Nov 5, 2018

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 RellstabFelix 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 p...Continue Reading

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Mentioned in this Paper

Study
Size
Autoimmune Lymphoproliferative Syndrome
Pinus sibirica
Genome
Bio-Informatics
Whole Exome Sequencing
Equilibrium
Genomics
Sequencing

About this Paper

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