Whole-genome sequencing of multiple Arabidopsis thaliana populations

Abstract

The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations

Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines

“…The amount of sequence variation among the five sequenced MA lines is roughly three orders of magnitude less than among 80 sequenced natural accessions when focused solely on the private mutations (21 mutations versus 22,000 private alleles) (Cao et al., 2011; Ossowski et al., 2010). Thus, the mutations in our study scale up to express heritable phenotypic variation about 40‐fold more than expected based on sequence differences alone (as above, phenotypic differences between accessions are about 25 times greater among accessions than MA lines).…”

Life at the extreme: lessons from the genome

“…With respect to individual genes, the result is termed copy number variation (CNV). From resequencing the genomes of 80 individual Arabidopsis ecotypes, it seems that natural selection has led to CNVs covering 2.2 Mb of the reference genome [30]. CNVs can also arise in a short time.…”

Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana

“…7c). This geographical pattern appears to be determined at least in part by A. thaliana demographic history, as Kas-1 haplogroup distribution overlaps markedly with the Asiandominant genetic group detected by genome-wide neutral singlenucleotide polymorphism 29 .…”

“…The first 24 amino acids of AtARQ1 were not included in these analyses, as they contain the two compensatory indel and have a higher sequencing error rate 29 .…”