ArticleBMC genomics2017
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 194 papers, 2 of them syntheses that pooled it.
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194 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genome-wide identification and expression analysis of peach multiple organellar RNA editing factors reveals the roles of RNA editing in plant immunity.BMC plant biology · 2022Pooled it
- Meta-analysis of RNA-Seq studies reveals genes with dominant functions during flower bud endo- to eco-dormancy transition in Prunus species.Scientific reports · 2021Pooled it
- PpAPRR2 regulates chlorophyll biosynthesis and chloroplast development during early fruit development in peach.Plant cell reports · 2026Article
- Regulatory structural variations upstream of a NAC transcription factor control fruit maturity timing in peach.Journal of experimental botany · 2026Article
- Dual regulation of anthocyanins and proanthocyanidins by PpBL and its linkage to acidity in peach.Molecular horticulture · 2026Article
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genetic dissection of apricot fruit skin color (Molecular breeding : new strategies in plant improvement · 2026Article
- Comparative transcriptomics among peach, almond and their interspecific F1 hybrid reveal key common and species-specific regulatory pathways involved in fruit development.BMC plant biology · 2026Article
- Improved genome assembly of double haploid Prunus persica siblings 'Lovell 2D' and 'Lovell 5D' and the peach NLRome.Scientific reports · 2026Article
- Chromosome-scale reference genome assembly and annotation of Prunus scopulorum.Scientific data · 2026Article
- Multi-Season Genome-Wide Association Study Reveals Loci and Candidate Genes for Fruit Quality and Maturity Traits in Peach.Plants (Basel, Switzerland) · 2026Article
- Identification of phenological QTLs using a combination of high- and low-coverage whole genome sequencing in Japanese plum (Horticulture research · 2026Article
- FT-like genes in Cannabis and hops: sex specific expression and copy-number variation may explain flowering time variation.BMC genomics · 2025Article
- Comparative genomic analyses reveal different genetic basis of two types of fruit in Maloideae.Nature communications · 2025Article
- Genetic architecture of key traits forHorticulture research · 2025Article
- PeachMD: a multi-omics database for peach.Molecular horticulture · 2025Article
- Integrating whole-genome resequencing and machine learning to refine QTL analysis for fruit quality traits in peach.Horticulture research · 2025Article
- Multi-environment GWAS uncovers markers associated to biotic stress response and genotype-by-environment interactions in stone fruit trees.Horticulture research · 2025Article
- The PeachSNP170K array facilitates insights into a large-scale population relatedness and genetic impacts on citrate content and flowering time.Communications biology · 2025Article
- Transcriptomic analysis of peaches and nectarines reveals alternative mechanism for trichome formation.BMC plant biology · 2025Article
134 more citing papers are in PubMed but not listed here.
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17 authors.
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Abstract
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.
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