Arabidopsis lyrata

A. lyrata on a cliff face in Minnesota, USA. Photo by Katy Chayka.

Arabidopsis lyrata is a member of the mustard family and is, of course, in the same genus as the widely used, and perhaps the best understood model plant, Arabidopsis thaliana. Its eXtreme plant bona fides stem from its preference is full or partial sun, mesic to dry conditions, and soil that is sandy, gravelly, or rocky. Like most small stature plants, however, it can not tolerate competition from taller ground vegetation. At some sites, it has been found seemingly growing out of the solid rock of the cliff face.

Why study A. lyrata

At the molecular level, the value of studying A. lyrata derives both from its close relation to A. thaliana, and from others of its unique biological properties. The two are close enough that ancestral states of polymorphisms in A. thaliana can be directly inferred from comparisons with A. lyrata; this should make it possible to advance the understanding of mutation and selection in plants. Furthermore, the A. lyrata genome is about 50% larger than that of A. thaliana. Their comparison affords an opportunity to discover how a plant can gain or lose a third or its genome in just five million years and if rapid changes are associated with performance.

On the other hand, A. lyrata is largely an outcrossing, insect pollinated, summer annual diploid which, on the edges of its range and late in the season, can become self-compatible. [1] It also has stable and spatially restricted populations or subspecies in small, isolated populations. These are not only genetically divergent, but have been shown to be metabolically different from each other. [2] A. lyrata may, thus, be particularly useful in understanding how populations diverge and how reproductive barriers arise. Because A. thaliana is more likely to inbreed than is A. lyrata, comparisons based of their genes and pathways may shed knowledge on the genome-level effects of inbreeding, the genetic basis of inbreeding depression, the potential for purging deleterious recessive alleles, and the transition from outcrossing to selfing.

A. lyrata is also a very close, interfertile relative of Arabidopsis halleri, a heavy metal accumulator and a tractable, laboratory model for studying phytoremediation. Understanding of the genome of A. lyrata is proceeding more quickly, but as knowledge can likely be directly transferred to A. halleri, A. lyrata is indirectly contributing to the understanding of metal tolerance.

Genomic and transcriptomic resources for A. lyrata

The assembly and annotation (Entrez Genome Project ID 41137) are available from GenBank and from JGI’s PHYTOZOME portal. Seeds of the MN47 strain have been deposited with the Arabidopsis Biological Resource Center under accession number CS22696.  The associated citation is in Nature Genetics[3]

 

Bibliography for the backstory

Bibliography for the backstory

1.
Griffin PC, Willi Y. Evolutionary shifts to self-fertilisation restricted to geographic range margins in North AmericanArabidopsis lyrata [Internet]. Ecol Lett2014;17:484–90. Available from: http://dx.doi.org/10.1111/ele.12248
2.
Davey MP, Burrell MM, Woodward FI, Quick WP. Population-specific metabolic phenotypes of Arabidopsis lyrata ssp. petraea [Internet]. New Phytol2007;0:071119221045001–??? Available from: http://dx.doi.org/10.1111/j.1469-8137.2007.02282.x
3.
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J-F, Clark RM, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change [Internet]. Nat Genet2011;43:476–81. Available from: http://dx.doi.org/10.1038/ng.807