New in G3: Drosophila doublesex, Shetland pony SHOX, and SNP-SNP interactions

Check out the July issue of G3!

ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity Between Studies in Meta-analysis

Eun Yong Kang, Yurang Park, Xiao Li, Ayellet V. Segrè, Buhm Han, and Eleazar Eskin

G3 July 2016 6:1793-1798; Early Online May 18, 2016

doi:10.1534/g3.116.029439

Abstract | Full Text | Full Text (PDF)

Sex Differences in Drosophila Somatic Gene Expression: Variation and Regulation by doublesex

Michelle N. Arbeitman, Felicia N. New, Justin M. Fear, Tiffany S. Howard, Justin E. Dalton, and Rita M. Graze

G3 July 2016 6:1799-1808; Early Online April 20, 2016

doi:10.1534/g3.116.027961

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

Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus

Jonathan Richards, Shiaoman Chao, Timothy Friesen, and Robert Brueggeman

G3 July 2016 6:1809-1818; Early Online April 20, 2016

doi:10.1534/g3.116.028902

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

Genomic Prediction of Gene Bank Wheat Landraces

José Crossa, Diego Jarquín, Jorge Franco, Paulino Pérez-Rodríguez, Juan Burgueño, Carolina Saint-Pierre, Prashant Vikram, Carolina Sansaloni, Cesar Petroli, Deniz Akdemir, Clay Sneller, Matthew Reynolds, Maria Tattaris, Thomas Payne, Carlos Guzman, Roberto J. Peña, Peter Wenzl, and Sukhwinder Singh

G3 July 2016 6:1819-1834; Early Online April 26, 2016

doi:10.1534/g3.116.029637

Abstract | Full Text | Full Text (PDF)

An Improved Genome Assembly of Azadirachta indica A. Juss.

Neeraja M. Krishnan, Prachi Jain, Saurabh Gupta, Arun K. Hariharan, and Binay Panda

G3 July 2016 6:1835-1840; Early Online April 20, 2016

doi:10.1534/g3.116.030056

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

The Drosophila melanogaster Muc68E Mucin Gene Influences Adult Size, Starvation Tolerance, and Cold Recovery

Micael Reis, Ana C. Silva, Cristina P. Vieira, and Jorge Vieira

G3 July 2016 6:1841-1851; Early Online April 26, 2016

doi:10.1534/g3.116.029934

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

Degradation Signals for Ubiquitin-Proteasome Dependent Cytosolic Protein Quality Control (CytoQC) in Yeast

Matthew J. Maurer, Eric D. Spear, Allen T. Yu, Evan J. Lee, Saba Shahzad, and Susan Michaelis

G3 July 2016 6:1853-1866; Early Online April 26, 2016

doi:10.1534/g3.116.027953

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

Copy Number Profiling of Brazilian Astrocytomas

Lucas Tadeu Bidinotto, Raul Torrieri, Alan Mackay, Gisele Caravina Almeida, Marta Viana-Pereira, Adriana Cruvinel-Carloni, Maria Luisa Spina, Nathalia Cristina Campanella, Weder Pereira de Menezes, Carlos Afonso Clara, Aline Paixão Becker, Chris Jones, and Rui Manuel Reis

G3 July 2016 6:1867-1878; Early Online April 26, 2016

doi:10.1534/g3.116.029884

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

Histone H1 Limits DNA Methylation in Neurospora crassa

Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, and Zachary A. Lewis

G3 July 2016 6:1879-1889; Early Online May 6, 2016

doi:10.1534/g3.116.028324

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

Cytotype Regulation Facilitates Repression of Hybrid Dysgenesis by Naturally Occurring KP Elements in Drosophila melanogaster

Michael J. Simmons, Craig D. Grimes, and Cody S. Czora

G3 July 2016 6:1891-1897; Early Online April 26, 2016

doi:10.1534/g3.116.028597

Abstract | Full Text | Full Text (PDF)

Patching Holes in the Chlamydomonas Genome

Frej Tulin and Frederick R. Cross

G3 July 2016 6:1899-1910; Early Online May 10, 2016

doi:10.1534/g3.116.029207

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

Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements

Aniruddha Chatterjee, Erin C. Macaulay, Euan J. Rodger, Peter A. Stockwell, Matthew F. Parry, Hester E. Roberts, Tania L. Slatter, Noelyn A. Hung, Celia J. Devenish, and Ian M. Morison

G3 July 2016 6:1911-1921; Early Online April 29, 2016

doi:10.1534/g3.116.030379

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

Fluorescent Beads Are a Versatile Tool for Staging Caenorhabditis elegans in Different Life Histories

Liberta Nika, Taylor Gibson, Rebecca Konkus, and Xantha Karp

G3 July 2016 6:1923-1933; Early Online April 29, 2016

doi:10.1534/g3.116.030163

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

Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Terry J. Felderhoff, Lauren M. McIntyre, Ana Saballos, and Wilfred Vermerris

G3 July 2016 6:1935-1946; Early Online May 18, 2016

doi:10.1534/g3.116.030510

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

Partial Functional Diversification of Drosophila melanogaster Septin Genes Sep2 and Sep5

Ryan S. O’Neill and Denise V. Clark

G3 July 2016 6:1947-1957; Early Online May 6, 2016

doi:10.1534/g3.116.028886

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

Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events in Drosophila melanogaster

Danny E. Miller, Kevin R. Cook, Alexandra V. Arvanitakis, and R. Scott Hawley

G3 July 2016 6:1959-1967; Early Online April 29, 2016

doi:10.1534/g3.116.029330

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

Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat

Huajing Teng, Yaohua Zhang, Chengmin Shi, Fengbiao Mao, Lingling Hou, Hongling Guo, Zhongsheng Sun, and Jianxu Zhang

G3 July 2016 6:1969-1977; Early Online April 29, 2016

doi:10.1534/g3.116.029504

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

Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies

Jun Chen, Thomas Källman, Xiao-Fei Ma, Giusi Zaina, Michele Morgante, and Martin Lascoux

G3 July 2016 6:1979-1989; Early Online May 6, 2016

doi:10.1534/g3.116.028753

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

Identification of Novel Regulators of the JAK/STAT Signaling Pathway that Control Border Cell Migration in the Drosophila Ovary

Afsoon Saadin and Michelle Starz-Gaiano

G3 July 2016 6:1991-2002; Early Online May 11, 2016

doi:10.1534/g3.116.028100

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

Evolution, Expression, and Function of Nonneuronal Ligand-Gated Chloride Channels in Drosophila melanogaster

Emily J. Remnant, Adam Williams, Chris Lumb, Ying Ting Yang, Janice Chan, Sebastian Duchêne, Phillip J. Daborn, Philip Batterham, and Trent Perry

G3 July 2016 6:2003-2012; Early Online May 6, 2016

doi:10.1534/g3.116.029546

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

Homeobox Is Pivotal for OsWUS Controlling Tiller Development and Female Fertility in Rice

Fredrick Mwamburi Mjomba, Yan Zheng, Huaqing Liu, Weiqi Tang, Zonglie Hong, Feng Wang, and Weiren Wu

G3 July 2016 6:2013-2021; Early Online May 18, 2016

doi:10.1534/g3.116.028837

Abstract | Full Text | Full Text (PDF)

Functional Genetic Screen to Identify Interneurons Governing Behaviorally Distinct Aspects of Drosophila Larval Motor Programs

Matt Q. Clark, Stephanie J. McCumsey, Sereno Lopez-Darwin, Ellie S. Heckscher, and Chris Q. Doe

G3 July 2016 6:2023-2031; Early Online May 6, 2016

doi:10.1534/g3.116.028472

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

Budding Yeast SLX4 Contributes to the Appropriate Distribution of Crossovers and Meiotic Double-Strand Break Formation on Bivalents During Meiosis

Mika Higashide and Miki Shinohara

G3 July 2016 6:2033-2042; Early Online May 6, 2016

doi:10.1534/g3.116.029488

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

Exhaustive Genome-Wide Search for SNP-SNP Interactions Across 10 Human Diseases

William Murk and Andrew T. DeWan

G3 July 2016 6:2043-2050; Early Online May 16, 2016

doi:10.1534/g3.116.028563

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

CRISPR/Cas9-Mediated Insertion of loxP Sites in the Mouse Dock7 Gene Provides an Effective Alternative to Use of Targeted Embryonic Stem Cells

Kathleen A. Bishop, Anne Harrington, Evguenia Kouranova, Edward J. Weinstein, Clifford J. Rosen, Xiaoxia Cui, and Lucy Liaw

G3 July 2016 6:2051-2061; Early Online May 11, 2016

doi:10.1534/g3.116.030601

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

Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae

Marc Krasovec, Adam Eyre-Walker, Nigel Grimsley, Christophe Salmeron, David Pecqueur, Gwenael Piganeau, and Sophie Sanchez-Ferandin

G3 July 2016 6:2063-2071; Early Online May 10, 2016

doi:10.1534/g3.116.029769

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

Analysis of Plasminogen Genetic Variants in Multiple Sclerosis Patients

A. Dessa Sadovnick, Anthony L. Traboulsee, Cecily Q. Bernales, Jay P. Ross, Amanda L. Forwell, Irene M. Yee, Lena Guillot-Noel, Bertrand Fontaine, Isabelle Cournu-Rebeix, Antonio Alcina, Maria Fedetz, Guillermo Izquierdo, Fuencisla Matesanz, Kelly Hilven, Bénédicte Dubois, An Goris, Ianire Astobiza, Iraide Alloza, Alfredo Antigüedad, Koen Vandenbroeck, Denis A. Akkad, Orhan Aktas, Paul Blaschke, Mathias Buttmann, Andrew Chan, Joerg T. Epplen, Lisa-Ann Gerdes, Antje Kroner, Christian Kubisch, Tania Kümpfel, Peter Lohse, Peter Rieckmann, Uwe K. Zettl, Frauke Zipp, Lars Bertram, Christina M Lill, Oscar Fernandez, Patricia Urbaneja, Laura Leyva, Jose Carlos Alvarez-Cermeño, Rafael Arroyo, Aroa M. Garagorri, Angel García-Martínez, Luisa M. Villar, Elena Urcelay, Sunny Malhotra, Xavier Montalban, Manuel Comabella, Thomas Berger, Franz Fazekas, Markus Reindl, Mascha C. Schmied, Alexander Zimprich, and Carles Vilariño-Güell

G3 July 2016 6:2073-2079; Early Online May 18, 2016

doi:10.1534/g3.116.030841

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

Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)

Manhong Ye, Bin Zhou, Shanshan Wei, MengMeng Ding, Xinghui Lu, Xuehao Shi, Jiatong Ding, Shengmei Yang, and Wanhong Wei

G3 July 2016 6:2081-2090; Early Online May 10, 2016

doi:10.1534/g3.116.029793

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

Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris)

Dongying Gao, Dongyan Zhao, Brian Abernathy, Aiko Iwata-Otsubo, Alfredo Herrera-Estrella, Ning Jiang, and Scott A. Jackson

G3 July 2016 6:2091-2101; Early Online May 16, 2016

doi:10.1534/g3.116.028761

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Improved Placement of Multi-mapping Small RNAs

Nathan R. Johnson, Jonathan M. Yeoh, Ceyda Coruh, and Michael J. Axtell

G3 July 2016 6:2103-2111; Early Online May 11, 2016

doi:10.1534/g3.116.030452

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

Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

Amelia R. I. Lindsey, John H. Werren, Stephen Richards, and Richard Stouthamer

G3 July 2016 6:2113-2123; Early Online May 18, 2016

doi:10.1534/g3.116.028449

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

UBR-5, a Conserved HECT-Type E3 Ubiquitin Ligase, Negatively Regulates Notch-Type Signaling in Caenorhabditis elegans

Komal Safdar, Anniya Gu, Xia Xu, Vinci Au, Jon Taylor, Stephane Flibotte, Donald G. Moerman, and Eleanor M. Maine

G3 July 2016 6:2125-2134; Early Online May 16, 2016

doi:10.1534/g3.116.027805

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

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Bingzhi Chen, Arend F. van Peer, Junjie Yan, Xiao Li, Bin Xie, Juan Miao, Qianhui Huang, Lei Zhang, Wei Wang, Junsheng Fu, Xiang Zhang, Xiaoyin Zhang, Fengli Hu, Qingfang Kong, Xianyun Sun, Feng Zou, Hanxing Zhang, Shaojie Li, and Baogui Xie

G3 July 2016 6:2135-2146; Early Online May 18, 2016

doi:10.1534/g3.116.030700

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

mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence

Gregory C. Finnigan and Jeremy Thorner

G3 July 2016 6:2147-2156; Early Online May 16, 2016

doi:10.1534/g3.116.029801

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

The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway

Sibel Kucukyildirim, Hongan Long, Way Sung, Samuel F. Miller, Thomas G. Doak, and Michael Lynch

G3 July 2016 6:2157-2163; Early Online May 18, 2016

doi:10.1534/g3.116.030130

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

Altered Function of the DnaJ Family Cochaperone DNJ-17 Modulates Locomotor Circuit Activity in a Caenorhabditis elegans Seizure Model

Seika Takayanagi-Kiya and Yishi Jin

G3 July 2016 6:2165-2171; Early Online May 16, 2016

doi:10.1534/g3.116.028928

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

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome

Hsin Y. Tsai, Diego Robledo, Natalie R. Lowe, Michael Bekaert, John B. Taggart, James E. Bron, and Ross D. Houston

G3 July 2016 6:2173-2179; Early Online May 18, 2016

doi:10.1534/g3.116.029009

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

Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling

Hao Song, Zheng-Lin Yu, Li-Na Sun, Dong-Xiu Xue, Tao Zhang, and Hai-Yan Wang

G3 July 2016 6:2181-2193; Early Online May 18, 2016

doi:10.1534/g3.116.029314

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

An Improved Binary Vector and Escherichia coli Strain for Agrobacterium tumefaciens-Mediated Plant Transformation

Michael R. Watson, Yu-fei Lin, Elizabeth Hollwey, Rachel E. Dodds, Peter Meyer, and Kenneth J. McDowall

G3 July 2016 6:2195-2201; Early Online May 18, 2016

doi:10.1534/g3.116.029405

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Genetic Mapping of Millions of SNPs in Safflower (Carthamus tinctorius L.) via Whole-Genome Resequencing

John E. Bowers, Stephanie A. Pearl, and John M. Burke

G3 July 2016 6:2203-2211; Early Online May 25, 2016

doi:10.1534/g3.115.026690

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

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies

Nima Rafati, Lisa S. Andersson, Sofia Mikko, Chungang Feng, Terje Raudsepp, Jessica Pettersson, Jan Janecka, Ove Wattle, Adam Ameur, Gunilla Thyreen, John Eberth, John Huddleston, Maika Malig, Ernest Bailey, Evan E. Eichler, Göran Dalin, Bhanu Chowdary, Leif Andersson, Gabriella Lindgren, and Carl-Johan Rubin

G3 July 2016 6:2213-2223; Early Online May 20, 2016

doi:10.1534/g3.116.029645

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Cilia-Associated Genes Play Differing Roles in Aminoglycoside-Induced Hair Cell Death in Zebrafish

Tamara M. Stawicki, Liana Hernandez, Robert Esterberg, Tor Linbo, Kelly N. Owens, Arish N. Shah, Nihal Thapa, Brock Roberts, Cecilia B. Moens, Edwin W. Rubel, and David W. Raible

G3 July 2016 6:2225-2235; Early Online May 20, 2016

doi:10.1534/g3.116.030080

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