PCI Genomics

333

Title *

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: *Phoxinus phoxinus*) provide evidence of haplotype diversityuse asterix (*) to get italics

Authors *

Temitope O. Oriowo, Ioannis Chrysostomakis, Sebastian Martin, Sandra Kukowka, Thomas Brown, Sylke Winkler, Eugene W. Myers, Astrid Boehne, Madlen StangePlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2024

Picture *

Abstract *

In this study we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C). We achieved a haploid size of 940 Megabase pairs (Mbp) for haplome one and 929 Mbp for haplome two with high scaffold N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, respectively, indicating a highly complete genome assembly. We detected notable heterozygosity (1.43%) and a high repeat content (approximately 54%), primarily consisting of DNA transposons, which contribute to genome rearrangements and variations. We found substantial structural variations within the genome, including insertions, deletions, inversions, and translocations. These variations affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, and stress response. In the annotation of protein-coding genes, 30,980 mRNAs and 23,497 protein-coding genes were identified with a high completeness score, which further underpins the high contiguity of our genome assemblies. We performed a gene family evolution analysis by comparing our proteome to ten other teleost species, which identified immune system gene families that prioritise histone-based disease prevention over NLR-based immune responses. Additionally, demographic analysis indicates historical fluctuations in the effective population size of P. phoxinus, likely correlating with past climatic changes. This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus Phoxinus and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterised by high heterozygosity.

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Keywords (optional)

Phoxinus, Haplotype-phased genome assembly, comparative genomics, structural variants, immune system, annotation, transposable elements

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Evolutionary genomics, Structural genomics, Vertebrates

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

Rui Borges ruiborges23@gmail.com, Alice Dennis alice.dennis@unamur.be, Lars Gabriel lars.gabriel@uni-greifswald.de, Henrik Lanz henrik.lantz@scilifelab.se, Fergal Martin fergal@ebi.ac.uk No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Opposed reviewers - Suggest up to 5 people not to invite as reviewers. (Optional)

e.g. John Doe [john@doe.com]

Submission date

2023-12-04 14:49:17

Recommender

Jitendra Narayan

Reviewers

Henrik Lanz, Rui Borges, Fergal Martin, Vinod Scaria, Mihai Pop, Alice Dennis, Jin-Wu Nam, Monya Baker, Giuseppe Narzisi

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