RT Journal Article
SR Electronic
T1 SMRT long-read sequencing and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (<em>Hirundo rustica rustica</em>)
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 374512
DO 10.1101/374512
A1 Giulio Formenti
A1 Matteo Chiara
A1 Lucy Poveda
A1 Kees-Jan Francoijs
A1 Andrea Bonisoli-Alquati
A1 Luca Canova
A1 Luca Gianfranceschi
A1 David Stephen Horner
A1 Nicola Saino
YR 2018
UL http://biorxiv.org/content/early/2018/07/23/374512.abstract
AB Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a high-quality genome for the European subspecies (Hirundo rustica rustica).Findings We have assembled a highly contiguous genome sequence using Single Molecule Real-Time (SMRT) DNA sequencing and Bionano optical maps. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from Direct Label and Stain technologies. For our SMRT-only assembly, the direct labelling system more than doubled the assembly N50 with respect to the nickase system. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with an N50 value of over 25.95 Mbp, representing an improvement in N50 of over 650 fold with respect to a previously reported assembly based on paired-end short read data.Conclusions This high-quality genome assembly represents a valuable resource for further studies of population genetics of the barn swallow and for studies concerning the evolution of avian genomes. It also represents the first genome assembled combining SMRT sequencing with the new Bionano Direct Label and Stain technology for scaffolding, highlighting the potential of this methodology to contribute to substantial increases in the contiguity of genome assemblies.DLSDirect Label and StainHMWHigh Molecular WeightHSHybrid ScaffoldNGSNext Generation SequencingNLRSNick, Label, Repair and StainN50the shortest sequence length at 50% of the genomeN90the shortest sequence length at 90% of the genomePFGEPulsed Field Gel ElectrophoresisQVQuality ValueSGSSecond Generation SequencingSMRTSingle Molecule Real-TimeTGSThird Generation SequencingVGPVertebrate Genomes Project