DOI: 10.5061/dryad.3xsj3txth
title: Data from: A prelude to conservation genomics: First chromosome-level genome assembly of a flying squirrel (Pteromyini: Pteromys volans)

description: The Siberian flying squirrel (Pteromys volans) represents the only
 European Pteromyini species. Thus, it is biogeographically unique due to
 its specialised anatomy and biology as a volant rodent. As a result of
 habitat fragmentation and destruction, Siberian flying squirrels
 experience severe and ongoing population declines throughout most of their
 distribution. While considered Least Concern throughout their immense
 Eurasian distribution, this species is red-listed as Vulnerable and even
 Critically Endangered in parts of its range. More knowledge about the
 population structure and overall biology is needed to improve conservation
 efforts for this umbrella and flagship species of old-growth boreal
 forests. Here, we present the first chromosome-level genome assembly of
 any Pteromyini, represented by P. volans (Uoulu_pteVol_1.0). The final
 assembly has a total length of 2.85 Gbp in 19 chromosome-scale scaffolds
 with only minor differences in the chromosomal structure compared to other
 Sciuridae. All chromosome-scale scaffolds show indications for telomeres
 at both ends; the N50 value and BUSCO, as well as k-mer completeness
 scores, are high with 157.39 Mbp and 97 – 99 %, respectively, indicating
 chromosome-level quality of the assembly. Based on whole-genome data from
 17 rodent species, P. volans clusters according to known evolutionary
 relationships. Additionally, we present a new 16,511 bp long mitogenome
 unveiling differences from known conspecific mitogenomes. We propose the
 utility of the new reference genome for further research and development
 of conservation-applied genetic methods.
description: # Data from: A prelude to conservation genomics: First chromosome-level
 genome assembly of a flying squirrel (Pteromyini: Pteromys volans) Dataset
 DOI: [10.5061/dryad.3xsj3txth](10.5061/dryad.3xsj3txth) ## Description of
 the data and file structure The presented data is related to the
 publication by Wehrenberg et al.: "A Prelude to Conservation
 Genomics: First Chromosome-Level Genome Assembly of a Flying Squirrel
 (Pteromyini: *Pteromys volans*)" available as a preprint at
 biorxiv.org (DOI:
 [https://doi.org/10.1101/2025.03.20.644356](https://doi.org/10.1101/2025.03.20.644356)). Any questions regarding this dataset or the publication can be addressed to the corresponding authors, Gerrit Wehrenberg ([gerrit.wehrenberg@oulu.fi](mailto:gerrit.wehrenberg@oulu.fi)) and Stefan Prost ([stefan.prost@oulu.fi](mailto:stefan.prost@oulu.fi)). ### Files and variables #### File: Pteromys_volans_PV54_hardmasked_genome_assembly.fasta.gz Description: Hard-masked genome assembly of *Pteromys volans volans* #### File: Pteromys_volans_PV54_interproscan_output.tsv.gz Description: Functional annotation results tab-separated values (TSV) output file by *InterProScan* v5.73-104.0 Column description of the T file: Column# 1: Protein Accession Column# 2: Sequence Column# 3: Sequence Length Column# 4: Analysis Column# 5: Signature Accession Column# 6: Signature Description Column# 7: Start Location Column# 8: End Location Column# 9: Score Column# 10: Status Column# 11: Date Column# 12: InterPro Accession Column# 13: InterPro Description Column# 14: GO Terms Column# 15: Pathways #### File: Pteromys_volans_PV54_interproscan_results.txt.gz Description: Functional annotation results TXT output file by *InterProScan* v5.73-104.0 #### File: Pteromys_volans_PV54_diamond_blastp_annotation_swiss-prot.out.gz Description: Functional annotation results output file by *diamond* (blastp mode) v2.1.6 utilising the database ‘Swiss-Prot’ (release: 04-2024; The UniProt Consortium, 2019) Column descriptions of the OUT file: Column# 1: Query ID Column# 2: Subject ID Column# 3: % Identity Column# 4: Alignment length Column# 5: Mismatches Column# 6: Gap opens Column# 7: Query start Column# 8: Query end Column# 9: Subject start Column# 10: Subject end Column# 11: e-value Column# 12: Bit score #### File: Pteromys_volans_PV54_final_annotation.gff.gz Description: GFF3 annotation of genes by *GeMoMa* v.1.9 #### File: Pteromys_volans_PV54_predicted_cds.fasta.gz Description: Nucleotide coding sequences (CDS) by *GeMoMa* v.1.9 #### File: Pteromys_volans_PV54_predicted_proteins.fasta.gz Description: Predicted amino acid sequences (proteins) by *GeMoMa* v.1.9 #### File: Pteromys_volans_PV54_functional_annotated_predicted_cds.fasta.gz Description: Functional annotated nucleotide coding sequences (CDS) #### File: Pteromys_volans_PV54_functional_annotated_predicted_proteins.fasta.gz Description: Functional annotated predicted amino acid sequences (proteins) ## Code/software *RepeatMasker* v4.1.6 (Smit et al., 2023) *GeMoMa* v.1.9 (Keilwagen et al., 2016, 2018) *diamond* (blastp mode) v2.1.6 (Buchfink et al., 2015) *InterProScan* v5.73-104.0 (Quevillon et al., 2005; Jones et al., 2014) *MAKER* v3.01.03 (Cantarel et al., 2008) database: ‘Swiss-Prot’ database (release: 04-2024; The UniProt Consortium, 2019) ## Access information The full chromosome-level genome assembly, the mitochondrial genome assembly and the assigned biosample information are available in BioProject PRJNA1141127. All files provided here were gzipped. **Repeat Annotation:** Hard-masking was executed with *RepeatMasker* v4.1.6 (Smit et al., 2023). **Gene annotation:** Genes in the masked assembly were predicted based on homology with Gene Model Mapper *GeMoMa* v.1.9 (Keilwagen et al., 2016, 2018) using the following publicly available assemblies at NCBI GenBank:* *human (Homo sapiens* Linnaeus, 1758; GCA_000001405.29), *house mouse (*Mus musculus* Linnaeus, 1758; GCA_000001635.9), eastern grey squirrel (*Sciurus carolinensis* Gmelin, 1788; GCA_902686445.2 (Mead et al., 2020a)), thirteen-lined ground squirrel (*Ictidomys tridecemlineatus* (Mitchill, 1821); GCA_016881025.1 (Fu et al., 2021)), Arctic ground squirrel (*Urocitellus parryii* Richardson, 1825; GCA_003426925.1), Alpine marmot (*Marmota marmota marmota* (Linnaeus, 1758); GCA_001458135.2), and groundhog or woodchuck (*Marmota monax *(Linnaeus, 1758); GCA_021218885.2 (Clarke and Bader, 2024)). The busco completeness of the transcript annotation was assessed with *BUSCO* v5.4.7 utilising the lineage dataset *mammalia_odb10*. Functional annotation of the predicted proteins by *GeMoMa* was conducted by *diamond* (blastp mode) v2.1.6 (Buchfink et al., 2015) with an e-value significance cutoff of ≤ 10−6 against the ‘Swiss-Prot’ database (release: 04-2024; The UniProt Consortium, 2019). Furthermore, we annotated gene ontology (GO) terms, domains, and motifs using *InterProScan* v5.73-104.0 (Quevillon et al., 2005; Jones et al., 2014). The gene annotation results were combined utilising modified functional annotation scripts from *MAKER* v3.01.03 (Cantarel et al., 2008; [https://github.com/schellt/maker-functional](https://github.com/schellt/maker-functional)). **References:** Buchfink, B., Xie, C., Huson, D.H., 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60. 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