DOI: 10.1101/462630Nov 5, 2018Paper

Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra

BioRxiv : the Preprint Server for Biology
Christian RellstabF. Gugerli


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 > 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, i.e. the 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...Continue Reading

Methods Mentioned

Illumina sequencing
exome capture
site-associated sequencing

Software Mentioned

R package POLYSAT
R package VEGAN
R Development Core Team

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