Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa

Genome duplication, which results in polyploidy, is disruptive to fundamental biological processes. Genome duplications occur spontaneously in a range of taxa and problems such as sterility, aneuploidy, and gene expression aberrations are common in newly formed polyploids. In mammals, genome duplication is associated with cancer and spontaneous abortion of embryos. Nevertheless, stable polyploid species occur in both plants and animals. Understanding how natural selection enabled these species to overcome early challenges can provide important insights into the mechanisms by which core cellular functions can adapt to perturbations of the genomic environment. Arabidopsis arenosa includes stable tetraploid populations and is related to well-characterized diploids A. lyrata and A. thaliana. It thus provides a rare opportunity to leverage genomic tools to investigate the genetic basis of polyploid stabilization. We sequenced the genomes of twelve A. arenosa individuals and found signatures suggestive of recent and ongoing selective sweeps throughout the genome. Many of these are at genes implicated in genome maintenance functions, including chromosome cohesion and segregation, DNA repair, homologous recombination, transcriptional regulation, and chromatin structure. Numerous encoded proteins are predicted to interact with one another. For a critical meiosis gene, ASYNAPSIS1, we identified a non-synonymous mutation that is highly differentiated by cytotype, but present as a rare variant in diploid A. arenosa, indicating selection may have acted on standing variation already present in the diploid. Several genes we identified that are implicated in sister chromatid cohesion and segregation are homologous to genes identified in a yeast mutant screen as necessary for survival of polyploid cells, and also implicated in genome instability in human diseases including cancer. This points to commonalities across kingdoms and supports the hypothesis that selection has acted on genes controlling genome integrity in A. arenosa as an adaptive response to genome doubling.Organismic and Evolutionary Biolog

Interlocking Natural and Social Systems - Resilience, Governance and Research Policy Considerations.: New Methodologies and Interdisciplinary Approaches in Global Change Research (International Symposium, Porquerolles, France 2008).

Fonds audiovisuel du programme "ESCoM-AAR" (Equipe Sémiotique Cognitive et nouveaux Médias - Archives Audiovisuelles de la Recherche. Paris, France, 2000 - 2016).In this presentation the start is made from the 2007 IPCC statement that it now seems consolidated that there is a clear sign of the importance of the anthropogenic factors in the climate change panorama in addition to the natural phenomena. Thus the current situation of civilisation seems to be characterised by the quickly growing interference and to some extent control by humans over natural flows e.g. the carbon or nitrogen cycles to an extent not earlier seen in history. This development is of recent date - maybe half a century - and could be regarded as the beginning of a new era that the Nobel Prize winner Paul Crutzen and others have labelled as the era of the "Anthropocen". This has research policy, risk management, governance and political consequences

Cytological evaluation of some doubled-haploid oat lines

Toisen tekijän sukunimi on abstraktissa kirjoitettu Tanhuanpaa. Poster: Cytology, in situ and microcloning P216vo

Site frequency spectra and SNP frequency for <i>NRPB1</i> and <i>ASY1</i>.

<p>(A) Polymorphism in <i>NRPB1</i>. Top graph shows unfolded SFS (top graph) relative to <i>A. lyrata</i>. Lower graph shows SNP frequencies along the gene's length relative to <i>A. lyrata</i> and <i>A. thaliana</i>. Light blue rectangle indicates region coding for C-terminal heptad repeat tail. (B) Polymorphism in <i>ASY1</i>. Top graph shows unfolded SFS (top graph) relative to <i>A. lyrata</i>. Lower graph shows SNP frequencies along the gene's length relative to <i>A. lyrata</i> and <i>A. thaliana</i>. Light blue rectangle indicates region encoding conserved HORMA domain. Non-synonymous sites are shown in red, synonymous in dark blue, and intronic sites in grey.</p

Predicted interactions among 27 putatively selected genes in <i>A. arenosa</i>.

<p>Network shows connections predicted by the AtPIN database (see methods) among selected genes in <i>A. arenosa</i>.</p

Polymorphism in <i>A. arenosa</i> genome data.

<p><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003093#pgen-1003093-t001" target="_blank">Table 1</a> notes: SNP = single nucleotide polymorphism within coding regions; S = number of segregating sites (S); For Watterson's θ and for pairwise diversity (π), we report mean values with median values in parentheses.</p