New genome assembly of the barn owl (Tyto alba alba)

Abstract

New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single‐Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.

Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles

“…As the available reference genome for the European Tyto alba was fragmented (Ducrest et al, 2020), a new reference was produced in order to achieve a near chromosome-level assembly. A full description of the process and its detailed results are given in Appendix 2.…”

“…Its assembly with FALCON and FALCON-Unzip resulted in 478 primary contigs partially phased, and 1736 fully phased haplotigs which represented divergent haplotypes. Optical mapping with Bionano produced a final assembly of 70 scaffolds, slightly more than the barn owl's karyotype of 46 chromosomes (Ducrest et al, 2020). The final assembly was 1.25 Gbp long, with an N50 of 36 Mbp and BUSCO score of 96.9% (see Appendix 2 Table 1 for full assembly metrics).…”

“…The final assembly was 1.25 Gbp long, with an N50 of 36 Mbp and BUSCO score of 96.9% (see Appendix 2 Table 1 for full assembly metrics). In comparison, the previous reference assembly (Ducrest et al, 2020) had 21,509 scaffolds, with an N50 of 4.6 Mbp.…”

Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology

“…In the last decade, the number of bird reference genomes has increased dramatically (e.g. Dalloul et al 2010 ; Warren et al 2010 ; Zhang et al 2012 ; Jarvis et al 2014 ; Poelstra et al 2014 ; Frankl-Vilches et al 2015 ; Friis et al 2018 ; Louha et al 2020 ; Peñalba et al 2020 ; Ducrest et al 2020 , Wang et al 2020 ), providing major scientific breakthroughs in phylogenetics ( Alström et al 2018 ; Braun et al 2019 ; Jarvis et al 2015 ), comparative genomics ( Zhang et al 2014 , Feng et al 2020 ), adaptation genomics ( Wirthlin et al 2014 ; Lawson and Petren 2017 ), and genomic architecture ( Poelstra et al 2014 ; Vijay et al 2016 ), among others. Moreover, the Ten-Thousand Bird Genomes (B10K) consortium has generated and analyzed over 300 avian genomes from 92.4% of bird families, providing an unprecedent genomic resource for avian comparative studies ( Zhang et al 2015 , Feng et al 2020 ).…”

Chromosome-level genome assembly of the common chaffinch (Aves: Fringilla coelebs): a valuable resource for evolutionary biology

“…In the last decade, the number of bird reference genomes has increased dramatically (e.g. Dalloul et al 2010;Warren et al 2010;Zhang et al 2012;Jarvis et al 2014;Poelstra et al 2014;Frankl-Vilches et al 2015;Friis et al 2018;Louha et al 2019;Peñalba et al 2019;Ducrest et al 2020, Wang et al 2020, providing major scientific breakthroughs in phylogenetics (e.g., Alström et al 2018;Braun et al 2019;Jarvis et al 2015), comparative genomics (Feng et al 2020), adaptation genomics (Wirthlin et al 2014;Lawson & Petren 2017), and genomic architecture (Poelstra et al 2014;Vijay et al 2016), among others. Moreover, the Ten-Thousand Bird Genomes (B10K) consortium is currently sequencing and assembling over 300 avian genomes that correspond to at least one representative per family (Zhang 2015).…”