DOI: 10.5061/dryad.qjq2bvqs3
title: Chromosome-Level genome assembly and transcriptome analysis of the ural owl, Strix uralensis Pallas, 1771

description: The Ural owl (Strix uralensis) is a large member of the Strigidae family
 and inhabits Eurasian forests ranging from Germany to Japan. However, it
 faces increased range reduction, particularly at its southwestern
 distribution edges. Despite being considered ‘Least Concern’ by the IUCN,
 local populations have become threatened in Central Europe due to severe
 habitat loss. Reintroduction programs aim to restore these populations by
 closing distribution gaps and facilitating natural recolonization of
 suitable habitats. To support these efforts, genomic resources have become
 an established tool to assess genetic diversity, geographic structure, and
 potential inbreeding, crucial for maintaining the genetic health and
 adaptability of newly established populations. Here, we present a de novo
 genome assembly and transcriptome of the Ural owl based on ONT long-reads,
 Omni-C Illumina short-reads, and RNASeq data. The final assembly has a
 total length of 1.26 Gb, of which 96.42% is anchored into the 42 largest
 scaffolds. The scaffold and contig N50 values of 88.65 Mb and 21.74 Mb,
 respectively, a BUSCO/compleasm completeness of 97.5%/99.65% and k-mer
 completeness of 95.18%, emphasize the high quality of this assembly.
 Furthermore, annotation of the assembly identified 17,650 genes and a
 repeat content of 12.48%. This new highly contiguous and chromosome-level
 assembly will greatly benefit Ural owl conservation management by
 informing reintroduction programs about the species’ genetic health and
 contributing a valuable resource to study genetic function in greater
 detail across the whole Strigidae family.
description: # Chromosome-level genome assembly and transcriptome analysis of the Ural
 owl, *Strix uralensis* PALLAS, 1771 Dataset DOI:
 [10.5061/dryad.qjq2bvqs3](10.5061/dryad.qjq2bvqs3) ## Description of the
 data and file structure Assembly: We assembled a high-quality reference
 genome and transcriptome for the Ural owl (*Strix uralensis*) from a
 female bird found dead in the municipality of Kuhmo near Lentiira,
 Finland. The assembly was generated from three Oxford Nanopore long-read
 libraries sequenced on either the MinION Mk1c or PromethION 2Solo. The
 resulting data was assembled with Flye v. 2.9.3, including one iteration
 of long-read polishing. Subsequently, the contigs of the polished assembly
 were anchored into chromosome-scale scaffolds with YaHS v.1.1 using
 Dovetail Omni-C data generated from the same individual, and prepared
 following the Arima Hi-C mapping pipeline
 ([https://github.com/VGP/vgp-assembly/blob/master/pipeline/salsa/arima_mapping_pipeline.sh](https://github.com/VGP/vgp-assembly/blob/master/pipeline/salsa/arima_mapping_pipeline.sh)). One iterations of gap-closing was performed with TGS-GapCloser v. 1.1.1 using the initial ONT reads. To further improve the assembly we performed a second round of both scaffolding and gap-closing. Annotation: Repeat Annotation Repeats in the genome assembly were masked in a three-step process. First, we masked known repeats for birds (‘-species aves’) based on the Repbase (release 20181026) (Bao et al., 2015) and Dfam (release 3.1-rb20181026) (Storer et al., 2021) databases with RepeatMasker v.4.1.0 (Smit et al., 2015a). Next, we identified the remaining repeats in the assembly de novo using RepeatModeler v.2.0.1 (Smit et al., 2015b). The resulting de novo repeat library was used in a second iteration of repeat masking to mask the remaining repeats in the assembly. Gene annotation Genes in the masked assembly were predicted based on homology with GeMoMa v.1.9 (Keilwagen et al., 2018) using the following eight annotated assemblies as evidence: Chicken (Gallus gallus) GCF_016699485.2, Japanese quail (Coturnix japonica) GCF_001577835.2, Burrowing owl (Athene cunicularia) GCF_003259725.1 (Mueller et al., 2018), Common barn owl (Tyto alba) GCF_018691265.1 (Cumer et al., 2022), Speckled mousebird (Colius striatus) GCF_028858725.1, California Condor (Gymnogypus californianus) GCF_018139145.2 (Robinson et al., 2021), Red-fronted tinkerbird (Pogoniulus pusillus) GCF_015220805.1, Downy woodpecker (Dryobates pubescens) GCF_014839835.1. In addition, the corrected and trimmed RNAseq data of the five different tissues were mapped against the masked reference with STAR v.2.7.9a (Dobin et al., 2013) and used as extrinsic evidence during the annotation. We functionally annotated the predicted proteins using InterProScan v.5.64.96 and a BLASTP v.2.15.0 search against the Swiss-Prot database (release 2024-04). For more details on assembly quality assessment please read the original manuscript, and the included list of commands in this dataset. ### Files and variables #### File: S3B\_Suralensis\_v1.3.3.fasta.tbl **Description:** RepeatMasker repeat table for the fully hard-masked assembly #### File: S3B\_Suralensis\_v1.3.3.fasta.out.gff **Description:** RepeatMasker repeat annotation in gff for the fully hard-masked assembly #### File: S3B\_Suralensis\_v1.3.3.fasta.out **Description:** RepeatMasker output for the fully hard-masked assembly #### File: S3B\_Suralensis\_v1.3.3.fasta **Description:** final *Strix uralensis* assembly (same as available under NCBI BioProject PRJNA1140424)  #### File: final\_annotation.gff\_summary **Description:** Summary of GeMoMa gene prediction results #### File: S3B\_Suralensis\_v1.3.3\_GeMoMa\_proteins.fun.fasta **Description:** protein sequences of predicted proteins with functional annotation results in fasta format #### File: S3B\_v1.3.3\_GeMoMa\_CDS.fun.fasta **Description:** Coding sequences of predicted and functionally annotated proteins #### File: S3B\_Suralensis\_v1.3.3\_GeMoMa\_all.fun.gff **Description:** GeMoMa annotation with functional annotation by InterProScan and Swiss-Prot in gff format #### File: S3B\_Suralensis\_transcriptome\_ncbi\_final3.fasta **Description:** final transcriptome assembly (same as available under NCBI BioProject PRJNA1140424)  #### File: Suralensis\_assembly\_commands.txt **Description:** detailed list of bioinformatics commands used to generate the assemblies and accompanying analyses #### File: uralowl\_masked\_db-families.fa **Description:** de novo repeat library generated by RepeatModeler #### File: functional\_annotation\_results.txt **Description:** Summary of the functional annotation results #### File: S3B\_Suralensis\_v1.3.3.fasta.masked.masked.fasta **Description:** genome assembly with hard-masked repeats ## Access information Other publicly accessible locations of the data: * The underlying raw data and the two assemblies (genome and transcriptome) can also be found under NCBI GenBank BioProject PRJNA1140424