A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set

Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B (2019)
PLOS ONE 14(5): e0216233.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
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.
Stichworte
sequence assembly tools; Arabidopsis thaliana; gene prediction; plant genomics; centromeres; sequence analysis; chromosomal inversion; comparative genomics
Erscheinungsjahr
2019
Zeitschriftentitel
PLOS ONE
Band
14
Ausgabe
5
Art.-Nr.
e0216233
eISSN
1932-6203
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
Page URI
https://pub.uni-bielefeld.de/record/2935698

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Pucker B, Holtgräwe D, Stadermann KB, et al. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLOS ONE. 2019;14(5): e0216233.
Pucker, B., Holtgräwe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., & Weisshaar, B. (2019). A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLOS ONE, 14(5), e0216233. doi:10.1371/journal.pone.0216233
Pucker, B., Holtgräwe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., and Weisshaar, B. (2019). A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLOS ONE 14:e0216233.
Pucker, B., et al., 2019. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLOS ONE, 14(5): e0216233.
B. Pucker, et al., “A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set”, PLOS ONE, vol. 14, 2019, : e0216233.
Pucker, B., Holtgräwe, D., Stadermann, K.B., Frey, K., Huettel, B., Reinhardt, R., Weisshaar, B.: A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLOS ONE. 14, : e0216233 (2019).
Pucker, Boas, Holtgräwe, Daniela, Stadermann, Kai Bernd, Frey, Katharina, Huettel, Bruno, Reinhardt, Richard, and Weisshaar, Bernd. “A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set”. PLOS ONE 14.5 (2019): e0216233.
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2019-05-22T03:44:47Z
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