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

被引：307

作者：

Verde, Ignazio ^{[1
]}

Jenkins, Jerry ^{[2
]}

Dondini, Luca ^{[3
]}

Micali, Sabrina ^{[1
]}

Pagliarani, Giulia ^{[3
]}

Vendramin, Elisa ^{[1
]}

Paris, Roberta ^{[3
,8
]}

Aramini, Valeria ^{[1
]}

Gazza, Laura ^{[1
]}

Rossini, Laura ^{[4
,5
]}

Bassi, Daniele ^{[4
]}

Troggio, Michela ^{[6
]}

Shu, Shengqiang ^{[7
]}

Grimwood, Jane ^{[2
]}

Tartarini, Stefano ^{[3
]}

Dettori, Maria Teresa ^{[1
]}

Schmutz, Jeremy ^{[2
,7
]}

机构：

[1] Ctr Ric Frutticoltura, Consiglio Ric agr analisi econ agraria CREA, Res Unit Cereal Qual, I-00134 Rome, Italy

[2] HudsonAlpha Inst Biotechnol, Huntsville, AL USA

[3] Univ Bologna, Dept Agr Sci DipSA, Bologna, Italy

[4] Univ Milan, Dept Agr & Environm Sci DISAA, Milan, Italy

[5] Parco Tecnol Padano, Via Einstein, I-26900 Lodi, Italy

[6] FEM, Res & Innovat Ctr, I-38010 San Michele All Adige, Italy

[7] Joint Genome Inst, US Dept Energy, Walnut Creek, CA 94598 USA

[8] Ctr Res Ind Crops, Consiglio Ric agr analisi econ agraria CREA, I-40128 Bologna, Italy

来源：

BMC GENOMICS | 2017年 / 18卷

关键词：

Prunus persica; WGS assembly; SNPs; SSRs; Linkage mapping; NGS resequencing; Gap patching; Recombination rates; Centromeric regions; GENOME PROVIDES INSIGHT; PRUNUS-PERSICA; DRAFT GENOME; SSR MARKERS; SEQUENCE; EVOLUTION; MAP; REVEALS; SET; DNA;

D O I：

10.1186/s12864-017-3606-9

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: 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. Results: 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%. Conclusions: 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.

引用

页数：18

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