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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #366256
Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: Pseudo-chromosome length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.)

Author
item LINSMITH, GARETH - Flanders Institute Of Biotechnology (VIB)
item ROMBAUTS, STEPHANE - Flanders Institute Of Biotechnology (VIB)
item MONATANARI, SARA - University Of California, Davis
item DENG, CECILIA - New Zealand Institute Of Plant & Food Research
item CELTON, JEAN-MARC - Institut National De La Recherche Agronomique (INRA)
item GUERIF, PHILIPPE - Institut National De La Recherche Agronomique (INRA)
item LIU, CHANG - University Of Tubingen
item LOHAUS, ROLF - Flanders Institute Of Biotechnology (VIB)
item Zurn, Jason
item CESTARO, ALESSANDRO - Fondazione Edmund Mach
item Bassil, Nahla
item BAKKER, LINDA - Wageningen University
item SCHIJLEN, ELIO - Wageningen University
item GARDINER, SUSAN - New Zealand Institute Of Plant & Food Research
item LESPINASSE, YVES - Institut National De La Recherche Agronomique (INRA)
item DUREL, CHARLES-ERIC - Institut National De La Recherche Agronomique (INRA)
item VELASCO, RICCARDO - Crea
item NEALE, DAVID - University Of California, Davis
item CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research
item VAN DE PEER, YVES - Flanders Institute Of Biotechnology (VIB)
item TROGGIO, MICHELA - Fondazione Edmund Mach
item BIANCO, LUCA - Fondazione Edmund Mach

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2019
Publication Date: 12/9/2019
Citation: Linsmith, G., Rombauts, S., Monatanari, S., Deng, C., Celton, J., Guerif, P., Liu, C., Lohaus, R., Zurn, J.D., Cestaro, A., Bassil, N.V., Bakker, L.V., Schijlen, E., Gardiner, S.E., Lespinasse, Y., Durel, C., Velasco, R., Neale, D.B., Chagne, D., Van De Peer, Y., Troggio, M., Bianco, L. 2019. Pseudo-chromosome length genome assembly of a double haploid 'Bartlett' pear (Pyrus communis L.). Gigascience. 8(12):138. https://doi.org/10.1093/gigascience/giz138.
DOI: https://doi.org/10.1093/gigascience/giz138

Interpretive Summary: In this study, we report an improved assembly of the European pear genome obtained using a combination of new techniques. These techniques allowed us to assemble the DNA sequences into the 17 chromosomes of the pear genome. About 50% of the genome consists of repetitive sequences. Comparison with previous assemblies of the European pear and the Asian pear confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

Technical Abstract: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.