AVAILABLE SNPs FROM PROJECTS / STUDIES
GENOAK : Sequencing of the oak genome and identification of genes that matter for forest tree adaptation
- 31.9 Millions SNPs detected using whole-genome sequence data from pools of individuals of 4 species (Q. robur, Q. petraea, Q. pyrenaica, Q. pubescens) resequenced at 400X coverage.
- 30 Millions SNPs detected using whole-genome sequence data from 18 Q. petraea populations resequenced at >100X coverage.
- Raw sequencing data are available here :
- 4 European white oak species (https://www.biorxiv.org/content/10.1101/246637v2) : PRJEB23847
- 18 sessile oak populations (https://www.biorxiv.org/content/10.1101/584847v1): PRJEB32209
SNP data available at : OAK GENOME SEQUENCING
Single-nucleotide polymorphism discovery and validation in high density SNP array for genetic analysis in European white oaks
An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered for SNP discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) and Roche 454 technology sequences from 5112 contigs (6542 putative in silico SNPs). The 7913 SNPs were genotyped across the six parental individuals, full-sib progenies (one within each species and two interspecific crosses between Q. petraea and Q. robur) and three natural populations from south-western France that included two additional interfertile white oak species (Q. pubescens and Q. pyrenaica).
SNP data available at : doi/10.1111/1755-0998.12407
High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)
Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects
SNP data available at : doi/10.1101/388447v4
