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Genes (Basel). 2019 Sep 2;10(9). pii: E671. doi: 10.3390/genes10090671.

Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome.

Author information

1
Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany. bpucker@cebitec.uni-bielefeld.de.
2
Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany.
3
Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany.

Abstract

Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Columbia-0 (Col-0) reference sequence were detected. The number of deletions exceeds the number of insertions, thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions, e.g., the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.

KEYWORDS:

copy number variations; long read sequencing; next generation sequencing; variant calling

PMID:
31480756
DOI:
10.3390/genes10090671
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