Articles
Achieving high quality rose pangenomics
Article number
1461_7
Pages
57 – 66
Language
English
Abstract
Rose breeding is a million-dollar industry, which increasingly relies on the efficient use of genetic variation.
For rose, as in many other species, the number of genome assemblies and resequenced accessions is steadily increasing, motivating the need for efficient analysis.
To capture and analyse all genetic variation in a species, genus or family in an unbiased fashion, genomics research is transitioning from reference-based approaches towards pangenomic approaches.
Here we discuss the technical challenges of constructing a genus-level rose pangenome and the benefits of pangenomes in the construction of high-quality genome assemblies of related species.
The substantial sequence-level variation among Rosa species renders alignment-based pangenome construction methods ineffective.
Thus, we adopt a k-mer-based pangenome approach, which effectively captures the genetic variations within the sampled Rosa species.
Our pangenome analysis delineates core, accessory, and unique genes across Rosa species, revealing substantial genomic differences, particularly within the repertoire of unique genes.
These unique genes may represent genuine biological variations contributing to the phenotypic diversity observed in roses.
However, discrepancies arising from variations in assembly/annotation quality across genomes may also appear as unique genes.
We adopted various approaches to identify and evaluate such technical artefacts.
Some of these consist of short, single-exon genes lacking supporting functional evidence.
These characteristics also provide valuable insights for developing approaches to enhance annotation quality.
The identification of technical variation within the pangenome underscores the importance of a pangenomic approach in enhancing genome annotation accuracy.
By distinguishing between biologically relevant unique genes and potential annotation errors, our study provides clearer insights into genetic variations among the sampled Rosa species.
Furthermore, understanding the nature of the technical artefacts offers valuable leads for improving genome quality, ultimately enabling a more reliable pangenomic analysis.
For rose, as in many other species, the number of genome assemblies and resequenced accessions is steadily increasing, motivating the need for efficient analysis.
To capture and analyse all genetic variation in a species, genus or family in an unbiased fashion, genomics research is transitioning from reference-based approaches towards pangenomic approaches.
Here we discuss the technical challenges of constructing a genus-level rose pangenome and the benefits of pangenomes in the construction of high-quality genome assemblies of related species.
The substantial sequence-level variation among Rosa species renders alignment-based pangenome construction methods ineffective.
Thus, we adopt a k-mer-based pangenome approach, which effectively captures the genetic variations within the sampled Rosa species.
Our pangenome analysis delineates core, accessory, and unique genes across Rosa species, revealing substantial genomic differences, particularly within the repertoire of unique genes.
These unique genes may represent genuine biological variations contributing to the phenotypic diversity observed in roses.
However, discrepancies arising from variations in assembly/annotation quality across genomes may also appear as unique genes.
We adopted various approaches to identify and evaluate such technical artefacts.
Some of these consist of short, single-exon genes lacking supporting functional evidence.
These characteristics also provide valuable insights for developing approaches to enhance annotation quality.
The identification of technical variation within the pangenome underscores the importance of a pangenomic approach in enhancing genome annotation accuracy.
By distinguishing between biologically relevant unique genes and potential annotation errors, our study provides clearer insights into genetic variations among the sampled Rosa species.
Furthermore, understanding the nature of the technical artefacts offers valuable leads for improving genome quality, ultimately enabling a more reliable pangenomic analysis.
Authors
Z.J. Yang, P. Arens, M.J.M. Smulders, R. van Velzen, J.J.B. Keurentjes, P.M. Bourke, S. Smit
Keywords
Rosa pangenome, quality, homology grouping, annotation discrepancy
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