Papers discussed.
Trung
Gherbi, H. et al. Homologous recombination in planta is stimulated in the absence of Rad50. EMBO Rep 2, 287–291 (2001).
Gherbi was able to produce plants that express the hyper-recombination phenotype by suppressing the nonhomologous end joining (NHEJ) pathway that is used by cells to repair double stranded breaks (DSB). It would be interesting to see if Daphnia exhibit the same increased rate of homologous recombination if the NHEJ pathway was suppressed and what effect it would have Daphnia living in a stressful environment that induces DSBs (ex. heavy metal pollution). This paper also helped me realize the importance of having a reliable and cost-effective recombination assay to further our recombination experiments.
Marelize
Flynn, Jullien M., et al. “Spontaneous Mutation Accumulation in Daphnia Pulex in Selection-Free Vs. Competitive Environments.” Molecular Biology and Evolution, vol. 34, no. 1, 2017, pp. 160-173.
In this paper the authors wanted to evaluate the influence of natural selection on the fate of de novo mutations in a population. They maintained a series of mutation accumulation lines and also a non-mutation accumulation population started by the same progenitor for an average of 82 generations. In total 30 Daphnia genomes were sequenced, 24 from the MA lines and 6 isolates from the non-MA lines. They estimated the rates for base substitutions and large scale deletions as well as the rates for ameiotic recombination in the 24 MA lines that were propagated strictly asexually. The mutation rates from the selection-free MA lines were then used to asses the level and type of selection in the non-MA population. They identified 477 single nucleotide mutations in the MA lines as well as a high overall rate of loss of heterozygosity, which they attributed to a large ameiotic recombination event spanning the entire arm of a chromosome and several hemizygous deletion events. In the non-MA lines they also found fewer mutations and more variability which they attributed to purifying selection and balancing selection respectively.
Swatantra
She, R., & Jarosz, D. F. (2018). Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change. Cell, 172(3), 478–490.e15.
The authors’ mathematical model provides an encouraging result: given the meiotic recombination rate in yeast and a typical density of polymorphism (once every 1,000 nucleotides), an attainable number of individuals (1,000clones) could deliver single-nucleotide precision mapping. They start with two natural strains: a wine strain and a clinical isolate. They cross them and inbreed offspring for six generations (F6). They collect more than a thousand F6ers, sequence their genomes, and phenotype their ability to withstand a diverse array of drugs. They found a locus of high association relating it to gene from related metabolic pathway. The gene features several mutations that differentiate between the parental strains. Their finding suggests that the eukaryotic chromosomes consist of ‘‘inheritance blocks’’ consisting of multiple genes each. Such blocks, are already present at the parental strains, and often contain combinations of mutations that neutralize each other’s potential deleterious effects. Also, the genes found here to affect a phenotype are largely different from the genes found in genetic perturbation experiments for the same phenotypes.
Sen
Fernandes, J.B., Séguéla-Arnaud, M., Larchevêque, C., Lloyd, A.H., and Mercier, R. (2018). Unleashing meiotic crossovers in hybrid plants. Proc. Natl. Acad. Sci. USA 115, 2431-2436.
Serra, H., Lambing, C., Griffin, C.H., Topp, S.D., Nageswaran, D.C., Underwood, C.J., Ziolkowski, P.A., Seguela-Arnaud, M., Fernandes, J.B., Mercier, R., et al. (2018). Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis. Proc. Natl. Acad. Sci. USA 115, 2437-2442.