title: The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.
abstract: The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches.
  
  
  
  Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%.
  
  
  
  The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy. ignazio.verde@crea.gov.it.
authors.forename: Ignazio
authors.identifier: 0000-0002-9139-955X
authors.initials: I
authors.lastname: Verde
authors.affiliation: HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Dondini
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Micali
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Pagliarani
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Vendramin
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.|Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centre of Research for Industrial Crops, 40128, Bologna, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Paris
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
authors.forename: Valeria
authors.initials: V
authors.lastname: Aramini
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.|Present address: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Research Unit for Cereal Quality, Rome, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Gazza
authors.affiliation: Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy.|Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Rossini
authors.affiliation: Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Bassi
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010, San Michele all'Adige, TN, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
authors.affiliation: U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Shengqiang
authors.initials: S
authors.lastname: Shu
authors.affiliation: HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Tartarini
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Dettori
authors.affiliation: HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.|U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D008040:Genetic Linkage; D023281:Genomics / Q000379:methods; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D000068239:Prunus persica / Q000235:genetics*
keywords: Centromeric regions; Gap patching; Linkage mapping; NGS resequencing; Prunus persica; Recombination rates; SNPs; SSRs; WGS assembly