Additional file 1: TableS1. of The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

SSR markers developed in this study from Peach v1.0. For each primer, the locus name, primer sequences, position in Peach v1.0 and v2.0, repeated motif, polymorphism in TxE (monomorphic, BIN or fully mapped) and location in genic or intergenic regions are reported. Table S2. SNP markers developed in this study from the resequencing of the CxA F1 parent. For each primer, the locus name, position in Peach v1.0 and v2.0, primer sequences, BIN position and location in genic or intergenic regions are reported. Table S3. Illumina short reads libraries. All libraries were sequenced as 2x250s using Illumina sequencing. Reads were filtered on quality, screening for reads that were predominantly simple sequence, and residual phix contamination. Table S4. TxE linkage map. For each locus, the genetic position in linkage groups and physical position in Peach v2.0 are reported. Only integrated markers are reported. Table S5. Sequenom SNP development and their efficiency with the SNP calling parameters used in this study. A posteriori efficiency was calculated using more stringent parameters as in Verde et al. 2013. Table S6. CxA linkage map. For each locus, the genetic position in linkage groups and physical position in Peach v2.0 are reported. Table S7. PxF linkage map. For each locus, the genetic position in linkage groups and physical position in Peach v2.0 are reported. Table S8. Linkage map of PxF F1 parent. For each locus, the genetic position in linkage groups and physical position in Peach v2.0 are reported. Table S9. Linkage map of PxF recurrent parent (IF7310828). For each locus, the genetic position in linkage groups and physical position in Peach v2.0 are reported. Table S10. Composition of the 8 Peach v2.0 pseudomolecules. Start and end of each scaffold, total scaffold length, scaffold denomination in v2.0 and in v1.0, v1.0 position of each v2.0 scaffold, length of the scaffold ends uncovered with markers and mapping and orientation information achieved with the linkage maps used in this study, are reported. Table S11. Linkage map of LG6 of MDxSD. For each locus, the genetic position (cM) in linkage groups and physical position in Peach v2.0 are reported. Table S12. Peach v2.0 assembly statistics (N/L) prior to the pseudomolecules build. Table S13. Peach v2.0 assembly statistics post chromosome-scale build. (XLSX 391Â kb)