PT  - JOURNAL ARTICLE
AU  - Boas Pucker
AU  - Daniela Holtgräwe
AU  - Kai Bernd Stadermann
AU  - Katharina Frey
AU  - Bruno Huettel
AU  - Richard Reinhardt
AU  - Bernd Weisshaar
TI  - A Chromosome-level Sequence Assembly Reveals the Structure of the <em>Arabidopsis thaliana</em> Nd-1 Genome and its Gene Set
AID  - 10.1101/407627
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 407627
4099  - http://biorxiv.org/content/early/2018/09/06/407627.short
4100  - http://biorxiv.org/content/early/2018/09/06/407627.full
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 allowed to access translocation and inversion polymorphisms between two genotypes of one species.Results Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2) based on SMRT sequencing data. The assembly comprises 26 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 200 fold increase in continuity was observed for AthNd-1_v2. To assign contig locations independent from the Col-0 reference sequence, we used genetic anchoring to generate a truly de novo assembly. In addition, we assembled the chondrome and plastome sequences.Conclusions Detailed analyses of AthNd-1_v2 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 reference sequence. This de novo assembly will extent the known proportion of the A. thaliana pan-genome.NGSnext generation sequencingNORnucleolus organizing regionRBHreciprocal best hitSMRTsingle molecule real time