New in G3: maize, master regulators, and mutagenesis

Check out the November issue of G3!

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, and Aaron J. Lorenz

G3 November 2016 6:3443-3453; Early Online September 19, 2016

doi:10.1534/g3.116.031286

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

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, and Joseph T. Nickels, Jr

G3 November 2016 6:3455-3465; Early Online August 31, 2016

doi:10.1534/g3.116.033969

Abstract | Full Text | Full Text (PDF)

Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent

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

G3 November 2016 6:3467-3474; Early Online September 7, 2016

doi:10.1534/g3.116.032227

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

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

Benjamin Neymotin, Victoria Ettorre, and David Gresham

G3 November 2016 6:3475-3483; Early Online September 15, 2016

doi:10.1534/g3.116.032276

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

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, and Steven L. Salzberg

G3 November 2016 6:3485-3495; Early Online September 12, 2016

doi:10.1534/g3.116.030411

Abstract | Full Text | Full Text (PDF)

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, and Jean-Luc Jannink

G3 November 2016 6:3497-3506; Early Online August 31, 2016

doi:10.1534/g3.116.033332

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

Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data

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

G3 November 2016 6:3507-3515; Early Online September 9, 2016

doi:10.1534/g3.116.034488

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

A Pedigree-Based Map of Recombination in the Domestic Dog Genome

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

G3 November 2016 6:3517-3524; Early Online September 2, 2016

doi:10.1534/g3.116.034678

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

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, and Mao Fu

G3 November 2016 6:3525-3532; Early Online September 7, 2016

doi:10.1534/g3.116.034702

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

Epidermal Growth Factor Receptor Cell Survival Signaling Requires Phosphatidylcholine Biosynthesis

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

G3 November 2016 6:3533-3540; Early Online September 7, 2016

doi:10.1534/g3.116.034850

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

The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition

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

G3 November 2016 6:3541-3551; Early Online September 2, 2016

doi:10.1534/g3.116.034199

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

Temporal Expression of a Master Regulator Drives Synchronous Sporulation in Budding Yeast

Minghao Chia and Folkert J. van Werven

G3 November 2016 6:3553-3560; Early Online September 7, 2016

doi:10.1534/g3.116.034983

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

The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum)

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

G3 November 2016 6:3561-3570; Early Online September 9, 2016

doi:10.1534/g3.116.032763

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

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, and Junhua Xiao

G3 November 2016 6:3571-3580; Early Online September 7, 2016

doi:10.1534/g3.116.033902

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

Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish

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

G3 November 2016 6:3581-3591; Early Online September 19, 2016

doi:10.1534/g3.116.032243

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

Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations

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

G3 November 2016 6:3593-3601; Early Online September 7, 2016

doi:10.1534/g3.116.032425

Abstract | Full Text | Full Text (PDF)

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, and Xingzhong Liu

G3 November 2016 6:3603-3613; Early Online September 15, 2016

doi:10.1534/g3.116.033308

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

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, and Xinyun Li

G3 November 2016 6:3615-3624; Early Online September 15, 2016

doi:10.1534/g3.116.032839

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

Sequential Turnovers of Sex Chromosomes in African Clawed Frogs (Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination

Benjamin L. S. Furman and Ben J. Evans

G3 November 2016 6:3625-3633; Early Online September 7, 2016

doi:10.1534/g3.116.033423

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

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, and Arend F. van Peer

G3 November 2016 6:3635-3645; Early Online September 12, 2016

doi:10.1534/g3.116.034637

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

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, and Fabien Nogué

G3 November 2016 6:3647-3653; Early Online September 9, 2016

doi:10.1534/g3.116.033266

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

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, and Antonis Rokas

G3 November 2016 6:3655-3662; Early Online September 16, 2016

doi:10.1534/g3.116.034249

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

Determinants in the LIN-12/Notch Intracellular Domain That Govern Its Activity and Stability During Caenorhabditis elegans Vulval Development

Yuting Deng and Iva Greenwald

G3 November 2016 6:3663-3670; Early Online September 19, 2016

doi:10.1534/g3.116.034363

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

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, and Dominique Gauguier

G3 November 2016 6:3671-3683; Early Online September 19, 2016

doi:10.1534/g3.116.033274

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

Non-Mendelian Dominant Maternal Effects Caused by CRISPR/Cas9 Transgenic Components in Drosophila melanogaster

Chun-Chieh Lin and Christopher J. Potter

G3 November 2016 6:3685-3691; Early Online September 16, 2016

doi:10.1534/g3.116.034884

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

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, and Luca Bargelloni

G3 November 2016 6:3693-3700; Early Online September 21, 2016

doi:10.1534/g3.116.035220

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

Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth

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

G3 November 2016 6:3701-3709; Early Online September 21, 2016

doi:10.1534/g3.116.034785

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

Distinct and Overlapping Requirements for Cyclins A, B, and B3 in Drosophila Female Meiosis

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

G3 November 2016 6:3711-3724; Early Online September 21, 2016

doi:10.1534/g3.116.033050

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

The Selective Maintenance of Allelic Variation Under Generalized Dominance

Hamish G. Spencer and Cuilodair Mitchell

G3 November 2016 6:3725-3732; Early Online September 21, 2016

doi:10.1534/g3.116.028076

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

Improvement of Predictive Ability by Uniform Coverage of the Target Genetic Space

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

G3 November 2016 6:3733-3747; Early Online September 26, 2016

doi:10.1534/g3.116.035410

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

A Simplified Strategy for Introducing Genetic Variants into Drosophila Compound Autosome Stocks

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

G3 November 2016 6:3749-3755; Early Online September 26, 2016

doi:10.1534/g3.116.035634

Abstract | Full Text | Full Text (PDF)

Mutant Screen Report

CRISPR/Cas9-Mediated Genome Editing and Mutagenesis of EcChi4 in Exopalaemon carinicauda

Tianshu Gui, Jiquan Zhang, Fengge Song, Yuying Sun, Shijun Xie, Kuijie Yu, and Jianhai Xiang

G3 November 2016 6:3757-3764; Early Online September 7, 2016

doi:10.1534/g3.116.034082

Abstract | Full Text | Full Text (PDF)