DOI: 10.5061/dryad.4bb5849
title: Data from: Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra

description: Despite decreasing sequencing costs, whole-genome sequencing for
 population-based genome scans for selection is still prohibitively
 expensive for organisms with large genomes. Moreover, the repetitive
 nature of large genomes often represents a challenge in bioinformatic and
 downstream analyses. Here we use in-depth transcriptome sequencing to
 design probes for exome capture in Swiss stone pine (Pinus cembra), a
 conifer with an estimated genome size of 29.3 Gbp and no reference genome
 available. We successfully applied around 55,000 self-designed probes,
 targeting 25,000 contigs, to DNA pools of seven populations from the Swiss
 Alps and identified &gt; 140,000 SNPs in around 13,000 contigs. The
 probes performed equally well in pools of the closely related species
 Pinus sibirica; in both species, more than 70% of the targeted contigs
 were sequenced at a depth ≥ 40x (number of haplotypes in the pool).
 However, a thorough analysis of individually sequenced P. cembra samples
 indicated that a majority of the contigs (63%) represented multi-copy
 genes. We therefore removed paralogous contigs based on heterozygote
 excess and deviation from allele balance. Without putatively paralogous
 contigs, allele frequencies of population pools represented accurate
 estimates of individually determined allele frequencies. We show that
 inferences of neutral and adaptive genetic variation may be biased when
 not accounting for such multi-copy genes. Without individual genotype
 data, it would have been nearly impossible to recognize and deal with the
 problem of multi-copy contigs. We advocate putting more emphasis on
 identifying paralogous loci, which will be facilitated by the
 establishment of additional high-quality reference genomes.
description: Probe
 sequencesSequences of the 54,870
 probes used in the exome capture. The probe name consists of the sequence
 number (subseq, alt1 and al2 refer to the second (alternative) approach
 used for probe design), contig name, the probes base region (start and
 stop position within the contig, 150bp), and the number of the tiled probe
 of the probe base.probe_sequences.fastaAllele frequencies of the seven populationsAlternative allele frequencies of the 13,228 SNPs in the seven population pools.allele_frequencies_7_populations.xlsxContigs attributed by HDplotList of the 10,675 contigs that could be attributed to either single-copy or multi-copy contigs using HDplot in the individually sequenced populations EC-HJ and WC-HJ.contigs_HDplot_filtering.xlsxPopulation informationEnvironmental information of the seven studied populations.population_information.xlsxRNA-Seq readcountsRaw read counts of the transcripts (length is also given) in the different libraries of the RNA-Seq. A = Adult, J = Juvenile, S = Seedling, Number = Replicate, C = Control treatment, F = Frost treatment, D = Drought treatment.RNAseq_readcounts.xlsxTranscriptome annotationFunctional annotation of the 34,010 transcripts of the transcriptome that could be annotated. Given is the putative gene name and GO-term ID, type, and description.transcriptome_annotation.xlsxTranscriptome assemblySequences of the 40,468 contigs of the assembled transcriptome.transcriptome_assembly.fasta