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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Pucker_2019_nd1pacbio.pdf
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Autor*in
Pucker, BoasUniBi 
;
Holtgräwe, DanielaUniBi ;
Stadermann, Kai BerndUniBi ;
Frey, KatharinaUniBi ;
Huettel, Bruno;
Reinhardt, Richard;
Weisshaar, BerndUniBi
;
Holtgräwe, DanielaUniBi ;
Stadermann, Kai BerndUniBi ;
Frey, KatharinaUniBi ;
Huettel, Bruno;
Reinhardt, Richard;
Weisshaar, BerndUniBi Einrichtung
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
Urheberrecht / Lizenzen
ISSN
1932-6203
eISSN
1932-6203
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2935698
Zitieren
Pucker B, Holtgräwe D, Stadermann KB, et al. 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). 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, Boas, Holtgräwe, Daniela, Stadermann, Kai Bernd, Frey, Katharina, Huettel, Bruno, Reinhardt, Richard, and Weisshaar, Bernd. 2019. “Chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set”. PLoS One 14 (5): e0216233.
Pucker, B., Holtgräwe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., and Weisshaar, B. (2019). 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. 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., “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.: 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. “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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Material in PUB:
Zitiert
Chromosome-level Assembly Reveals the Niederzenz (Nd-1) Genome Structure and Gene Set
Pucker B, Holtgräwe D, Stadermann KB, Weisshaar B (2019)
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben.
Pucker B, Holtgräwe D, Stadermann KB, Weisshaar B (2019)
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben.
Teil dieser Dissertation
De novo Nd-1 genome assembly reveals genomic diversity of Arabidopsis thaliana and facilitates genome-wide non-canonical splice site analysis across plant species
Pucker B (2019)
Bielefeld: Universität Bielefeld.
Pucker B (2019)
Bielefeld: Universität Bielefeld.
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