Listed below are the selected highlights for the April 2013 issue of the Genetics Society of America’s journal, Genetics. The April issue is available online.*
Methods, Technology and Resources
1. 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 genotyping 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.
2. 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 regulator 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.
Genetics of Complex Traits
3. 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.
Genome Integrity and Transmission
4. 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, Raffi Hagopian, 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.
Population and Evolutionary Genetics
5. 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 – ALDER – and applied to human data, yielding new insights into the admixture history of Sardinians, Pygmies, and Japanese.
Population and Evolutionary Genetics
6. 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 population size and other parameters; culling low-frequency SNPs makes the bias worse. This article offers corrections allowing accurate estimation of population parameters from panel-based and frequency-culled SNPs, and recommends strategies for SNP-based data collection and analysis.
7. Nonself recognition through intermolecular disulfide bond formation of ribonucleotide reductase in Neurospora, pp. 1175-1183
Robert P. Smith, Kenji Wellman, Leila Haidari, Hirohisa Masuda, and Myron L. Smith
In addition to its task of manufacturing DNA nucleotides, ribonucleotide reductase has a surprising function in Neurospora crassa: nonself recognition. These investigators discovered that the flexible tail of the enzyme irreversibly crosslinks two alternative forms of the enzyme via an unusual disulfide bond. Their observation that different versions of this tail inhibit the growth of cells that carry the other allelic form offers the possibility of developing specific chemotherapeutic drugs using this system as a prototype.
Genome and Systems Biology
8. The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle, pp. 1279-1295
Jagan Srinivasan, Adler R. Dillman, Marissa G. Macchietto, Liisa Heikkinen, Merja Lakso, Kelley M. Fracchia, Igor Antoshechkin, Ali Mortazavi, Garry Wong, and Paul W. Sternberg
This article presents analysis of the draft genome sequence of a free-living nematode. It reveals striking protein family expansions that likely result from selection in a harsh environment with pathogens. For example, expansion of a eukaryotic release factor protein family suggests an ongoing evolutionary arms race with viruses and transposons. The authors describe a resource that will enable experimental analysis of interesting developmental and behavioral features of this worm, such as its gonad development and use of ascaroside social signals.
Genetics, Vol. 193, April 2013, Copyright © 2013.
Genetics Society of America