New in G3: a beaver genome, some sparkling yeast, and neon proteins

Check out the February issue of G3!

Table of Contents

Genome Report

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology

Bryan T. Welly, Michael R. Miller, Jeffrey L. Stott, Myra T. Blanchard, Alma D. Islas-Trejo, Sean M. O’Rourke, Amy E. Young, Juan F. Medrano, and Alison L. Van Eenennaam

G3 February 2017 7:321-331; Early Online December 30, 2016

doi:10.1534/g3.116.036673

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

Mutant Screen Reports

A High Copy Suppressor Screen for Autophagy Defects in Saccharomyces arl1 and ypt6 Strains

Shu Yang and Anne Rosenwald

G3 February 2017 7:333-341; Early Online December 14, 2016

doi:10.1534/g3.116.035998

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

A Network of Chromatin Factors Is Regulating the Transition to Postembryonic Development in Caenorhabditis elegans

Peter Erdelyi, Xing Wang, Marina Suleski, and Chantal Wicky

G3 February 2017 7:343-353; Early Online December 22, 2016

doi:10.1534/g3.116.037747

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

Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

Julien Chaillot, Michael A. Cook, Jacques Corbeil, and Adnane Sellam

G3 February 2017 7:355-360; Early Online December 30, 2016

doi:10.1534/g3.116.037986

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

Investigations

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

Christina A. Cuomo, Guus Bakkeren, Hala Badr Khalil, Vinay Panwar, David Joly, Rob Linning, Sharadha Sakthikumar, Xiao Song, Xian Adiconis, Lin Fan, Jonathan M. Goldberg, Joshua Z. Levin, Sarah Young, Qiandong Zeng, Yehoshua Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent McCallum, Les J. Szabo, Scot Hulbert, Xianming Chen, and John P. Fellers

G3 February 2017 7:361-376; Early Online December 2, 2016

doi:10.1534/g3.116.032797

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

The Effect of Temperature on Drosophila Hybrid Fitness

Charles J. J. Miller and Daniel R. Matute

G3 February 2017 7:377-385; Early Online December 2, 2016

doi:10.1534/g3.116.034926

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

The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development

Rafael D. Rosengarten, Balaji Santhanam, Janez Kokosar, and Gad Shaulsky

G3 February 2017 7:387-398; Early Online December 7, 2016

doi:10.1534/g3.116.037150

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

Genetic Causes of Phenotypic Adaptation to the Second Fermentation of Sparkling Wines in Saccharomyces cerevisiae

Maria Martí-Raga, Emilien Peltier, Albert Mas, Gemma Beltran, and Philippe Marullo

G3 February 2017 7:399-412; Early Online November 30, 2016

doi:10.1534/g3.116.037283

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

Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines

Charles Addo-Quaye, Elizabeth Buescher, Norman Best, Vijay Chaikam, Ivan Baxter, and Brian P. Dilkes

G3 February 2017 7:413-425; Early Online December 30, 2016

doi:10.1534/g3.116.029660

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

Genomics of Compensatory Adaptation in Experimental Populations of Aspergillus nidulans

Jeremy R. Dettman, Nicolas Rodrigue, Sijmen E. Schoustra, and Rees Kassen

G3 February 2017 7:427-436; Early Online November 30, 2016

doi:10.1534/g3.116.036152

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

Screening and Analysis of Janelia FlyLight Project Enhancer-Gal4 Strains Identifies Multiple Gene Enhancers Active During Hematopoiesis in Normal and Wasp-Challenged Drosophila Larvae

Tsuyoshi Tokusumi, Yumiko Tokusumi, Mark S. Brahier, Victoria Lam, Jessica R. Stoller-Conrad, Paul T. Kroeger, and Robert A. Schulz

G3 February 2017 7:437-448; Early Online December 2, 2016

doi:10.1534/g3.116.034439

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

Alternative Oxidase Transcription Factors AOD2 and AOD5 of Neurospora crassa Control the Expression of Genes Involved in Energy Production and Metabolism

Zhigang Qi, Kristina M. Smith, Erin L. Bredeweg, Natasa Bosnjak, Michael Freitag, and Frank E. Nargang

G3 February 2017 7:449-466; Early Online December 16, 2016

doi:10.1534/g3.116.035402

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

Transcriptome Analysis of Drosophila melanogaster Third Instar Larval Ring Glands Points to Novel Functions and Uncovers a Cytochrome p450 Required for Development

Danielle Christesen, Ying Ting Yang, Jason Somers, Charles Robin, Tamar Sztal, Philip Batterham, and Trent Perry

G3 February 2017 7:467-479; Early Online December 14, 2016

doi:10.1534/g3.116.037333

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

Genomic Prediction with Pedigree and Genotype x Environment Interaction in Spring Wheat Grown in South and West Asia, North Africa, and Mexico

Sivakumar Sukumaran, Jose Crossa, Diego Jarquin, Marta Lopes, and Matthew P. Reynolds

G3 February 2017 7:481-495; Early Online November 30, 2016

doi:10.1534/g3.116.036251

Abstract | Full Text | Full Text (PDF)

Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

Amir Fallahsharoudi, Neil de Kock, Martin Johnsson, Lejla Bektic, S. J. Kumari A. Ubhayasekera, Jonas Bergquist, Dominic Wright, and Per Jensen

G3 February 2017 7:497-504; Early Online December 14, 2016

doi:10.1534/g3.116.037721

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

From Embryo to Adult: piRNA-Mediated Silencing throughout Germline Development in Drosophila

Pauline P. Marie, Stéphane Ronsseray, and Antoine Boivin

G3 February 2017 7:505-516; Early Online December 7, 2016

doi:10.1534/g3.116.037291

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

The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

Miguel A. Hernández-Prieto, Yuankui Lin, and Min Chen

G3 February 2017 7:517-532; Early Online December 14, 2016

doi:10.1534/g3.116.036855

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

Expression Patterns of Atlantic Sturgeon (Acipenser oxyrinchus) During Embryonic Development

Elisavet Kaitetzidou, Arne Ludwig, Jörn Gessner, and Elena Sarropoulou

G3 February 2017 7:533-542; Early Online December 14, 2016

doi:10.1534/g3.116.036699

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

A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication

Cameron M. Nugent, Anne A. Easton, Joseph D. Norman, Moira M. Ferguson, and Roy G. Danzmann

G3 February 2017 7:543-556; Early Online December 16, 2016

doi:10.1534/g3.116.038026

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

Fine Mapping of Ur-3, a Historically Important Rust Resistance Locus in Common Bean

Oscar P. Hurtado-Gonzales, Giseli Valentini, Thiago A. S. Gilio, Alexandre M. Martins, Qijian Song, and Marcial A. Pastor-Corrales

G3 February 2017 7:557-569; Early Online December 27, 2016

doi:10.1534/g3.116.036061

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

Exon-Enriched Libraries Reveal Large Genic Differences Between Aedes aegypti from Senegal, West Africa, and Populations Outside Africa

Laura B. Dickson, Corey L. Campbell, Punita Juneja, Francis M. Jiggins, Massamba Sylla, and William C. Black IV

G3 February 2017 7:571-582; Early Online December 22, 2016

doi:10.1534/g3.116.036053

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

Single Locus Maintains Large Variation of Sex Reversal in Half-Smooth Tongue Sole (Cynoglossus semilaevis)

Li Jiang and Hengde Li

G3 February 2017 7:583-589; Early Online December 22, 2016

doi:10.1534/g3.116.036822

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

Paralog-Specific Functions of RPL7A and RPL7B Mediated by Ribosomal Protein or snoRNA Dosage in Saccharomyces cerevisiae

Ryan J. Palumbo, Gabriele Fuchs, Sheila Lutz, and M. Joan Curcio

G3 February 2017 7:591-606; Early Online December 22, 2016

doi:10.1534/g3.116.035931

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

The Bright Fluorescent Protein mNeonGreen Facilitates Protein Expression Analysis In Vivo

Lola Hostettler, Laura Grundy, Stéphanie Käser-Pébernard, Chantal Wicky, William R. Schafer, and Dominique A. Glauser

G3 February 2017 7:607-615; Early Online January 20, 2017

doi:10.1534/g3.116.038133

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

Predictability of Genetic Interactions from Functional Gene Modules

Jonathan H. Young and Edward M. Marcotte

G3 February 2017 7:617-624; Early Online December 22, 2016

doi:10.1534/g3.116.035915

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

upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks

Kyle A. McElroy, Youngsook L. Jung, Barry M. Zee, Charlotte I. Wang, Peter J. Park, and Mitzi I. Kuroda

G3 February 2017 7:625-635; Early Online January 6, 2017

doi:10.1534/g3.116.037788

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

Comparative High-Density Linkage Mapping Reveals Conserved Genome Structure but Variation in Levels of Heterochiasmy and Location of Recombination Cold Spots in the Common Frog

Gemma Palomar, Freed Ahmad, Anti Vasemägi, Chikako Matsuba, Alfredo G. Nicieza, and José Manuel Cano

G3 February 2017 7:637-645; Early Online December 30, 2016

doi:10.1534/g3.116.036459

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

Caenorhabditis elegans Male Copulation Circuitry Incorporates Sex-Shared Defecation Components To Promote Intromission and Sperm Transfer

Brigitte LeBoeuf and L. Rene Garcia

G3 February 2017 7:647-662; Early Online December 27, 2016

doi:10.1534/g3.116.036756

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

A Missense Variant in KCNJ10 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA1)

Nico Mauri, Miriam Kleiter, Michael Leschnik, Sandra Högler, Elisabeth Dietschi, Michaela Wiedmer, Joëlle Dietrich, Diana Henke, Frank Steffen, Simone Schuller, Corinne Gurtner, Nadine Stokar-Regenscheit, Donal O’Toole, Thomas Bilzer, Christiane Herden, Anna Oevermann, Vidhya Jagannathan, and Tosso Leeb

G3 February 2017 7:663-669; Early Online December 22, 2016

doi:10.1534/g3.116.038455

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

An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy

Alexandre M. Harris and Michael DeGiorgio

G3 February 2017 7:671-691; Early Online December 30, 2016

doi:10.1534/g3.116.037168

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

Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex

Madhav Jagannathan, Natalie Warsinger-Pepe, George J. Watase, and Yukiko M. Yamashita

G3 February 2017 7:693-704; Early Online December 22, 2016

doi:10.1534/g3.116.035352

Abstract | Full Text | Full Text (PDF)

The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior, and Fertility of Resynthesized Allotetraploid Brassica napus L.

Mathieu Rousseau-Gueutin, Jérôme Morice, Olivier Coriton, Virginie Huteau, Gwenn Trotoux, Sylvie Nègre, Cyril Falentin, Gwennaëlle Deniot, Marie Gilet, Frédérique Eber, Alexandre Pelé, Sonia Vautrin, Joëlle Fourment, Maryse Lodé, Hélène Bergès, and Anne-Marie Chèvre

G3 February 2017 7:705-717; Early Online December 22, 2016

doi:10.1534/g3.116.036517

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

Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection

Dawn E. Watkins-Chow, Gaurav K. Varshney, Lisa J. Garrett, Zelin Chen, Erin A. Jimenez, Cecilia Rivas, Kevin S. Bishop, Raman Sood, Ursula L. Harper, William J. Pavan, and Shawn M. Burgess

G3 February 2017 7:719-722; Early Online December 30, 2016

doi:10.1534/g3.116.038091

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

Latrunculin A-Induced Perturbation of the Actin Cytoskeleton Mediates Pap1p-Dependent Induction of the Caf5p Efflux Pump in Schizosaccharomyces pombe

Farzad Asadi, Bidhan Chakraborty, and Jim Karagiannis

G3 February 2017 7:723-730; Early Online December 30, 2016

doi:10.1534/g3.116.037903

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

Polygenic Control of Carotid Atherosclerosis in a BALB/cJ × SM/J Intercross and a Combined Cross Involving Multiple Mouse Strains

Andrew T. Grainger, Michael B. Jones, Mei-Hua Chen, and Weibin Shi

G3 February 2017 7:731-739; Early Online December 30, 2016

doi:10.1534/g3.116.037879

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

Genetic Analysis of the Lambda Spanins Rz and Rz1: Identification of Functional Domains

Jesse Cahill, Manoj Rajaure, Chandler O’Leary, Jordan Sloan, Armando Marrufo, Ashley Holt, Aneesha Kulkarni, Oscar Hernandez, and Ry Young

G3 February 2017 7:741-753; Early Online December 30, 2016

doi:10.1534/g3.116.037192

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

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)

Si Lok, Tara A. Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K. C. Yuen, Wilson W. L. Sung, Joseph Whitney, Janet A. Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J. Dawson, Karen Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arun Shipstone, Fiona Tsoi, Ting Wang, Sergio L. Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T. Simpson, Burton K. Lim, Mark D. Engstrom, Christopher J. Dutton, Kevin C. R. Kerr, Maria Franke, William Rapley, Richard F. Wintle, and Stephen W. Scherer

G3 February 2017 7:755-773; Early Online January 13, 2017

doi:10.1534/g3.116.038208

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