBio HiFi long-read sequencing alone can produce complete, chromosome-level plant genome assemblies.
• This approach offers an efficient alternative to multi-technology methods for plant genome sequencing.
• The methodology is potentially transferable for high-quality genome assembly in other plant species.