New in G3: coffee genome, dog diseases, and mouse infertility

Check out the September issue of G3!

Investigations

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus

Alex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna, and Jim Leebens-Mack

G3 September 2016 6:2679-2685; Early Online June 24, 2016

doi:10.1534/g3.116.030239

Abstract | Full Text | Full Text (PDF) | Supplemental Material

An Inversion Disrupting FAM134B Is Associated with Sensory Neuropathy in the Border Collie Dog Breed

Oliver P. Forman, Rebekkah J. Hitti, Louise Pettitt, Christopher A. Jenkins, Dennis P. O’Brien, G. Diane Shelton, Luisa De Risio, Rodrigo Gutierrez Quintana, Elsa Beltran, and Cathryn Mellersh

G3 September 2016 6:2687-2692; Early Online August 15, 2016

doi:10.1534/g3.116.027896

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genomic Signatures of North American Soybean Improvement Inform Diversity Enrichment Strategies and Clarify the Impact of Hybridization

Justin N. Vaughn and Zenglu Li

G3 September 2016 6:2693-2705; Early Online July 8, 2016

doi:10.1534/g3.116.029215

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Microsporidia Intracellular Development Relies on Myc Interaction Network Transcription Factors in the Host

Michael R. Botts, Lianne B. Cohen, Christopher S. Probert, Fengting Wu, and Emily R. Troemel

G3 September 2016 6:2707-2716; Early Online July 8, 2016

doi:10.1534/g3.116.029983

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton

Lianguang Shang, Yumei Wang, Xiaocui Wang, Fang Liu, Abdugheni Abduweli, Shihu Cai, Yuhua Li, Lingling Ma, Kunbo Wang, and Jinping Hua

G3 September 2016 6:2717-2724; Early Online June 24, 2016

doi:10.1534/g3.116.031302

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Genomic Bayesian Multi-trait and Multi-environment Model

Osval A. Montesinos-López, Abelardo Montesinos-López, José Crossa, Fernando H. Toledo, Oscar Pérez-Hernández, Kent M. Eskridge, and Jessica Rutkoski

G3 September 2016 6:2725-2744; Early Online June 24, 2016

doi:10.1534/g3.116.032359

Abstract | Full Text | Full Text (PDF)

Identification of QTLs Associated with Virulence Related Traits and Drug Resistance in Cryptococcus neoformans

Aaron A. Vogan, Jordan Khankhet, Himeshi Samarasinghe, and Jianping Xu

G3 September 2016 6:2745-2759; Early Online July 2, 2016

doi:10.1534/g3.116.029595

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Covariance Between Genotypic Effects and its Use for Genomic Inference in Half-Sib Families

Dörte Wittenburg, Friedrich Teuscher, Jan Klosa, and Norbert Reinsch

G3 September 2016 6:2761-2772; Early Online July 8, 2016

doi:10.1534/g3.116.032409

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Comparative Analysis of 5-Azacytidine- and Zebularine-Induced DNA Demethylation

Patrick T. Griffin, Chad E. Niederhuth, and Robert J. Schmitz

G3 September 2016 6:2773-2780; Early Online July 8, 2016

doi:10.1534/g3.116.030262

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Sources of Error in Mammalian Genetic Screens

Laura Magill Sack, Teresa Davoli, Qikai Xu, Mamie Z. Li, and Stephen J. Elledge

G3 September 2016 6:2781-2790; Early Online July 8, 2016

doi:10.1534/g3.116.030973

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principle Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

Walter J. Müller, Nokuthula Tlalajoe, Errol D. Cason, Derek Litthauer, Oleg Reva, Elzbieta Brzuszkiewicz, and Esta van Heerden

G3 September 2016 6:2791-2797; Early Online July 13, 2016

doi:10.1534/g3.116.032953

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Canopy Temperature and Vegetation Indices from High-Throughput Phenotyping Improve Accuracy of Pedigree and Genomic Selection for Grain Yield in Wheat

Jessica Rutkoski, Jesse Poland, Suchismita Mondal, Enrique Autrique, Lorena González Pérez, José Crossa, Matthew Reynolds, and Ravi Singh

G3 September 2016 6:2799-2808; Early Online July 8, 2016

doi:10.1534/g3.116.032888

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Split-Ubiquitin Based Strategy Selecting for Protein Complex-Interfering Mutations

Thomas Gronemeyer, Julian Chollet, Stefan Werner, Oliver Glomb, Anne Bäuerle, and Nils Johnsson

G3 September 2016 6:2809-2815; Early Online July 8, 2016

doi:10.1534/g3.116.031369

Abstract | Full Text | Full Text (PDF) | Supplemental Material

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress

Benoît Castandet, Amber M. Hotto, Susan R. Strickler, and David B. Stern

G3 September 2016 6:2817-2827; Early Online July 8, 2016

doi:10.1534/g3.116.030783

Abstract | Full Text | Full Text (PDF) | Supplemental Material

rDNA Copy Number Variants Are Frequent Passenger Mutations in Saccharomyces cerevisiae Deletion Collections and de Novo Transformants

Elizabeth X. Kwan, Xiaobin S. Wang, Haley M. Amemiya, Bonita J. Brewer, and M. K. Raghuraman

G3 September 2016 6:2829-2838; Early Online July 22, 2016

doi:10.1534/g3.116.030296

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Ligand-Bound GeneSwitch Causes Developmental Aberrations in Drosophila that Are Alleviated by the Alternative Oxidase

Ana Andjelkovic, Kia K. Kemppainen, and Howard T. Jacobs

G3 September 2016 6:2839-2846; Early Online July 13, 2016

doi:10.1534/g3.116.030882

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain

Andreas J. Stroehlein, Neil D. Young, Pasi K. Korhonen, Bill C. H. Chang, Paul W. Sternberg, Giuseppe La Rosa, Edoardo Pozio, and Robin B. Gasser

G3 September 2016 6:2847-2856; Early Online July 13, 2016

doi:10.1534/g3.116.032961

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge

Samir N. P. Kelada

G3 September 2016 6:2857-2865; Early Online July 22, 2016

doi:10.1534/g3.116.032912

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

Kevin C. Deitz, Giridhar A. Athrey, Musa Jawara, Hans J. Overgaard, Abrahan Matias, and Michel A. Slotman

G3 September 2016 6:2867-2879; Early Online July 27, 2016

doi:10.1534/g3.116.031906

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants

Andrew D. L. Nelson, Evan S. Forsythe, Upendra K. Devisetty, David S. Clausen, Asher K. Haug-Batzell, Ari M. R. Meldrum, Michael R. Frank, Eric Lyons, and Mark A. Beilstein

G3 September 2016 6:2881-2891; Early Online July 20, 2016

doi:10.1534/g3.116.030338

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Identification of Genes in Candida glabrata Conferring Altered Responses to Caspofungin, a Cell Wall Synthesis Inhibitor

Anne G. Rosenwald, Gaurav Arora, Rocco Ferrandino, Erica L. Gerace, Maedeh Mohammednetej, Waseem Nosair, Shemona Rattila, Amanda Zirzow Subic, and Ronda Rolfes

G3 September 2016 6:2893-2907; Early Online July 22, 2016

doi:10.1534/g3.116.032490

Abstract | Full Text | Full Text (PDF) | Supplemental Material

From Genotype to Phenotype: Nonsense Variants in SLC13A1 Are Associated with Decreased Serum Sulfate and Increased Serum Aminotransferases

Christina G. Tise, James A. Perry, Leslie E. Anforth, Mary A. Pavlovich, Joshua D. Backman, Kathleen A. Ryan, Joshua P. Lewis, Jeffrey R. O’Connell, Laura M. Yerges-Armstrong, and Alan R. Shuldiner

G3 September 2016 6:2909-2918; Early Online July 13, 2016

doi:10.1534/g3.116.032979

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Optimizing Training Population Data and Validation of Genomic Selection for Economic Traits in Soft Winter Wheat

Amber Hoffstetter, Antonio Cabrera, Mao Huang, and Clay Sneller

G3 September 2016 6:2919-2928; Early Online July 20, 2016

doi:10.1534/g3.116.032532

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Genome-Wide Association Mapping for Female Infertility in Inbred Mice

Ji-Long Liu, Tong-Song Wang, and Miao Zhao

G3 September 2016 6:2929-2935; Early Online July 22, 2016

doi:10.1534/g3.116.031575

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.)

Philippe Lashermes, Yann Hueber, Marie-Christine Combes, Dany Severac, and Alexis Dereeper

G3 September 2016 6:2937-2948; Early Online July 20, 2016

doi:10.1534/g3.116.030858

Abstract | Full Text | Full Text (PDF) | Supplemental Material

A Splice Defect in the EDA Gene in Dogs with an X-Linked Hypohidrotic Ectodermal Dysplasia (XLHED) Phenotype

Dominik P. Waluk, Gila Zur, Ronnie Kaufmann, Monika M. Welle, Vidhya Jagannathan, Cord Drögemüller, Eliane J. Müller, Tosso Leeb, and Arnaud Galichet

G3 September 2016 6:2949-2954; Early Online July 22, 2016

doi:10.1534/g3.116.033225

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Sensitivity of Allelic Divergence to Genomic Position: Lessons from the Drosophila tan Gene

Alisha V. John, Lisa L. Sramkoski, Elizabeth A. Walker, Arielle M. Cooley, and Patricia J. Wittkopp

G3 September 2016 6:2955-2962; Early Online July 22, 2016

doi:10.1534/g3.116.032029

Abstract | Full Text | Full Text (PDF) | Supplemental Material

An Intronic MBTPS2 Variant Results in a Splicing Defect in Horses with Brindle Coat Texture

Leonardo Murgiano, Dominik P. Waluk, Rachel Towers, Natalie Wiedemar, Joëlle Dietrich, Vidhya Jagannathan, Michaela Drögemüller, Pierre Balmer, Tom Druet, Arnaud Galichet, M. Cecilia Penedo, Eliane J. Müller, Petra Roosje, Monika M. Welle, and Tosso Leeb

G3 September 2016 6:2963-2970; Early Online July 22, 2016

doi:10.1534/g3.116.032433

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Evidence for Regulation of ECM3 Expression by Methylation of Histone H3 Lysine 4 and Intergenic Transcription in Saccharomyces cerevisiae

Elizabeth A. Raupach, Joseph A. Martens, and Karen M. Arndt

G3 September 2016 6:2971-2981; Early Online July 22, 2016

doi:10.1534/g3.116.033118

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Aspergillus fumigatus MADS-Box Transcription Factor rlmA Is Required for Regulation of the Cell Wall Integrity and Virulence

Marina Campos Rocha, João Henrique Tadini Marilhano Fabri, Krissia Franco de Godoy, Patrícia Alves de Castro, Juliana Issa Hori, Anderson Ferreira da Cunha, Mark Arentshorst, Arthur F. J. Ram, Cees A. M. J. J. van den Hondel, Gustavo Henrique Goldman, and Iran Malavazi

G3 September 2016 6:2983-3002; Early Online July 29, 2016

doi:10.1534/g3.116.031112

Abstract | Full Text | Full Text (PDF) | Supplemental Material

Mutant Screen Report

Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale

Martin Zackrisson, Johan Hallin, Lars-Göran Ottosson, Peter Dahl, Esteban Fernandez-Parada, Erik Ländström, Luciano Fernandez-Ricaud, Petra Kaferle, Andreas Skyman, Simon Stenberg, Stig Omholt, Uroš Petrovic, Jonas Warringer, and Anders Blomberg

G3 September 2016 6:3003-3014; Early Online July 2, 2016

doi:10.1534/g3.116.032342

Abstract | Full Text | Full Text (PDF) | Supplemental Material