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.
Highlights
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
A weakness of the WGS sequencing approach is it tends to produce a more fragmented assembly with reduced contiguity, coupled with the risk of largescale misassemblies. This is especially true for complex eukaryotic genomes and the assembly process can be confounded with recent duplication events, large regions of expanded repeats, and residual heterozygosity
We describe the efforts aimed at improving the peach chromosome-scale build (Peach v1.0 [20]) using a set of linkage maps and resequencing the reference accession (‘Lovell’ double haploid)
Summary
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. A weakness of the WGS sequencing approach is it tends to produce a more fragmented assembly with reduced contiguity, coupled with the risk of largescale misassemblies This is especially true for complex eukaryotic genomes and the assembly process can be confounded with recent duplication events (either segmental or Whole Genome Duplication, WGD), large regions of expanded repeats (up to 85% of the genome in species such as corn and wheat [8, 9]), and residual heterozygosity. Inconsistencies between the position of markers on the map and in the assembly can highlight putative misassembled sequences that can be further resolved by breaking the chimeric scaffolds and rearranging the broken pieces in their correct order and orientation Fragmented genome assemblies, such as those obtained with short reads NGS data, need dense genetic maps for a large fraction of the assembled sequence to be anchored on chromosomes
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