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

Publication Overview
TitleThe Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
AuthorsVerde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J
TypeJournal Article
Journal NameBMC genomics
Volume18
Issue1
Year2017
Page(s)225
CitationVerde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC genomics. 2017 Mar 11; 18(1):225.

Abstract

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.

Features
This publication contains information about 533 features:
Feature NameUniquenameType
DCAS1_1088574DCAS1_1088574genetic_marker
DCAS1_12251759DCAS1_12251759genetic_marker
DCAS1_1520277DCAS1_1520277genetic_marker
DCAS1_16202261DCAS1_16202261genetic_marker
DCAS1_17800568DCAS1_17800568genetic_marker
DCAS1_18511715DCAS1_18511715genetic_marker
DCAS1_21445863DCAS1_21445863genetic_marker
DCAS1_23841301DCAS1_23841301genetic_marker
DCAS1_2546779DCAS1_2546779genetic_marker
DCAS1_32513219DCAS1_32513219genetic_marker
DCAS1_33489785DCAS1_33489785genetic_marker
DCAS1_35422376DCAS1_35422376genetic_marker
DCAS1_36528021DCAS1_36528021genetic_marker
DCAS1_37248927DCAS1_37248927genetic_marker
DCAS1_39573544DCAS1_39573544genetic_marker
DCAS1_41822497DCAS1_41822497genetic_marker
DCAS1_42772641DCAS1_42772641genetic_marker
DCAS1_44849381DCAS1_44849381genetic_marker
DCAS1_46853702DCAS1_46853702genetic_marker
DCAS1_4951731DCAS1_4951731genetic_marker
DCAS1_5748455DCAS1_5748455genetic_marker
DCAS1_9614192DCAS1_9614192genetic_marker
DCAS10_435830DCAS10_435830genetic_marker
DCAS10_63954DCAS10_63954genetic_marker
DCAS10_742540DCAS10_742540genetic_marker

Pages

Featuremaps
This publication contains information about 6 maps:
Map Name
Prunus-TxE-peachV2.0
Peach-CA-BC1-2017
Peach-PF-BC1-2017
Peach-PF-F1-2017
Peach-PF-Recurrent-2017
Prunus-MDxSD-2017
Stocks
This publication contains information about 4 stocks:
Stock NameUniquenameType
Texas_x_Earligold-F2Texas_x_Earligold-F2population
IF7310828_x_Ferganensis-BC1IF7310828_x_Ferganensis-BC1population
Contender_x _Ambra-F2Contender_x _Ambra-F2population
Maria Dolce_x_SD81-F1Maria Dolce_x_SD81-F1population