FrangiPANe, a tool for creating a panreference using left behind reads

Area of Science:

• Genomics
• Bioinformatics

Background:

• Pangenomics aims to capture the full genetic diversity within a species.
• Short-read sequencing is cost-effective but challenges comprehensive genome assembly.

Purpose of the Study:

• To develop FrangiPANe, a novel pipeline for constructing pan-genome references using short reads.
• To identify novel genomic sequences and genes in African rice using this pipeline.

Main Methods:

• FrangiPANe employs a map-then-assemble strategy.
• The pipeline was applied to 248 African rice genomes utilizing an improved CG14 reference genome.
• Validation was performed using long-read sequencing data.

Main Results:

• An average of 8 Mb of new sequences and 5290 contigs were identified per individual.
• A total of 1.4 Gb of new sequences comprising 1,306,676 contigs were assembled.
• 3252 novel genes absent from the reference genome were annotated, with 31.5% of new contigs anchored accurately.

Conclusions:

• FrangiPANe effectively leverages short-read data to build robust pan-genome references.
• The pipeline facilitates the discovery of substantial novel genomic content, including genes.
• This approach is valuable for large-scale pangenome studies, including Genome-Wide Association Studies (GWAS) and selection detection.