RT Journal Article SR Electronic T1 A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set JF bioRxiv FD Cold Spring Harbor Laboratory SP 407627 DO 10.1101/407627 A1 Boas Pucker A1 Daniela Holtgräwe A1 Kai Bernd Stadermann A1 Katharina Frey A1 Bruno Huettel A1 Richard Reinhardt A1 Bernd Weisshaar YR 2019 UL http://biorxiv.org/content/early/2019/04/14/407627.abstract AB Background In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species.Results Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2c) based on SMRT sequencing data. The best assembly comprises 69 nucleome sequences and displays a contig length of up to 16 Mbp. Compared to an earlier Illumina short read-based NGS assembly (AthNd-1_v1), a 75 fold increase in contiguity was observed for AthNd-1_v2c. To assign contig locations independent from the Col-0 gold standard reference sequence, we used genetic anchoring to generate a de novo assembly. In addition, we assembled the chondrome and plastome sequences.Conclusions Detailed analyses of AthNd-1_v2c allowed reliable identification of large genomic rearrangements between A. thaliana accessions contributing to differences in the gene sets that distinguish the genotypes. One of the differences detected identified a gene that is lacking from the Col-0 gold standard sequence. This de novo assembly extends the known proportion of the A. thaliana pan-genome.NGSnext generation sequencingNORnucleolus organizing regionRBHreciprocal best hitSMRTsingle molecule real time