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

Abstract

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

BETA
genotyping
RAD-Seq
RNA-Seq
Illumina sequencing
exome capture
site-associated sequencing
restriction

Software Mentioned

BLAST
LFMM
R package POLYSAT
R package VEGAN
perl
R
R Development Core Team
TRIMMOMATIC
HDPLOT
R package VENNDIAGRAM

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