New in G3: sequencing in schizophrenia, fine-mapping in wheat, and cloning in C. elegans

Check out the November issue of G3!

Investigations

Genes with Restricted Introgression in a Field Cricket (Gryllus firmus/Gryllus pennsylvanicus) Hybrid Zone Are Concentrated on the X Chromosome and a Single Autosome

Luana S. Maroja, Erica L. Larson, Steven M. Bogdanowicz, and Richard G. Harrison

G3 November 2015 5:2219-2227; Early Online August 26, 2015, doi:10.1534/g3.115.021246

Abstract | Full Text | Full Text (PDF) | Supporting Information

Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize

Ashley N. Lough, Kaitlyn M. Faries, Dal-Hoe Koo, Abid Hussain, Leah M. Roark, Tiffany L. Langewisch, Teresa Backes, Karl A. G. Kremling, Jiming Jiang, James A. Birchler, and Kathleen J. Newton

G3 November 2015 5:2229-2239; Early Online September 1, 2015, doi:10.1534/g3.115.020677

Abstract | Full Text | Full Text (PDF) | Supporting Information

High-Throughput Cloning of Temperature-Sensitive Caenorhabditis elegans Mutants with Adult Syncytial Germline Membrane Architecture Defects

Josh Lowry, John Yochem, Chien-Hui Chuang, Kenji Sugioka, Amy A. Connolly, and Bruce Bowerman

G3 November 2015 5:2241-2255; Early Online August 26, 2015, doi:10.1534/g3.115.021451

Abstract | Full Text | Full Text (PDF) | Supporting Information

Fine-Mapping the Wheat Snn1 Locus Conferring Sensitivity to the Parastagonospora nodorum Necrotrophic Effector SnTox1 Using an Eight Founder Multiparent Advanced Generation Inter-Cross Population

James Cockram, Alice Scuderi, Toby Barber, Eiko Furuki, Keith A. Gardner, Nick Gosman, Radoslaw Kowalczyk, Huyen P. Phan, Gemma A. Rose, Kar-Chun Tan, Richard P. Oliver, and Ian J. Mackay

G3 November 2015 5:2257-2266; Early Online September 28, 2015, doi:10.1534/g3.115.021584

Abstract | Full Text | Full Text (PDF) | Supporting Information

Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci

Tomoyuki Furuta, Norio Komeda, Kenji Asano, Kanako Uehara, Rico Gamuyao, Rosalyn B. Angeles-Shim, Keisuke Nagai, Kazuyuki Doi, Diane R. Wang, Hideshi Yasui, Atsushi Yoshimura, Jianzhong Wu, Susan R. McCouch, and Motoyuki Ashikari

G3 November 2015 5:2267-2274; Early Online September 2, 2015, doi:10.1534/g3.115.020834

Abstract | Full Text | Full Text (PDF) | Supporting Information

Evolutionary Fate of the Androgen Receptor-Signaling Pathway in Ray-Finned Fishes with a Special Focus on Cichlids

Thibault Lorin, Walter Salzburger, and Astrid Böhne

G3 November 2015 5:2275-2283; Early Online September 1, 2015, doi:10.1534/g3.115.020685

Abstract | Full Text | Full Text (PDF) | Supporting Information

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

Qijian Song, Gaofeng Jia, David L. Hyten, Jerry Jenkins, Eun-Young Hwang, Steven G. Schroeder, Juan M. Osorno, Jeremy Schmutz, Scott A. Jackson, Phillip E. McClean, and Perry B. Cregan

G3 November 2015 5:2285-2290; Early Online August 28, 2015, doi:10.1534/g3.115.020594

Abstract | Full Text | Full Text (PDF) | Supporting Information

Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis

Jeanine M. Refsnider, Thomas J. Poorten, Penny F. Langhammer, Patricia A. Burrowes, and Erica Bree Rosenblum

G3 November 2015 5:2291-2298; Early Online September 1, 2015, doi:10.1534/g3.115.021808

Abstract | Full Text | Full Text (PDF) | Supporting Information

Persistent Activation of the Innate Immune Response in Adult Drosophila Following Radiation Exposure During Larval Development

Lisa J. Sudmeier, Sai-Suma Samudrala, Steven P. Howard, and Barry Ganetzky

G3 November 2015 5:2299-2306; Early Online September 1, 2015, doi:10.1534/g3.115.021782

Abstract | Full Text | Full Text (PDF) | Supporting Information

Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea

Carrie A. Whittle and Cassandra G. Extavour

G3 November 2015 5:2307-2321; Early Online September 17, 2015, doi:10.1534/g3.115.021402

Abstract | Full Text | Full Text (PDF) | Supporting Information

bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis

Alexandre Gillet-Markowska, Guillaume Louvel, and Gilles Fischer

G3 November 2015 5:2323-2327; Early Online September 2, 2015, doi:10.1534/g3.115.019836

Abstract | Full Text | Full Text (PDF)

The Genetic Architecture of Hearing Impairment in Mice: Evidence for Frequency-Specific Genetic Determinants

Amanda L. Crow, Jeffrey Ohmen, Juemei Wang, Joel Lavinsky, Jaana Hartiala, Qingzhong Li, Xin Li, Pezhman Salehide, Eleazar Eskin, Calvin Pan, Aldons J. Lusis, Hooman Allayee, and Rick A. Friedman

G3 November 2015 5:2329-2339; Early Online September 4, 2015, doi:10.1534/g3.115.021592

Abstract | Full Text | Full Text (PDF) | Supporting Information

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

Theresa Hill, Hamid Ashrafi, Sebastian Reyes Chin-Wo, Kevin Stoffel, Maria-Jose Truco, Alexander Kozik, Richard Michelmore, and Allen Van Deynze

G3 November 2015 5:2341-2355; Early Online September 8, 2015, doi:10.1534/g3.115.020040

Abstract | Full Text | Full Text (PDF) | Supporting Information

Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.)

Alicia N. Massa, Norma C. Manrique-Carpintero, Joseph J. Coombs, Daniel G. Zarka, Anne E. Boone, William W. Kirk, Christine A. Hackett, Glenn J. Bryan, and David S. Douches

G3 November 2015 5:2357-2364; Early Online September 14, 2015, doi:10.1534/g3.115.019646

Abstract | Full Text | Full Text (PDF) | Supporting Information

Exact Inference for Hardy-Weinberg Proportions with Missing Genotypes: Single and Multiple Imputation

Jan Graffelman, S. Nelson, S. M. Gogarten, and B. S. Weir

G3 November 2015 5:2365-2373; Early Online September 15, 2015, doi:10.1534/g3.115.022111

Abstract | Full Text | Full Text (PDF)

Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms

Darin R. Rokyta, Mark J. Margres, and Kate Calvin

G3 November 2015 5:2375-2382; Early Online September 9, 2015, doi:10.1534/g3.115.020578

Abstract | Full Text | Full Text (PDF)

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

Daniel Money, Kyle Gardner, Zoë Migicovsky, Heidi Schwaninger, Gan-Yuan Zhong, and Sean Myles

G3 November 2015 5:2383-2390; Early Online September 15, 2015, doi:10.1534/g3.115.021667

Abstract | Full Text | Full Text (PDF) | Supporting Information

Genome-Wide Association Study of Ureide Concentration in Diverse Maturity Group IV Soybean [Glycine max (L.) Merr.] Accessions

Jeffery D. Ray, Arun Prabhu Dhanapal, Shardendu K. Singh, Valerio Hoyos-Villegas, James R. Smith, Larry C. Purcell, C. Andy King, Debbie Boykin, Perry B. Cregan, Qijian Song, and Felix B. Fritschi

G3 November 2015 5:2391-2403; Early Online September 14, 2015, doi:10.1534/g3.115.021774

Abstract | Full Text | Full Text (PDF) | Supporting Information

The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila

Clinton Rice, Danielle Beekman, Liping Liu, and Albert Erives

G3 November 2015 5:2405-2419; Early Online September 10, 2015, doi:10.1534/g3.115.021659

Abstract | Full Text | Full Text (PDF) | Supporting Information

Flux Control in a Defense Pathway in Arabidopsis thaliana Is Robust to Environmental Perturbations and Controls Variation in Adaptive Traits

Carrie F. Olson-Manning, Christopher F. Strock, and Thomas Mitchell-Olds

G3 November 2015 5:2421-2427; Early Online September 10, 2015, doi:10.1534/g3.115.021816

Abstract | Full Text | Full Text (PDF) | Supporting Information

Slit Binding via the Ig1 Domain Is Essential for Midline Repulsion by Drosophila Robo1 but Dispensable for Receptor Expression, Localization, and Regulation in Vivo

Haley E. Brown, Marie C. Reichert, and Timothy A. Evans

G3 November 2015 5:2429-2439; Early Online September 10, 2015, doi:10.1534/g3.115.022327

Abstract | Full Text | Full Text (PDF)

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

Sheila A. Kitchen, Camerron M. Crowder, Angela Z. Poole, Virginia M. Weis, and Eli Meyer

G3 November 2015 5:2441-2452; Early Online September 17, 2015, doi:10.1534/g3.115.020164

Abstract | Full Text | Full Text (PDF) | Supporting Information

Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome

Daniele Merico, Mehdi Zarrei, Gregory Costain, Lucas Ogura, Babak Alipanahi, Matthew J. Gazzellone, Nancy J. Butcher, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Eva W. C. Chow, Danielle M. Andrade, Brendan J. Frey, Christian R. Marshall, Stephen W. Scherer, and Anne S. Bassett

G3 November 2015 5:2453-2461; Early Online September 16, 2015, doi:10.1534/g3.115.021345

Abstract | Full Text | Full Text (PDF) | Supporting Information

Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data

Morten T. Limborg, Ryan K. Waples, Fred W. Allendorf, and James E. Seeb

G3 November 2015 5:2463-2473; Early Online September 18, 2015, doi:10.1534/g3.115.020222

Abstract | Full Text | Full Text (PDF) | Supporting Information

Long-Lasting Gene Conversion Shapes the Convergent Evolution of the Critical Methanogenesis Genes

Sishuo Wang, Youhua Chen, Qinhong Cao, and Huiqiang Lou

G3 November 2015 5:2475-2486; Early Online September 16, 2015, doi:10.1534/g3.115.020180

Abstract | Full Text | Full Text (PDF) | Supporting Information

RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi

Martha Nigg, Jérôme Laroche, Christian R. Landry, and Louis Bernier

G3 November 2015 5:2487-2495; Early Online September 17, 2015, doi:10.1534/g3.115.021022

Abstract | Full Text | Full Text (PDF) | Supporting Information

Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly

Gregory A. Cary, Dani B. N. Vinh, Patrick May, Rolf Kuestner, and Aimée M. Dudley

G3 November 2015 5:2497-2511; Early Online September 21, 2015, doi:10.1534/g3.115.021444

Abstract | Full Text | Full Text (PDF) | Supporting Information

Genomic Instability of the Sex-Determining Locus in Atlantic Salmon (Salmo salar)

Krzysztof P. Lubieniecki, Song Lin, Emily I. Cabana, Jieying Li, Yvonne Y. Y. Lai, and William S. Davidson

G3 November 2015 5:2513-2522; Early Online September 22, 2015, doi:10.1534/g3.115.020115

Abstract | Full Text | Full Text (PDF) | Supporting Information