Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species ...

• Main Authors: Bringloe, Trevor T., Parent, Geneviève J.
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: figshare 2023
• Subjects: Genetics; FOS Biological sciences; Beluga; Beluga*; Delphinapterus leucas; Monodon monoceros; narwhal*
• Online Access: https://dx.doi.org/10.6084/m9.figshare.c.6940518.v1; https://springernature.figshare.com/collections/Contrasting_new_and_available_reference_genomes_to_highlight_uncertainties_in_assemblies_and_areas_for_future_improvement_an_example_with_monodontid_species/6940518/1

Abstract Background Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies. Results The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2–3.7% of the total genome ...