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Abstract

Much of our knowledge about genome structure and function in Arabidopsis comes from studies with the single reference accession, Col-0. To broadly understand both sequence and functional variation in Arabidopsis, we have Illumina sequenced the genomes of 18 diverse accessions that are the founders of the Multiparent Advanced Generation Inter-Cross (MAGIC) nested association mapping population. Using a combination of read alignment and de novo methods, we assembled the unique to moderately repetitive fraction (~80%) of each accession's genome with an error rate of about 1 nucleotide error per 10kb. From the assemblies, we identified more than 3 million SNPs, and more than 1 million indels that (non-redundantly) alter more than 10% of the reference genome sequence. To inform the genome assemblies, we also produced the seedling transcriptomes of each accession (Illumina RNA-seq), and we are now extending this work to also produce floral bud and root transcriptomes. By combining computational methods with the RNA-seq data, we annotated each of the MAGIC founder genomes, in the process identifying thousands of alternative gene models or new genes not predicted in or absent from the Col-0 genome. In an initial analysis, we have used the DNA sequence and transcriptome data to understand the genetic basis of gene expression variation in unprecedented detail. We identify more than 9,000 differentially expressed genes at the seedling stage alone. Much of this expression variation is obviously explained by structural changes, or is associated with other cis polymorphisms, often nearby transcriptional start sites. Moreover, with strand-specific RNA-seq, we find extensive antisense transcription, including at genes for which antisense or non-coding transcripts have not previously been reported. The comprehensive DNA sequence, gene annotation and expression data will be fundamental for studies to understand phenotypic variation of ecological and agronomic relevance in these lines, and in other Arabidopsis populations.