SRP005499 PRJNA132409 GSE24569 Homology-guided Assembly of the Genomes of the Four Diverse Accessions Ler, C24, Bur-0 and Kro-0 Here we present the first whole-genome assemblies of Arabidopsis thaliana strains since the release of the 125 Mb reference genome sequence a decade ago. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Overall design: A. thaliana Col-0, Bur-0 & C24 small RNA-seq data, 2 biological replicates each GSE24569 pubmed 21252301