The shrunken genome of Arabidopsis thaliana

Abstract

This paper examines macro and micro-level patterns of genome size evolution in the Brassicaceae. A phylogeny of 25 relatives of Arabidopsis thaliana was reconstructed using four molecular markers under both parsimony and Bayesian methods. Reconstruction of genome size (C value) evolution as a discrete character and as a continuous character was also performed. In addition, size dynamics in small chromosomal regions were assessed by comparing genomic clones generated for Arabidopsis lyrata and for Boechera stricta to the fully sequenced genome of A. thaliana. The results reveal a sevenfold variation in genome size among the taxa investigated and that the small genome size of A. thaliana is derived. Our results also indicate that the genome is free to increase or decrease in size across these evolutionary lineages without a directional bias. These changes are accomplished by insertions and deletions at both large and small-scales occurring mostly in intergenic regions, with repetitive sequences and transposable elements implicated in genome size increases. The focus upon taxa relatively closely related to the model organism A. thaliana, and the combination of complementary approaches, allows for unique insights into the processes driving genome size changes.

Multilocus Patterns of Nucleotide Diversity, Population Structure and Linkage Disequilibrium inBoechera stricta, a Wild Relative of Arabidopsis

“…Within the limits of available data, our comparative studies support this hypothesis. The genome size of inbreeding B. stricta is only 5% larger than outcrossing A. lyrata ( Johnston et al 2005;Windsor et al 2006;Oyama et al 2008), with similar numbers of chromosomes (7 vs. 8, respectively), but B. stricta has a linkage map that is $50% longer than A. lyrata (Kuittinen et al 2004;Yogeeswaran et al 2005;Schranz et al 2007b). Likewise, the DNA content of A. lyrata is $50% greater than A. thaliana, but the linkage maps of both Arabidopsis species are of similar length (Kuittinen et al 2004;Yogeeswaran et al 2005).…”

Spatiotemporal Seed Development Analysis Provides Insight into Primary Dormancy Induction and Evolution of theLepidium DELAY OF GERMINATION1Genes

“…However, providing that the LepaDOG1a and LepaDOG1c transcripts are translated, at least two similar DOG1 proteins are expressed in L. papillosum seeds. It is tempting to speculate that in L. papillosum, the two LepaDOG1a and LepaDOG1c proteins provide functional roles in dormancy regulation that are fulfilled by different splice variants of the single AtDOG1 gene (Bentsink et al, 2006;Nakabayashi et al, 2012) in the shrunken genome of Arabidopsis, which is characterized by extensive gene loss (Thomas et al, 2006;Oyama et al, 2008). Furthermore, polyploidization can form the basis for neofunctionalization or subfunctionalization of multiplied and retained genes (homeologs; Erdmann et al, 2010;Liu and Adams, 2010;Franzke et al, 2011), providing a mechanism for potentially diversified or more complex functions of the individual LepaDOG1 proteins in a putatively conserved dormancy mechanism.…”

MicroRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana

“…Additionally, young A. thaliana MIRNA may be associated with more transposons. However, analysis of A. lyrata MIRNA was less clear because all conservation groups were associated with flanking regions containing thaliana has evolved a reduced genome size through both large and small deletion events (Oyama et al, 2008) These deletions, which appear as unaligned nucleotides in A. lyrata, may mask patterns of variability found near young A. lyrata MIRNA. Future comparisons between A. lyrata and additional Arabidopsis species that share the ancestral genome architecture will be helpful in elucidating this possibility.…”