The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

By T. Hu, P. Pattyn, E. Bakker, Jun Cao, Jan-Fang Cheng, Richard M. Clark, Noah Fahlgren, Jeffrey A. Fawcett, J. Grimwood, H. Gundlach and 20 more. Nature Genetics, 2011

879 citations recorded by the source corpus.

We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/80c8fe9ed248841e7a07458c87895b885c2e5ef9

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In Molecular Biology

1. Jinfeng Chen
2. Shujun Ou
3. Ning Jiang
4. B. Mueller‐Roeber
5. Y. Van de Peer

In Plant Science

1. Jinfeng Chen
2. Shujun Ou
3. Ning Jiang
4. Y. Van de Peer

Citations in the corpus

• Phytozome: a comparative platform for green plant genomics (2011, background): “0 (13) Arabidopsis thaliana Thale cress TAIR v10 (1) Brachypodium distachyon Purple false brome JGI /MIPS v1.”
• Epigenomic diversity in a global collection of Arabidopsis thaliana accessions (2016, neutral): “This is expected if A. thaliana genomes are continuing to shrink, as suggested before (Hu et al., 2011).”
• Evolution of Selfing: Recurrent Patterns in Molecular Adaptation (2015, neutral): “lyrata (Hu et al. 2011).”
• PLAZA 3.0: an access point for plant comparative genomics (2014, background): “In addition to Arabidopsis thaliana (36) and Arabidopsis lyrata (37), which were already included in PLAZA, D ow naded rom http/academ ic.”
• Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, background): “Intra-element recombination is thought to be the major process facilitating the removal of LTR sequence in genomes of rice (Oryza sativa) and Arabidopsis lyrata (8,9), resulting in the formation of solo LTRs that consist of only one of the LTR regions.”