TY  - JOUR
AB  - 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. 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. 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.
DA  - 2019
DO  - 10.1371/journal.pone.0216233
KW  - sequence assembly tools
KW  - Arabidopsis thaliana
KW  - gene prediction
KW  - plant genomics
KW  - centromeres
KW  - sequence analysis
KW  - chromosomal inversion
KW  - comparative genomics
LA  - eng
IS  - 5
PY  - 2019
SN  - 1932-6203
T2  - PLoS One
TI  - Chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
UR  - https://nbn-resolving.org/urn:nbn:de:0070-pub-29356986
Y2  - 2024-11-22T00:54:12
ER  -