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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3606-9) contains supplementary material, which is available to authorized users.

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Apple scab, caused by the ascomycete Venturia inaequalis, is the most damaging fungal disease of commercial apple orchards. Functional scab resistance genes are present in some wild Malus species. The HcrVf2 gene, derived from the Vf-region of the wild apple Malus floribunda 821 and encoding a receptor-like protein, has proved to confer scab resistance in a transgenic susceptible cultivar. In order to minimize nonplant DNA in genetically modified apple and to go a step toward the development of cisgenic apples, we have studied the capability of the HcrVf2 gene to confer apple scab resistance when it is controlled by its own promoter. Three promoter deletion constructs containing 115, 288, and 779 bp of the 5′ untranslated region and the HcrVf2 gene were used to transform the scab susceptible apple cvs. 'Gala' and 'Elstar.' The influence of the promoter length on both the HcrVf2 expression level and the response to V. inaequalis was analyzed in different transgenic lines. Promoter length was found to influence both the constitutive transcription levels of HcrVf2 in transgenic lines and the resistance level. Highly scab resistant 'Elstar' and 'Gala' plants were obtained, proving that the HcrVf2 gene controlled by its native promoter is effective in conferring resistance to V. inaequalis similarly as Vf introgressed in apple cvs. through classical breeding.