GENETICS, Vol. 193, APRIL 2013, Copyright © 2013
Marker density and read depth for genotyping populations using genotyping-by-sequencing, pp. 1073-1081
Timothy M. Beissinger, Candice N. Hirsch, Rajandeep S. Sekhon, Jillian M. Foerster, James M. Johnson, German Muttoni, Brieanne Vaillancourt, C. Robin Buell, Shawn M. Kaeppler, and Natalia de Leon
Genotyping-by-sequencing enables rapid and efficient geno typing of any species, but it must be appropriately implemented to provide the desired information. This article describes what constitutes sufficient marker information for a variety of genetic studies, and tells how best to obtain that information with genotyping-by-sequencing.
Novel sexual-cycle-specific gene silencing in Aspergillus nidulans, pp. 1149-1162
Wioletta Czaja, Karen Y. Miller, and Bruce L. Miller
Homology-dependent gene silencing operates in many fungi, plants, and animals. This article reports a novel gene silencing system in the fungus Aspergillus nidulans that is sexual-cycle-specific. Duplication of the matA gene encoding a master regu lator of sexual differentiation triggers Mat-induced silencing of mating type function and aborts gametogenesis. Mat-induced silencing offers a valuable insight into genome surveillance in eukaryotes.
The protein chaperone HSP90 can facilitate the divergence of gene duplicates, pp. 1269-1277
Jennifer Lachowiec, Tzitziki Lemus, James H. Thomas, Patrick J. M. Murphy, Jennifer L. Nemhauser, and Christine Queitsch
Because protein chaperones facilitate folding and stability of their client proteins, clients may be free to accumulate more mutations than nonclients experiencing similar evolutionary pressures. These investigators found that a plant HSP90 client protein shows relaxed selection and hallmarks of neo- and subfunctionalization compared to its nonclient paralog. In addition, they show that systematically identified yeast HSP90 clients also tend to evolve faster than their nonclient paralogs.
Limited RNA editing in exons of mouse liver and adipose, pp. 1107-1115
Sandrine Lagarrigue, Farhad Hormozdiari, Lisa J. Martin, Frédéric Lecerf, Yehudit Hasin, Christoph Rau, RaffiHagopian, Yu Xiao, Jun Yan, Thomas A. Drake, Anatole Ghazalpour, Eleazar Eskin, and Aldons J. Lusis
How prevalent is RNA editing? Several recent studies of RNA editing of exons in humans and mice reached very different conclusions. This article should quiet the controversy. Employing stringent criteria, the authors identified only 63 examples of editing in liver and 188 in adipose tissue of mice. Their results suggest that exonic RNA editing in these tissues is limited to perhaps a few hundred events.
Inferring admixture histories of human populations using linkage disequilibrium, pp. 1233-1254
Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich, and Bonnie Berger
Admixture between previously separated populations shapes patterns of genetic diversity. These investigators present new methods for analyzing data from admixed populations and show how statistics based on linkage disequilibrium can be used to construct a robust test for admixture and to infer admixture-related parameters such as dates, mixture proportions, and phylogenetic relationships. These tools are offered in a fast and flexible software package- LDER-and applied to human data, yielding new insights into the admixture history of Sardinians, Pygmies, and Japanese.
Correcting coalescent analyses for panel-based SNP ascertainment, pp. 1185-1196
James R. McGill, Elizabeth A. Walkup, and Mary K. Kuhner
SNP chips only detect previously identified variants. Analyzing them as if they are fully ascertained leads to biased estimates of SNP chips only detect previously identified variants. …