New in G3: chicken genome assembly, Drosophila co-CRISPR, and more

Check out the January issue of G3!

Table of Contents

Investigations

The CgHaa1-Regulon Mediates Response and Tolerance to Acetic Acid Stress in the Human Pathogen Candida glabrata

Ruben T. Bernardo, Diana V. Cunha, Can Wang, Leonel Pereira, Sónia Silva, Sara B. Salazar, Markus S. Schröder, Michiyo Okamoto, Azusa Takahashi-Nakaguchi, Hiroji Chibana, Toshihiro Aoyama, Isabel Sá-Correia, Joana Azeredo, Geraldine Butler, and Nuno Pereira Mira

G3 January 2017 7:1-18; Early Online November 4, 2016

doi:10.1534/g3.116.034660

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

Using Next-Generation Sequencing for DNA Barcoding: Capturing Allelic Variation in ITS2

Jana Batovska, Noel O. I. Cogan, Stacey E. Lynch, and Mark J. Blacket

G3 January 2017 7:19-29; Early Online October 31, 2016

doi:10.1534/g3.116.036145

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

Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export

Emily K. Tsang, Nathan S. Abell, Xin Li, Vanessa Anaya, Konrad J. Karczewski, David A. Knowles, Raymond G. Sierra, Kevin S. Smith, and Stephen B. Montgomery

G3 January 2017 7:31-39; Early Online October 31, 2016

doi:10.1534/g3.116.036137

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

Bayesian Genomic Prediction with Genotype x Environment Interaction Kernel Models

Jaime Cuevas, José Crossa, Osval A. Montesinos-López, Juan Burgueo, Paulino Pérez-Rodríguez, and Gustavo de los Campos

G3 January 2017 7:41-53; Early Online October 28, 2016

doi:10.1534/g3.116.035584

Abstract | Full Text | Full Text (PDF)

Assortative Mating and Linkage Disequilibrium

Philip W. Hedrick

G3 January 2017 7:55-62; Early Online October 26, 2016

doi:10.1534/g3.116.034967

Abstract | Full Text | Full Text (PDF)

The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations

Florian Mattenberger, Beatriz Sabater-Muñoz, Christina Toft, and Mario A. Fares

G3 January 2017 7:63-75; Early Online October 31, 2016

doi:10.1534/g3.116.035329

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

Cytogenetic and Molecular Characterization of B-Genome Introgression Lines of Brassica napus L.

Inderpreet Dhaliwal, Annaliese S. Mason, Shashi Banga, Sakshi Bharti, Beerpal Kaur, Allison Mary Gurung, Phillip Anthony Salisbury, Jacqueline Batley, and Surinder Singh Banga

G3 January 2017 7:77-86; Early Online November 7, 2016

doi:10.1534/g3.116.036442

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

Efficient Screening of CRISPR/Cas9-Induced Events in Drosophila Using a Co-CRISPR Strategy

Nanci S. Kane, Mehul Vora, Krishna J. Varre, and Richard W. Padgett

G3 January 2017 7:87-93; Early Online October 28, 2016

doi:10.1534/g3.116.036723

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

Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity

Michelle D. Leach, TaeHyung Kim, Sonja E. DiGregorio, Cathy Collins, Zhaolei Zhang, Martin L. Duennwald, and Leah E. Cowen

G3 January 2017 7:95-108; Early Online November 2, 2016

doi:10.1534/g3.116.035675

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

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Wesley C. Warren, LaDeana W. Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D. Pruitt, Francoise Thibaud-Nissen, Valerie Schneider, Tamer A. Mansour, C. Titus Brown, Aleksey Zimin, Rachel Hawken, Mitch Abrahamsen, Alexis B. Pyrkosz, Mireille Morisson, Valerie Fillon, Alain Vignal, William Chow, Kerstin Howe, Janet E. Fulton, Marcia M. Miller, Peter Lovell, Claudio V. Mello, Morgan Wirthlin, Andrew S. Mason, Richard Kuo, David W. Burt, Jerry B. Dodgson, and Hans H. Cheng

G3 January 2017 7:109-117; Early Online November 14, 2016

doi:10.1534/g3.116.035923

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

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci

Monika Brandt, Muhammad Ahsan, Christa F. Honaker, Paul B. Siegel, and örjan Carlborg

G3 January 2017 7:119-128; Early Online October 31, 2016

doi:10.1534/g3.116.036012

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

The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion

Rigzin Dekhang, Cheng Wu, Kristina M. Smith, Teresa M. Lamb, Matthew Peterson, Erin L. Bredeweg, Oneida Ibarra, Jillian M. Emerson, Nirmala Karunarathna, Anna Lyubetskaya, Elham Azizi, Jennifer M. Hurley, Jay C. Dunlap, James E. Galagan, Michael Freitag, Matthew S. Sachs, and Deborah Bell-Pedersen

G3 January 2017 7:129-142; Early Online November 16, 2016

doi:10.1534/g3.116.034298

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

iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast

Mia Jaffe, Gavin Sherlock, and Sasha F. Levy

G3 January 2017 7:143-153; Early Online November 7, 2016

doi:10.1534/g3.116.034207

Abstract | Full Text | Full Text (PDF) | Supporting Information

The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles

Gleb N. Artemov, Ashley N. Peery, Xiaofang Jiang, Zhijian Tu, Vladimir N. Stegniy, Maria V. Sharakhova, and Igor V. Sharakhov

G3 January 2017 7:155-164; Early Online November 7, 2016

doi:10.1534/g3.116.034959

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

Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus

Victoria L. Pritchard, Heidi M. Viitaniemi, R. J. Scott McCairns, Juha Merilä, Mikko Nikinmaa, Craig R. Primmer, and Erica H. Leder

G3 January 2017 7:165-178; Early Online November 11, 2016

doi:10.1534/g3.116.033241

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

Cfs1p, a Novel Membrane Protein in the PQ-Loop Family, Is Involved in Phospholipid Flippase Functions in Yeast

Takaharu Yamamoto, Konomi Fujimura-Kamada, Eno Shioji, Risa Suzuki, and Kazuma Tanaka

G3 January 2017 7:179-192; Early Online November 9, 2016

doi:10.1534/g3.116.035238

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

CRISPR/Cas9-Induced Double-Strand Break Repair in Arabidopsis Nonhomologous End-Joining Mutants

Hexi Shen, Gary D. Strunks, Bart J. P. M. Klemann, Paul J. J. Hooykaas, and Sylvia de Pater

G3 January 2017 7:193-202; Early Online November 18, 2016

doi:10.1534/g3.116.035204

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

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

Dongyan Zhao, John P. Hamilton, Michael Hardigan, Dongmei Yin, Tao He, Brieanne Vaillancourt, Mauricio Reynoso, Germain Pauluzzi, Scott Funkhouser, Yuehua Cui, Julia Bailey-Serres, Jiming Jiang, C. Robin Buell, and Ning Jiang

G3 January 2017 7:203-219; Early Online November 14, 2016

doi:10.1534/g3.116.036020

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

Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response

Nasrine Bendjilali, Samuel MacLeon, Gurmannat Kalra, Stephen D. Willis, A. K. M. Nawshad Hossian, Erica Avery, Olivia Wojtowicz, and Mark J. Hickman

G3 January 2017 7:221-231; Early Online November 9, 2016

doi:10.1534/g3.116.034991

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

Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch

Gareth A. Cromie, Zhihao Tan, Michelle Hays, Eric W. Jeffery, and Aimée M. Dudley

G3 January 2017 7:233-246; Early Online November 11, 2016

doi:10.1534/g3.116.036160

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

Multiplex shRNA Screening of Germ Cell Development by in Vivo Transfection of Mouse Testis

Nicholas R. Y. Ho, Abul R. Usmani, Yan Yin, Liang Ma, and Donald F. Conrad

G3 January 2017 7:247-255; Early Online November 16, 2016

doi:10.1534/g3.116.036087

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

Caenorhabditis elegans DAF-2 as a Model for Human Insulin Receptoropathies

David A. Bulger, Tetsunari Fukushige, Sijung Yun, Robert K. Semple, John A. Hanover, and Michael W. Krause

G3 January 2017 7:257-268; Early Online November 16, 2016

doi:10.1534/g3.116.037184

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

First in Vivo Batrachochytrium dendrobatidis Transcriptomes Reveal Mechanisms of Host Exploitation, Host-Specific Gene Expression, and Expressed Genotype Shifts

Amy R. Ellison, Graziella V. DiRenzo, Caitlin A. McDonald, Karen R. Lips, and Kelly R. Zamudio

G3 January 2017 7:269-278; Early Online November 16, 2016

doi:10.1534/g3.116.035873

Abstract | Full Text | Full Text (PDF) | Supporting Information

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

Thurston Herricks, David J. Dilworth, Fred D. Mast, Song Li, Jennifer J. Smith, Alexander V. Ratushny, and John D. Aitchison

G3 January 2017 7:279-288; Early Online November 16, 2016

doi:10.1534/g3.116.037044

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

Correlations of Genotype with Climate Parameters Suggest Caenorhabditis elegans Niche Adaptations

Kathryn S. Evans, Yuehui Zhao, Shannon C. Brady, Lijiang Long, Patrick T. McGrath, and Erik C. Andersen

G3 January 2017 7:289-298; Early Online November 18, 2016

doi:10.1534/g3.116.035162

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

Genotyping-by-Sequencing-Based Investigation of the Genetic Architecture Responsible for a ~Sevenfold Increase in Soybean Seed Stearic Acid

Crystal B. Heim and Jason D. Gillman

G3 January 2017 7:299-308; Early Online November 18, 2016

doi:10.1534/g3.116.035741

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

Mutant Screen Report

Identification of Genes Mediating Drosophila Follicle Cell Progenitor Differentiation by Screening for Modifiers of GAL4::UAS Variegation

Ming-Chia Lee, Andrew D. Skora, and Allan C. Spradling

G3 January 2017 7:309-318; Early Online November 18, 2016

doi:10.1534/g3.116.036038

Abstract | Full Text | Full Text (PDF)

Corrigendum

Corrigendum

G3 January 2017 7:319;

doi:10.1534/g3.116.037358

Full Text | Full Text (PDF)