Data from: Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst)

Heer, Katrin, Philipp University of Marburg

Ullrich, Kristian Karsten

Liepelt, Sascha, Philipp University of Marburg

Rensing, Stefan Andreas

Zhou, Jiabin, Philipp University of Marburg

Ziegenhagen, Birgit, Philipp University of Marburg

Opgenoorth, Lars, Philipp University of Marburg

Publication date: January 26, 2017

Publisher: Dryad

https://doi.org/10.5061/dryad.f3r35

Citation

Heer, Katrin et al. (2017), Data from: Detection of SNPs based on transcriptome sequencing in Norway spruce (Picea abies (L.) Karst), Dryad, Dataset, https://doi.org/10.5061/dryad.f3r35

Abstract

A novel set of SNPs was derived from transcriptome data of ten Norway spruce (Picea abies) trees from the Bavarian Forest National Park in Germany (BaFoNP). SNPs were identified by mapping against a de-novo transcriptome assembly and against pre-mRNAs of predicted genes of the reference genome assembly. This resulted in 111,849 and 366,577 SNPs, respectively. Out of these, 311 were either randomly selected or chosen because of their pronounced divergence between sampling sites and genotyped in 218 trees with an Illumina Infinium HD iSelect BeadChip.

Usage notes

Pabies1.0-all.phase.changed.gff3

gene feature format (gff3) file from Picea abies v1.0 with phase information

cont_plastids_mito_plants_ribosome_dna

chloroplast genomes, mitochondrial genomes and ribosomal DNA sequences for NGS data filtering combined and obtained from NCBI