The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

BMC Genomics

Research Article

Sabrina Micali¹  Ignazio Verde¹  Valeria Aramini¹  Maria Teresa Dettori¹  Elisa Vendramin¹  Laura Gazza²  Luca Dondini³  Giulia Pagliarani³  Stefano Tartarini³  Roberta Paris⁴  Daniele Bassi⁵  Laura Rossini⁶  Jane Grimwood⁷  Jerry Jenkins⁷  Jeremy Schmutz⁸  Michela Troggio⁹  Shengqiang Shu^1,10 

[1] Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Centro di Ricerca per la Frutticoltura, 00134, Rome, Italy;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;Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy;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;Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy;Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy;Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy;HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA;HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA;U.S. Department of Energy, Joint Genome Institute, 94598, Walnut Creek, CA, USA;Research and Innovation Centre, Fondazione Edmund Mach (FEM), 38010, San Michele all’Adige, TN, Italy;U.S. Department of Energy, Joint Genome Institute, 94598, Walnut Creek, CA, USA;

关键词: Prunus persica;    WGS assembly;    SNPs;    SSRs;    Linkage mapping;    NGS resequencing;    Gap patching;    Recombination rates;    Centromeric regions;   

DOI  :  10.1186/s12864-017-3606-9

 received in 2016-10-25, accepted in 2017-03-03,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsFour 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%.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017