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

Tranchant-Dubreuil Christine1, Chenal Clothilde1,2,3, Blaison Mathieu1

  • 1DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France.

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Summary

FrangiPANe pipeline builds comprehensive pan-genome references from short-read sequencing data. This approach significantly expands the known rice genome, identifying novel sequences and genes for pangenome studies.

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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.