Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank)

Tsangaras Kyriakos, Wales Nathan, Sicheritz-Pontén Thomas, Rasmussen Simon, Michaux Johan, Ishida Yasuko, Morand Serge, Kampmann Marie-Louise, Gilbert M. Thomas P., Greenwood Alex. 2014. Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank). PloS One, 9 (10):e109101, 10 p.

Url - jeu de données - Entrepôt autre : http://www.ncbi.nlm.nih.gov/nuccore/KJ530551 / Url - jeu de données - Entrepôt autre : http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP040713 / Url - jeu de données - Entrepôt autre : http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP041271

Quartile : Q1, Sujet : MULTIDISCIPLINARY SCIENCES

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Note générale : Jeux de données enregistrés dans la base GenBank du numéro d'accès KJ530551 au KJ530565.

Résumé : Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.

Classification Agris : U30 - Méthodes de recherche
L72 - Organismes nuisibles des animaux

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

• Tsangaras Kyriakos, Leibniz IZW (DEU)
• Wales Nathan, Natural History Museum (DNK)
• Sicheritz-Pontén Thomas, Technical University of Denmark (DNK)
• Rasmussen Simon, Technical University of Denmark (DNK)
• Michaux Johan, CIRAD-ES-UPR AGIRs (FRA)
• Ishida Yasuko, University of Illinois (USA)
• Morand Serge, CIRAD-ES-UPR AGIRs (LAO) ORCID: 0000-0003-3986-7659
• Kampmann Marie-Louise, Leibniz IZW (DEU)
• Gilbert M. Thomas P., Technical University of Denmark (DNK)
• Greenwood Alex, Leibniz IZW (DEU)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/578501/)

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