New in G3: resistant bed bugs, stressed cotton, and outbred mice

Check out the December issue of G3!

Table of Contents

Meeting Report

Meeting Report: The Allied Genetics Conference 2016

Organizers of The Allied Genetics Conference 2016

G3 December 2016 6:3765-3786;

doi:10.1534/g3.116.036848

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Investigations

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

Daniel Gonzalez-Ibeas, Pedro J. Martinez-Garcia, Randi A. Famula, Annette Delfino-Mix, Kristian A. Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, and Jill L. Wegrzyn

G3 December 2016 6:3787-3802; Early Online October 31, 2016

doi:10.1534/g3.116.032805

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

Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

Jiafa Chen, Rosemary Shrestha, Junqiang Ding, Hongjian Zheng, Chunhua Mu, Jianyu Wu, and George Mahuku

G3 December 2016 6:3803-3815; Early Online October 14, 2016

doi:10.1534/g3.116.034561

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

Tissue Culture as a Source of Replicates in Nonmodel Plants: Variation in Cold Response in Arabidopsis lyrata ssp. petraea

Tanaka Kenta, Jessica E. M. Edwards, Roger K. Butlin, Terry Burke, W. Paul Quick, Peter Urwin, and Matthew P. Davey

G3 December 2016 6:3817-3823; Early Online October 11, 2016

doi:10.1534/g3.116.034314

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

Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

Ratan Chopra, Gloria Burow, Charles E. Simpson, Jennifer Chagoya, Joann Mudge, and Mark D. Burow

G3 December 2016 6:3825-3836; Early Online October 11, 2016

doi:10.1534/g3.115.026898

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Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes

Wanlong Li, Ghana S. Challa, Huilan Zhu, and Wenjie Wei

G3 December 2016 6:3837-3847; Early Online October 11, 2016

doi:10.1534/g3.116.035089

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

Drosophila CG2469 Encodes a Homolog of Human CTR9 and Is Essential for Development

Dhananjay Chaturvedi, Mayu Inaba, Shane Scoggin, and Michael Buszczak

G3 December 2016 6:3849-3857; Early Online September 27, 2016

doi:10.1534/g3.116.035196

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

The GATOR1 Complex Regulates Metabolic Homeostasis and the Response to Nutrient Stress in Drosophila melanogaster

Youheng Wei, Brad Reveal, Weili Cai, and Mary A. Lilly

G3 December 2016 6:3859-3867; Early Online September 26, 2016

doi:10.1534/g3.116.035337

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

Prevention of DNA Rereplication Through a Meiotic Recombination Checkpoint Response

Nicole A. Najor, Layne Weatherford, and George S. Brush

G3 December 2016 6:3869-3881; Early Online September 27, 2016

doi:10.1534/g3.116.033910

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

A Natural Mutation Involving both Pathogenicity and Perithecium Formation in the Fusarium graminearum Species Complex

Haruhisha Suga, Koji Kageyama, Masafumi Shimizu, and Misturo Hyakumachi

G3 December 2016 6:3883-3892; Early Online September 27, 2016

doi:10.1534/g3.116.033951

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

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

Elissa J. Chesler, Daniel M. Gatti, Andrew P. Morgan, Marge Strobel, Laura Trepanier, Denesa Oberbeck, Shannon McWeeney, Robert Hitzemann, Martin Ferris, Rachel McMullan, Amelia Clayshultle, Timothy A. Bell, Fernando Pardo Manuel de Villena, and Gary A. Churchill

G3 December 2016 6:3893-3902; Early Online September 30, 2016

doi:10.1534/g3.116.035527

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

Autosomal and X-Linked Additive Genetic Variation for Lifespan and Aging: Comparisons Within and Between the Sexes in Drosophila melanogaster

Robert M. Griffin, Holger Schielzeth, and Urban Friberg

G3 December 2016 6:3903-3911; Early Online September 27, 2016

doi:10.1534/g3.116.028308

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

X Chromosome Crossover Formation and Genome Stability in Caenorhabditis elegans Are Independently Regulated by xnd-1

T. Brooke McClendon, Rana Mainpal, Francis R. G. Amrit, Michael W. Krause, Arjumand Ghazi, and Judith L. Yanowitz

G3 December 2016 6:3913-3925; Early Online September 27, 2016

doi:10.1534/g3.116.035725

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

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Cletus P. Kurtzman, Chris Todd Hittinger, and Antonis Rokas

G3 December 2016 6:3927-3939; Early Online September 26, 2016

doi:10.1534/g3.116.034744

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

On Robust Association Testing for Quantitative Traits and Rare Variants

Peng Wei, Ying Cao, Yiwei Zhang, Zhiyuan Xu, Il-Youp Kwak, Eric Boerwinkle, and Wei Pan

G3 December 2016 6:3941-3950; Early Online September 27, 2016

doi:10.1534/g3.116.035485

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

Characterization, Expression, and Functional Analysis of a Novel NAC Gene Associated with Resistance to Verticillium Wilt and Abiotic Stress in Cotton

Weina Wang, Youlu Yuan, Can Yang, Shuaipeng Geng, Quan Sun, Lu Long, Chaowei Cai, Zongyan Chu, Xin Liu, Guanghao Wang, Xiongming Du, Chen Miao, Xiao Zhang, and Yingfan Cai

G3 December 2016 6:3951-3961; Early Online October 26, 2016

doi:10.1534/g3.116.034512

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

A Novel Frizzled-Based Screening Tool Identifies Genetic Modifiers of Planar Cell Polarity in Drosophila Wings

Jose Maria Carvajal-Gonzalez, Sonia Mulero-Navarro, Michael Smith, and Marek Mlodzik

G3 December 2016 6:3963-3973; Early Online October 11, 2016

doi:10.1534/g3.116.035535

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

Male-Specific Transcription Factor Occupancy Alone Does Not Account for Differential Methylation at Imprinted Genes in the mouse Germ Cell Lineage

Edward J. Romasko Nora Engel

G3 December 2016 6:3975-3983; Early Online September 30, 2016

doi:10.1534/g3.116.033613

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

Evolutionary Genomics of Peach and Almond Domestication

Dianne Velasco, Josh Hough, Mallikarjuna Aradhya, and Jeffrey Ross-Ibarra

G3 December 2016 6:3985-3993; Early Online October 5, 2016

doi:10.1534/g3.116.032672

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

Genome-Wide Association Study of Meiotic Recombination Phenotypes

Ferdouse Begum, Reshmi Chowdhury, Vivian G. Cheung, Stephanie L. Sherman, and Eleanor Feingold

G3 December 2016 6:3995-4007; Early Online October 12, 2016

doi:10.1534/g3.116.035766

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

Epigenetic Control of Phenotypic Plasticity in the Filamentous Fungus Neurospora crassa

Ilkka Kronholm, Hanna Johannesson, and Tarmo Ketola

G3 December 2016 6:4009-4022; Early Online September 30, 2016

doi:10.1534/g3.116.033860

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

Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus

Abigail L. Lind, Timothy D. Smith, Timothy Saterlee, Ana M. Calvo, and Antonis Rokas

G3 December 2016 6:4023-4033; Early Online September 30, 2016

doi:10.1534/g3.116.033084

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

The First Scube3 Mutant Mouse Line with Pleiotropic Phenotypic Alterations

Helmut Fuchs, Sibylle Sabrautzki, Gerhard K. H. Przemeck, Stefanie Leuchtenberger, Bettina Lorenz-Depiereux, Lore Becker, Birgit Rathkolb, Marion Horsch, Lillian Garrett, Manuela A. Östereicher, Wolfgang Hans, Koichiro Abe, Nobuho Sagawa, Jan Rozman, Ingrid L. Vargas-Panesso, Michael Sandholzer, Thomas S. Lisse, Thure Adler, Juan Antonio Aguilar-Pimentel, Julia Calzada-Wack, Nicole Ehrhard, Ralf Elvert, Christine Gau, Sabine M. Hölter, Katja Micklich, Kristin Moreth, Cornelia Prehn, Oliver Puk, Ildiko Racz, Claudia Stoeger, Alexandra Vernaleken, Dian Michel, Susanne Diener, Thomas Wieland, Jerzy Adamski, Raffi Bekeredjian, Dirk H. Busch, John Favor, Jochen Graw, Martin Klingenspor, Christoph Lengger, Holger Maier, Frauke Neff, Markus Ollert, Tobias Stoeger, Ali Önder Yildirim, Tim M. Strom, Andreas Zimmer, Eckhard Wolf, Wolfgang Wurst, Thomas Klopstock, Johannes Beckers, Valerie Gailus-Durner, and Martin Hrabé de Angelis

G3 December 2016 6:4035-4046; Early Online November 4, 2016

doi:10.1534/g3.116.033670

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

Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis

Igor Zeman, Martina Nebohácová, Gabriela Gérecová, Kornélia Katonová, Eva Jánošíková, Michaela Jakúbková, Ivana Centárová, Ivana Dunková, L’ubomír Tomáška, Leszek P. Pryszcz, Toni Gabaldón, and Jozef Nosek

G3 December 2016 6:4047-4058; Early Online October 5, 2016

doi:10.1534/g3.116.034389

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

A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius

Toby Fountain, Mark Ravinet, Richard Naylor, Klaus Reinhardt, and Roger K. Butlin

G3 December 2016 6:4059-4066; Early Online October 12, 2016

doi:10.1534/g3.116.033092

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

Multiple Genes Cause Postmating Prezygotic Reproductive Isolation in the Drosophila virilis Group

Yasir H. Ahmed-Braimah

G3 December 2016 6:4067-4076; Early Online October 11, 2016

doi:10.1534/g3.116.033340

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

Analysis of a lin-42/period Null Allele Implicates All Three Isoforms in Regulation of Caenorhabditis elegans Molting and Developmental Timing

Theresa L. B. Edelman, Katherine A. McCulloch, Angela Barr, Christian Frøkjær-Jensen, Erik M. Jorgensen, and Ann E. Rougvie

G3 December 2016 6:4077-4086; Early Online October 11, 2016

doi:10.1534/g3.116.034165

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

snpGeneSets: An R Package for Genome-Wide Study Annotation

Hao Mei, Lianna Li, Fan Jiang, Jeannette Simino, Michael Griswold, Thomas Mosley, and Shijian Liu

G3 December 2016 6:4087-4095; Early Online November 2, 2016

doi:10.1534/g3.116.034694

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

Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes

Gregory P. Way, James Rudd, Chen Wang, Habib Hamidi, Brooke L. Fridley, Gottfried E. Konecny, Ellen L. Goode, Casey S. Greene, and Jennifer A. Doherty

G3 December 2016 6:4097-4103; Early Online October 11, 2016

doi:10.1534/g3.116.033514

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

Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice

Yongxia Cui, Beng Kah Song, Lin-Feng Li, Ya-Ling Li, Zhongyun Huang, Ana L. Caicedo, Yulin Jia, and Kenneth M. Olsen

G3 December 2016 6:4105-4114; Early Online October 11, 2016

doi:10.1534/g3.116.035881

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

Robust Transgene Expression from Bicistronic mRNA in the Green Alga Chlamydomonas reinhardtii

Masayuki Onishi John R. Pringle

G3 December 2016 6:4115-4125; Early Online October 21, 2016

doi:10.1534/g3.116.033035

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

cdc-25.4, a Caenorhabditis elegans Ortholog of cdc25, Is Required for Male Mating Behavior

Sangmi Oh, Ichiro Kawasaki, Jae-Hyung Park, and Yhong-Hee Shim

G3 December 2016 6:4127-4138; Early Online October 21, 2016

doi:10.1534/g3.116.036129

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

New Insights into the Roles of Host Gene-Necrotrophic Effector Interactions in Governing Susceptibility of Durum Wheat to Tan Spot and Septoria nodorum Blotch

Simerjot K. Virdi, Zhaohui Liu, Megan E. Overlander, Zengcui Zhang, Steven S. Xu, Timothy L. Friesen, and Justin D. Faris

G3 December 2016 6:4139-4150; Early Online October 24, 2016

doi:10.1534/g3.116.036525

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

Age and Diet Affect Genetically Separable Secondary Injuries that Cause Acute Mortality Following Traumatic Brain Injury in Drosophila

Rebeccah J. Katzenberger, Barry Ganetzky, and David A. Wassarman

G3 December 2016 6:4151-4166; Early Online October 17, 2016

doi:10.1534/g3.116.036194

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

Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes

Porfirio Quintero-Cadena Paul W. Sternberg

G3 December 2016 6:4167-4174; Early Online October 31, 2016

doi:10.1534/g3.116.036228

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

The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome

Alexandra Asaro, Gregory Ziegler, Cathrine Ziyomo, Owen A. Hoekenga, Brian P. Dilkes, and Ivan Baxter

G3 December 2016 6:4175-4183; Early Online October 21, 2016

doi:10.1534/g3.116.034827

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

Evolutionary Insights into Taste Perception of the Invasive Pest Drosophila suzukii

Cristina M. Crava, Sukanya Ramasamy, Lino Ometto, Gianfranco Anfora, and Omar Rota-Stabelli

G3 December 2016 6:4185-4196; Early Online October 19, 2016

doi:10.1534/g3.116.036467

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

Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster

Yanzhu Lin, Zhen-Xia Chen, Brian Oliver, and Susan T. Harbison

G3 December 2016 6:4197-4210; Early Online October 21, 2016

doi:10.1534/g3.116.035444

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

Genome Report

Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers

Andrew P. Morgan, John P. Didion, Anthony G. Doran, James M. Holt, Leonard McMillan, Thomas M. Keane, and Fernando Pardo-Manuel de Villena

G3 December 2016 6:4211-4216; Early Online October 7, 2016

doi:10.1534/g3.116.034751

Abstract | Full Text | Full Text (PDF)

Mutant Screen Report

A Genetic Screen To Assess Dopamine Receptor (DopR1) Dependent Sleep Regulation in Drosophila

Yiqin Jiang, Elise Pitmon, Jack Berry, Fred W. Wolf, Zach McKenzie, and Tim J. Lebestky

G3 December 2016 6:4217-4226; Early Online October 19, 2016

doi:10.1534/g3.116.032136

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

An RNAi Screen To Identify Protein Phosphatases That Function Within the Drosophila Circadian Clock

Parul Agrawal Paul E. Hardin

G3 December 2016 6:4227-4238; Early Online October 26, 2016

doi:10.1534/g3.116.035345

Abstract | Full Text | Full Text (PDF)

Corrigendum

Corrigendum

G3 December 2016 6:4239;

doi:10.1534/g3.116.035956

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Reviewer Index

G3 Reviewer Index 2016

G3 December 2016 6:4241-4244;

doi:10.1534/g3.116.036715

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