November 2016 Table of Contents

Investigations

• Genomic Prediction of Single Crosses in the Early Stages of a Maize Hybrid Breeding Pipeline

  Dnyaneshwar C. Kadam, Sarah M. Potts, Martin O. Bohn, Alexander E. Lipka, Aaron J. Lorenz

  G3: Genes, Genomes, Genetics November 2016 6: 3443-3453; https://doi.org/10.1534/g3.116.031286
• Proper Sterol Distribution Is Required for Candida albicans Hyphal Formation and Virulence

  Paula McCourt, Hsing-Yin Liu, Josie E. Parker, Christina Gallo-Ebert, Melissa Donigan, Adam Bata, Caroline Giordano, Steven L. Kelly, Joseph T. Nickels

  G3: Genes, Genomes, Genetics November 2016 6: 3455-3465; https://doi.org/10.1534/g3.116.033969
• Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent

  Chuyue Yang, Adam J. Hockenberry, Michael C. Jewett, Luís A. N. Amaral

  G3: Genes, Genomes, Genetics November 2016 6: 3467-3474; https://doi.org/10.1534/g3.116.032227
• Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

  Benjamin Neymotin, Victoria Ettorre, David Gresham

  G3: Genes, Genomes, Genetics November 2016 6: 3475-3483; https://doi.org/10.1534/g3.116.032276
• First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae)

  Victoria L. Sork, Sorel T. Fitz-Gibbon, Daniela Puiu, Marc Crepeau, Paul F. Gugger, Rachel Sherman, Kristian Stevens, Charles H. Langley, Matteo Pellegrini, Steven L. Salzberg

  G3: Genes, Genomes, Genetics November 2016 6: 3485-3495; https://doi.org/10.1534/g3.116.030411
• Marker-Based Estimates Reveal Significant Nonadditive Effects in Clonally Propagated Cassava (Manihot esculenta): Implications for the Prediction of Total Genetic Value and the Selection of Varieties

  Marnin D. Wolfe, Peter Kulakow, Ismail Y. Rabbi, Jean-Luc Jannink

  G3: Genes, Genomes, Genetics November 2016 6: 3497-3506; https://doi.org/10.1534/g3.116.033332
• Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data

  Robert Kofler, Anna Maria Langmüller, Pierre Nouhaud, Kathrin Anna Otte, Christian Schlötterer

  G3: Genes, Genomes, Genetics November 2016 6: 3507-3515; https://doi.org/10.1534/g3.116.034488
• A Pedigree-Based Map of Recombination in the Domestic Dog Genome

  Christopher L. Campbell, Claude Bhérer, Bernice E. Morrow, Adam R. Boyko, Adam Auton

  G3: Genes, Genomes, Genetics November 2016 6: 3517-3524; https://doi.org/10.1534/g3.116.034678
• Effect of Two Lipoprotein (a)-Associated Genetic Variants on Plasminogen Levels and Fibrinolysis

  Hong Wang, Chan E. Hong, Joshua P. Lewis, Yanbei Zhu, Xing Wang, Xin Chu, Joshua Backman, Ziying Hu, Peixin Yang, Christopher D. Still, Glenn S. Gerhard, Mao Fu

  G3: Genes, Genomes, Genetics November 2016 6: 3525-3532; https://doi.org/10.1534/g3.116.034702
• Epidermal Growth Factor Receptor Cell Survival Signaling Requires Phosphatidylcholine Biosynthesis

  Matt Crook, Awani Upadhyay, Liyana J. Ido, Wendy Hanna-Rose

  G3: Genes, Genomes, Genetics November 2016 6: 3533-3540; https://doi.org/10.1534/g3.116.034850
• The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition

  Hua Luo, Xiao Li, Julie M. Claycomb, Howard D. Lipshitz

  G3: Genes, Genomes, Genetics November 2016 6: 3541-3551; https://doi.org/10.1534/g3.116.034199
• Temporal Expression of a Master Regulator Drives Synchronous Sporulation in Budding Yeast

  Minghao Chia, Folkert J. van Werven

  G3: Genes, Genomes, Genetics November 2016 6: 3553-3560; https://doi.org/10.1534/g3.116.034983
• The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)

  Elizabeth R. Milano, David B. Lowry, Thomas E. Juenger

  G3: Genes, Genomes, Genetics November 2016 6: 3561-3570; https://doi.org/10.1534/g3.116.032763
• Genome Sequencing of Chromosome 1 Substitution Lines Derived from Chinese Wild Mice Revealed a Unique Resource for Genetic Studies of Complex Traits

  Fuyi Xu, Tianzhu Chao, Yingming Liang, Kai Li, Shixian Hu, Maochun Wang, Yuxun Zhou, Hongyan Xu, Junhua Xiao

  G3: Genes, Genomes, Genetics November 2016 6: 3571-3580; https://doi.org/10.1534/g3.116.033902
• Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish

  Zaixuan Zhong, Kang Du, Qian Yu, Yong E. Zhang, Shunping He

  G3: Genes, Genomes, Genetics November 2016 6: 3581-3591; https://doi.org/10.1534/g3.116.032243
• Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations

  Aurora García-Dorado, Jinliang Wang, Eugenio López-Cortegano

  G3: Genes, Genomes, Genetics November 2016 6: 3593-3601; https://doi.org/10.1534/g3.116.032425
• Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila

  Yao Su, Xianzhi Jiang, Wenping Wu, Manman Wang, M. Imran Hamid, Meichun Xiang, Xingzhong Liu

  G3: Genes, Genomes, Genetics November 2016 6: 3603-3613; https://doi.org/10.1534/g3.116.033308
• Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs

  Yunxia Zhao, Ye Hou, Fei Liu, An Liu, Lu Jing, Changzhi Zhao, Yu Luan, Yuanxin Miao, Shuhong Zhao, Xinyun Li

  G3: Genes, Genomes, Genetics November 2016 6: 3615-3624; https://doi.org/10.1534/g3.116.032839
• Sequential Turnovers of Sex Chromosomes in African Clawed Frogs (Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination

  Benjamin L. S. Furman, Ben J. Evans

  G3: Genes, Genomes, Genetics November 2016 6: 3625-3633; https://doi.org/10.1534/g3.116.033423
• Advances in Understanding Mating Type Gene Organization in the Mushroom-Forming Fungus Flammulina velutipes

  Wei Wang, Lingdan Lian, Ping Xu, Tiansheng Chou, Irum Mukhtar, Aron Osakina, Muhammad Waqas, Bingzhi Chen, Xinrui Liu, Fang Liu, Baogui Xie, Arend F. van Peer

  G3: Genes, Genomes, Genetics November 2016 6: 3635-3645; https://doi.org/10.1534/g3.116.034637
• Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens

  Mauricio Lopez-Obando, Beate Hoffmann, Carine Géry, Anouchka Guyon-Debast, Evelyne Téoulé, Catherine Rameau, Sandrine Bonhomme, Fabien Nogué

  G3: Genes, Genomes, Genetics November 2016 6: 3647-3653; https://doi.org/10.1534/g3.116.033266
• In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

  Xiaofan Zhou, David Peris, Jacek Kominek, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas

  G3: Genes, Genomes, Genetics November 2016 6: 3655-3662; https://doi.org/10.1534/g3.116.034249
• Determinants in the LIN-12/Notch Intracellular Domain That Govern Its Activity and Stability During Caenorhabditis elegans Vulval Development

  Yuting Deng, Iva Greenwald

  G3: Genes, Genomes, Genetics November 2016 6: 3663-3670; https://doi.org/10.1534/g3.116.034363
• Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression

  Pamela J. Kaisaki, Georg W. Otto, Karène Argoud, Stephan C. Collins, Robert H. Wallis, Steven P. Wilder, Anthony C. Y. Yau, Christophe Hue, Sophie Calderari, Marie-Thérèse Bihoreau, Jean-Baptiste Cazier, Richard Mott, Dominique Gauguier

  G3: Genes, Genomes, Genetics November 2016 6: 3671-3683; https://doi.org/10.1534/g3.116.033274
• Non-Mendelian Dominant Maternal Effects Caused by CRISPR/Cas9 Transgenic Components in Drosophila melanogaster

  Chun-Chieh Lin, Christopher J. Potter

  G3: Genes, Genomes, Genetics November 2016 6: 3685-3691; https://doi.org/10.1534/g3.116.034884
• Genomic Prediction of Resistance to Pasteurellosis in Gilthead Sea Bream (Sparus aurata) Using 2b-RAD Sequencing

  Christos Palaiokostas, Serena Ferraresso, Rafaella Franch, Ross D. Houston, Luca Bargelloni

  G3: Genes, Genomes, Genetics November 2016 6: 3693-3700; https://doi.org/10.1534/g3.116.035220
• Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth

  Matthew V. Cannon, Genay Pilarowski, Xiuli Liu, David Serre

  G3: Genes, Genomes, Genetics November 2016 6: 3701-3709; https://doi.org/10.1534/g3.116.034785
• Distinct and Overlapping Requirements for Cyclins A, B, and B3 in Drosophila Female Meiosis

  Mohammed Bourouh, Rajdeep Dhaliwal, Ketki Rana, Sucheta Sinha, Zhihao Guo, Andrew Swan

  G3: Genes, Genomes, Genetics November 2016 6: 3711-3724; https://doi.org/10.1534/g3.116.033050
• The Selective Maintenance of Allelic Variation Under Generalized Dominance

  Hamish G. Spencer, Cuilodair Mitchell

  G3: Genes, Genomes, Genetics November 2016 6: 3725-3732; https://doi.org/10.1534/g3.116.028076
• Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space

  Daniela Bustos-Korts, Marcos Malosetti, Scott Chapman, Ben Biddulph, Fred van Eeuwijk

  G3: Genes, Genomes, Genetics November 2016 6: 3733-3747; https://doi.org/10.1534/g3.116.035410
• A Simplified Strategy for Introducing Genetic Variants into Drosophila Compound Autosome Stocks

  William D. Gilliland, Dennis P. May, Eileen M. Colwell, James A. Kennison

  G3: Genes, Genomes, Genetics November 2016 6: 3749-3755; https://doi.org/10.1534/g3.116.035634