Abstract
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.
Footnotes
Email addresses: BP: bpucker{at}cebitec.uni-bielefeld.de, DH: dholtgra{at}cebitec.uni-bielefeld.de, KS: kstaderm{at}cebitec.uni-bielefeld.de, KF: katharina.frey{at}uni-bielefeld.de., BH: huettel{at}mpipz.mpg.de, RR: reinhardt{at}mpipz.mpg.de, BW: bernd.weisshaar{at}uni-bielefeld.de
List of abbreviations
- NGS
- next generation sequencing
- NOR
- nucleolus organizing region
- RBH
- reciprocal best hit
- SMRT
- single molecule real time
