Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

  1. Gareth Linsmith
  2. Stephane Rombauts
  3. Sara Montanari
  4. Cecilia H. Deng
  5. Jean-Marc Celton
  6. Philippe Guérif
  7. Chang Liu
  8. Rolf Lohaus
  9. Jason D. Zurn
  10. Alessandro Cestaro
  11. Nahla V. Bassil
  12. Linda V. Bakker
  13. Elio Schijlen
  14. Susan E. Gardiner
  15. Yves Lespinasse
  16. Charles-Eric Durel
  17. Riccardo Velasco
  18. David B. Neale
  19. David Chagné
  20. Yves Van de Peer
  21. Michela Troggio
  22. Luca Bianco
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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.

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