High quality genome assembly of the brown hare (*Lepus europaeus*) with chromosome-level scaffoldinguse asterix (*) to get italics

Craig Michell, Joanna Collins, Pia K. Laine, Zsofia Fekete, Riikka Tapanainen, Jonathan M. D. Wood, Steffi Goffart, Jaakko L. O. PohjoismakiPlease 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"

2024

<p style="text-align: justify;">We present here a high-quality genome assembly of the brown hare (Lepus europaeus Pallas), based on a fibroblast cell line of a male specimen from Liperi, Eastern Finland. This brown hare genome represents the first Finnish contribution to the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity.<br>The genome was assembled using 25X PacBio HiFi sequencing data and scaffolded utilizing a Hi-C chromosome structure capture approach. After manual curation, the assembled genome length was 2,930,972,003 bp with N50 scaffold of 125.8 Mb. 93.16% of the assembly could be assigned to 25 identified chromosomes (23 autosomes plus X and Y), matching the published karyotype. The chromosomes were numbered according to size. The genome has a high degree of completeness based on the BUSCO score (mammalia_odb10 database), Complete: 96.1% [Single copy: 93.1%, Duplicated: 3.0%], Fragmented 0.8%, and Missing 2.9%. The mitochondrial genome of the cell line was sequenced and assembled separately.<br>The brown hare genome is particularly interesting as this species readily hybridizes with the mountain hare (Lepus timidus L.) at the species contact zone in northern Eurasia, producing fertile offspring and resulting in gene flow between the two species. In addition to providing a useful comparison for population studies, the genome can offer insight into the chromosomal evolution among Glires in general and Lagomorpha in particular. The chromosomal assembly of the genome also demonstrates that the cell line has not acquired karyotypic changes during culture.&nbsp;</p>

https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_029958975.1/You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Lagomorpha, reference genome, chromosome structure, phylogeny, fibroblast cell line

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ERGA Pilot, Vertebrates

Sylke Winkler suggested: Dear Ed, apologies for declining - I simply won't manage due to time constrains until the end of November. , Sylke Winkler suggested: Best regards, , Sylke Winkler suggested: sylke, Sylke Winkler suggested: an alternative reviewer: Michael Hiller (michael.hiller@senckenberg.de) 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

2023-10-16 20:46:39

Ed Hollox