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A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.
Pucker, Boas; Holtgräwe, Daniela; Stadermann, Kai Bernd; Frey, Katharina; Huettel, Bruno; Reinhardt, Richard; Weisshaar, Bernd.
Afiliación
  • Pucker B; Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany.
  • Holtgräwe D; Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany.
  • Stadermann KB; Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany.
  • Frey K; Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany.
  • Huettel B; Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
  • Reinhardt R; Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
  • Weisshaar B; Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany.
PLoS One ; 14(5): e0216233, 2019.
Article en En | MEDLINE | ID: mdl-31112551
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.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genoma de Planta Idioma: En Revista: PLoS One Asunto de la revista: CIENCIA / MEDICINA Año: 2019 Tipo del documento: Article País de afiliación: Alemania

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genoma de Planta Idioma: En Revista: PLoS One Asunto de la revista: CIENCIA / MEDICINA Año: 2019 Tipo del documento: Article País de afiliación: Alemania
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