SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)
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Abstract
Background
The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica).
Findings
As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp.
Conclusions
This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Now published in GigaScience doi: 10.1093/gigascience/giy142
Giulio Formenti 1Department of Environmental Science and Policy, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Giulio FormentiFor correspondence: giulio.formenti@unimi.itMatteo Chiara 2Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matteo ChiaraFor correspondence: matteo.chiara@unimi.itLucy Poveda 3Functional Genomics Center of Zurich, University of Zurich, (Zurich, Switzerland) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucy PovedaFor correspondence: lucy.poveda@fgcz.uzh.chKees-Jan …
Now published in GigaScience doi: 10.1093/gigascience/giy142
Giulio Formenti 1Department of Environmental Science and Policy, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Giulio FormentiFor correspondence: giulio.formenti@unimi.itMatteo Chiara 2Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matteo ChiaraFor correspondence: matteo.chiara@unimi.itLucy Poveda 3Functional Genomics Center of Zurich, University of Zurich, (Zurich, Switzerland) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lucy PovedaFor correspondence: lucy.poveda@fgcz.uzh.chKees-Jan Francoijs 4Bionano Genomics (San Diego, CA, USA) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kees-Jan FrancoijsFor correspondence: kfrancoijs@bionanogenomics.comAndrea Bonisoli-Alquati 5Department of Biological Sciences, California State Polytechnic University, Pomona (Pomona, CA, USA) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Andrea Bonisoli-AlquatiFor correspondence: kfrancoijs@bionanogenomics.comLuca Canova 6Department of Biochemistry, University of Pavia (Pavia, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca CanovaFor correspondence: canova@unipv.itLuca Gianfranceschi 7Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca GianfranceschiFor correspondence: luca.gianfranceschi@unimi.itDavid Stephen Horner 8Department of Biosciences, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David Stephen HornerFor correspondence: david.horner@unimi.itNicola Saino 9Department of Environmental Science and Policy, University of Milan (Milan, Italy) Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Nicola SainoFor correspondence: nicola.saino@unimi.it
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy142 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101444 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101445
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