New in G3: Yorkie signaling, rice hybrid incompatibility, and a wasp genome

Check out the August issue of G3!

Table of Contents

Genome Reports

Whole Genome Sequencing of the Braconid Parasitoid Wasp Fopius arisanus, an Important Biocontrol Agent of Pest Tepritid Fruit Flies

Scott M. Geib, Guang Hong Liang, Terence D. Murphy, Sheina B. Sim

G3: Genes, Genomes, Genetics August 2017 7: 2407-2411;

DOI: https://doi.org/10.1534/g3.117.040741

Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates

Luis Vale-Silva, Emmanuel Beaudoing, Van Du T. Tran, Dominique Sanglard

G3: Genes, Genomes, Genetics August 2017 7: 2413-2426;

DOI: https://doi.org/10.1534/g3.117.042887

Mutant Screen Report

A Genetic Screen Reveals an Unexpected Role for Yorkie Signaling in JAK/STAT-Dependent Hematopoietic Malignancies in Drosophila melanogaster

Abigail M. Anderson, Alessandro A. Bailetti, Elizabeth Rodkin, Atish De, Erika A. Bach

G3: Genes, Genomes, Genetics August 2017 7: 2427-2438;

DOI: https://doi.org/10.1534/g3.117.044172

Investigations

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

Mathieu Siol, Françoise Jacquin, Marianne Chabert-Martinello, Petr Smýkal, Marie-Christine Le Paslier, Grégoire Aubert, Judith Burstin

G3: Genes, Genomes, Genetics August 2017 7: 2461-2471;

DOI: https://doi.org/10.1534/g3.117.043471

A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus) Using 2b-RAD Sequencing

Haiyang Liu, Beide Fu, Meixia Pang, Xiu Feng, Xiaomu Yu, Jingou Tong

G3: Genes, Genomes, Genetics August 2017 7: 2473-2487;

DOI: https://doi.org/10.1534/g3.117.041376

A Duplicated, Truncated amh Gene Is Involved in Male Sex Determination in an Old World Silverside

Dilip Kumar Bej, Kaho Miyoshi, Ricardo S. Hattori, Carlos A. Strüssmann, Yoji Yamamoto

G3: Genes, Genomes, Genetics August 2017 7: 2489-2495;

DOI: https://doi.org/10.1534/g3.117.042697

A Kinome RNAi Screen in Drosophila Identifies Novel Genes Interacting with Lgl, aPKC, and Crb Cell Polarity Genes in Epithelial Tissues

Linda M. Parsons, Nicola A. Grzeschik, Kasun Amaratunga, Peter Burke, Leonie M. Quinn, Helena E. Richardson

G3: Genes, Genomes, Genetics August 2017 7: 2497-2509;

DOI: https://doi.org/10.1534/g3.117.043513

RNA Binding Protein Vigilin Collaborates with miRNAs To Regulate Gene Expression for Caenorhabditis elegans Larval Development

Rebecca A. Zabinsky, Brett M. Weum, Mingxue Cui, Min Han

G3: Genes, Genomes, Genetics August 2017 7: 2511-2518;

DOI: https://doi.org/10.1534/g3.117.043414

Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization in Arabidopsis thaliana

Basten L. Snoek, Penka Pavlova, Federico Tessadori, Anton J. M. Peeters, Clara Bourbousse, Fredy Barneche, Hans de Jong, Paul F. Fransz, Martijn van Zanten

G3: Genes, Genomes, Genetics August 2017 7: 2519-2531;

DOI: https://doi.org/10.1534/g3.117.043539

Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression

Biao Zeng, Luke R. Lloyd-Jones, Alexander Holloway, Urko M. Marigorta, Andres Metspalu, Grant W. Montgomery, Tonu Esko, Kenneth L. Brigham, Arshed A. Quyyumi, Youssef Idaghdour, Jian Yang, Peter M. Visscher, Joseph E. Powell, Greg Gibson

G3: Genes, Genomes, Genetics August 2017 7: 2533-2544;

DOI: https://doi.org/10.1534/g3.117.043752

Multidimensional Genetic Analysis of Repeated Seizures in the Hybrid Mouse Diversity Panel Reveals a Novel Epileptogenesis Susceptibility Locus

Russell J. Ferland, Jason Smith, Dominick Papandrea, Jessica Gracias, Leah Hains, Sridhar B. Kadiyala, Brittany O’Brien, Eun Yong Kang, Barbara S. Beyer, Bruce J. Herron

G3: Genes, Genomes, Genetics August 2017 7: 2545-2558;

DOI: https://doi.org/10.1534/g3.117.042234

Mouse Chromosome 4 Is Associated with the Baseline and Allergic IgE Phenotypes

Cynthia Kanagaratham, Pierre Camateros, John Ren, Robert Sladek, Silvia M. Vidal, Danuta Radzioch

G3: Genes, Genomes, Genetics August 2017 7: 2559-2564;

DOI: https://doi.org/10.1534/g3.117.042739

Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice

Giao Ngoc Nguyen, Yoshiyuki Yamagata, Yuko Shigematsu, Miyako Watanabe, Yuta Miyazaki, Kazuyuki Doi, Kosuke Tashiro, Satoru Kuhara, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Hideshi Yasui, Atsushi Yoshimura

G3: Genes, Genomes, Genetics August 2017 7: 2565-2575;

DOI: https://doi.org/10.1534/g3.117.043943

Transcriptional Complexity and Distinct Expression Patterns of auts2 Paralogs in Danio rerio

Igor Kondrychyn, Lena Robra, Vatsala Thirumalai

G3: Genes, Genomes, Genetics August 2017 7: 2577-2593;

DOI: https://doi.org/10.1534/g3.117.042622

Unique Allelic eQTL Clusters in Human MHC Haplotypes

Tze Hau Lam, Meixin Shen, Matthew Zirui Tay, Ee Chee Ren

G3: Genes, Genomes, Genetics August 2017 7: 2595-2604;

DOI: https://doi.org/10.1534/g3.117.043828

Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice (Oryza sativa L.)

Lihua Zhang, Jieqiong Lou, Michael E. Foley, Xing-You Gu

G3: Genes, Genomes, Genetics August 2017 7: 2605-2614;

DOI: https://doi.org/10.1534/g3.117.040451

Characterizing the Pyrenophora teres f. maculata–Barley Interaction Using Pathogen Genetics

Steven A. Carlsen, Anjan Neupane, Nathan A. Wyatt, Jonathan K. Richards, Justin D. Faris, Steven S. Xu, Robert S. Brueggeman, Timothy L. Friesen

G3: Genes, Genomes, Genetics August 2017 7: 2615-2626;

DOI: https://doi.org/10.1534/g3.117.043265

Cytonuclear Epistasis Controls the Density of Symbiont Wolbachia pipientis in Nongonadal Tissues of Mosquito Culex quinquefasciatus

Kevin J. Emerson, Robert L. Glaser

G3: Genes, Genomes, Genetics August 2017 7: 2627-2635;

DOI: https://doi.org/10.1534/g3.117.043422

Daily Activity of the Housefly, Musca domestica, Is Influenced by Temperature Independent of 3′ UTR period Gene Splicing

Olga Bazalova, David Dolezel

G3: Genes, Genomes, Genetics August 2017 7: 2637-2649;

DOI: https://doi.org/10.1534/g3.117.042374

Sex and Genetic Background Influence Superoxide Dismutase (cSOD)-Related Phenotypic Variation in Drosophila melanogaster

Courtney E. Lessel, Tony L. Parkes, Joel Dickinson, Thomas J. S. Merritt

G3: Genes, Genomes, Genetics August 2017 7: 2651-2664;

DOI: https://doi.org/10.1534/g3.117.043836

Fine Mapping, Transcriptome Analysis, and Marker Development for Y₂, the Gene That Conditions ß-Carotene Accumulation in Carrot (Daucus carota L.)

Shelby Ellison, Douglas Senalik, Hamed Bostan, Massimo Iorizzo, Philipp Simon

G3: Genes, Genomes, Genetics August 2017 7: 2665-2675;

DOI: https://doi.org/10.1534/g3.117.043067

Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species

Jesper Bechsgaard, Tove Hedegaard Jorgensen, Mikkel Heide Schierup

G3: Genes, Genomes, Genetics August 2017 7: 2677-2683;

DOI: https://doi.org/10.1534/g3.117.043984

The Accuracy and Bias of Single-Step Genomic Prediction for Populations Under Selection

Wan-Ling Hsu, Dorian J. Garrick, Rohan L. Fernando

G3: Genes, Genomes, Genetics August 2017 7: 2685-2694;

DOI: https://doi.org/10.1534/g3.117.043596

rRNA Pseudogenes in Filamentous Ascomycetes as Revealed by Genome Data

Yi Li, Rui-Heng Yang, Lan Jiang, Xiao-Di Hu, Zu-Jian Wu, Yi-Jian Yao

G3: Genes, Genomes, Genetics August 2017 7: 2695-2703;

DOI: https://doi.org/10.1534/g3.117.044016

Simple Expression Domains Are Regulated by Discrete CRMs During Drosophila Oogenesis

Nicole T. Revaitis, Robert A. Marmion, Maira Farhat, Vesile Ekiz, Wei Wang, Nir Yakoby

G3: Genes, Genomes, Genetics August 2017 7: 2705-2718;

DOI: https://doi.org/10.1534/g3.117.043810

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

Traver Hart, Amy Hin Yan Tong, Katie Chan, Jolanda Van Leeuwen, Ashwin Seetharaman, Michael Aregger, Megha Chandrashekhar, Nicole Hustedt, Sahil Seth, Avery Noonan, Andrea Habsid, Olga Sizova, Lyudmila Nedyalkova, Ryan Climie, Leanne Tworzyanski, Keith Lawson, Maria Augusta Sartori, Sabriyeh Alibeh, David Tieu, Sanna Masud, Patricia Mero, Alexander Weiss, Kevin R. Brown, Matej Usaj, Maximilian Billmann, Mahfuzur Rahman, Michael Constanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Daniel Durocher, Jason Moffat

G3: Genes, Genomes, Genetics August 2017 7: 2719-2727;

DOI: https://doi.org/10.1534/g3.117.041277

A SINE Insertion in ATP1B2 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA2)

Nico Mauri, Miriam Kleiter, Elisabeth Dietschi, Michael Leschnik, Sandra Högler, Michaela Wiedmer, Joëlle Dietrich, Diana Henke, Frank Steffen, Simone Schuller, Corinne Gurtner, Nadine Stokar-Regenscheit, Donal O’Toole, Thomas Bilzer, Christiane Herden, Anna Oevermann, Vidhya Jagannathan, Tosso Leeb

G3: Genes, Genomes, Genetics August 2017 7: 2729-2737;

DOI: https://doi.org/10.1534/g3.117.043018

The R148.3 Gene Modulates Caenorhabditis elegans Lifespan and Fat Metabolism

Catherine Roy-Bellavance, Jennifer M. Grants, Stéphanie Miard, Kayoung Lee, Évelyne Rondeau, Chantal Guillemette, Martin J. Simard, Stefan Taubert, Frédéric Picard

G3: Genes, Genomes, Genetics August 2017 7: 2739-2747;

DOI: https://doi.org/10.1534/g3.117.041681

Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis

Ben J.G. Sutherland, Ciro Rico, Céline Audet, Louis Bernatchez

G3: Genes, Genomes, Genetics August 2017 7: 2749-2762;

DOI: https://doi.org/10.1534/g3.117.040915

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

Michael G. Nelson, Raquel S. Linheiro, Casey M. Bergman

G3: Genes, Genomes, Genetics August 2017 7: 2763-2778;

DOI: https://doi.org/10.1534/g3.117.043893

Bayesian Networks Illustrate Genomic and Residual Trait Connections in Maize (Zea mays L.)

Katrin Töpner, Guilherme J. M. Rosa, Daniel Gianola, Chris-Carolin Schön

G3: Genes, Genomes, Genetics August 2017 7: 2779-2789;

DOI: https://doi.org/10.1534/g3.117.044263

FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila

Sudhir Kumar, Charlotte Konikoff, Maxwell Sanderford, Li Liu, Stuart Newfeld, Jieping Ye, Rob J. Kulathinal

G3: Genes, Genomes, Genetics August 2017 7: 2791-2797;

DOI: https://doi.org/10.1534/g3.117.040345

Two Variants in SLC24A5 Are Associated with “Tiger-Eye” Iris Pigmentation in Puerto Rican Paso Fino Horses

Maura Mack, Elizabeth Kowalski, Robert Grahn, Dineli Bras, Maria Cecilia T. Penedo, Rebecca Bellone

G3: Genes, Genomes, Genetics August 2017 7: 2799-2806;

DOI: https://doi.org/10.1534/g3.117.043786

Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding

Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya

G3: Genes, Genomes, Genetics August 2017 7: 2807-2820;

DOI: https://doi.org/10.1534/g3.117.044099

Genome-Wide Associations for Water-Soluble Carbohydrate Concentration and Relative Maturity in Wheat Using SNP and DArT Marker Arrays

Ben Ovenden, Andrew Milgate, Len J. Wade, Greg J. Rebetzke, James B. Holland

G3: Genes, Genomes, Genetics August 2017 7: 2821-2830;

DOI: https://doi.org/10.1534/g3.117.039842

Dissecting the Satellite DNA Landscape in Three Cactophilic Drosophila Sequenced Genomes

Leonardo G. de Lima, Marta Svartman, Gustavo C. S. Kuhn

G3: Genes, Genomes, Genetics August 2017 7: 2831-2843;

DOI: https://doi.org/10.1534/g3.117.042093

Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae

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

G3: Genes, Genomes, Genetics August 2017 7: 2845-2854;

DOI: https://doi.org/10.1534/g3.117.042440

Gene2Function: An Integrated Online Resource for Gene Function Discovery

Yanhui Hu, Aram Comjean, Stephanie E. Mohr, The FlyBase Consortium, Norbert Perrimon

G3: Genes, Genomes, Genetics August 2017 7: 2855-2858;

DOI: https://doi.org/10.1534/g3.117.043885

A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer (Cervus elaphus)

Susan E. Johnston, Jisca Huisman, Philip A. Ellis, Josephine M. Pemberton

G3: Genes, Genomes, Genetics August 2017 7: 2859-2870;

DOI: https://doi.org/10.1534/g3.117.044198

An RNA Recognition Motif-Containing Protein Functions in Meiotic Silencing by Unpaired DNA

Dilini A. Samarajeewa, Pennapa Manitchotpisit, Miranda Henderson, Hua Xiao, David G. Rehard, Kevin A. Edwards, Patrick K. T. Shiu, Thomas M. Hammond

G3: Genes, Genomes, Genetics August 2017 7: 2871-2882;

DOI: https://doi.org/10.1534/g3.117.041848

Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

Wilson Leung, Christopher D. Shaffer, Elizabeth J. Chen, Thomas J. Quisenberry, Kevin Ko, John M. Braverman, Thomas C. Giarla, Nathan T. Mortimer, Laura K. Reed, Sheryl T. Smith, Srebrenka Robic, Shannon R. McCartha, Danielle R. Perry, Lindsay M. Prescod, Zenyth A. Sheppard, Ken J. Saville, Allison McClish, Emily A. Morlock, Victoria R. Sochor, Brittney Stanton, Isaac C. Veysey-White, Dennis Revie, Luis A. Jimenez, Jennifer J. Palomino, Melissa D. Patao, Shane M. Patao, Edward T. Himelblau, Jaclyn D. Campbell, Alexandra L. Hertz, Maddison F. McEvilly, Allison R. Wagner, James Youngblom, Baljit Bedi, Jeffery Bettincourt, Erin Duso, Maiye Her, William Hilton, Samantha House, Masud Karimi, Kevin Kumimoto, Rebekah Lee, Darryl Lopez, George Odisho, Ricky Prasad, Holly Lyn Robbins, Tanveer Sandhu, Tracy Selfridge, Kara Tsukashima, Hani Yosif, Nighat P. Kokan, Latia Britt, Alycia Zoellner, Eric P. Spana, Ben T. Chlebina, Insun Chong, Harrison Friedman, Danny A. Mammo, Chun L. Ng, Vinayak S. Nikam, Nicholas U. Schwartz, Thomas Q. Xu, Martin G. Burg, Spencer M. Batten, Lindsay M. Corbeill, Erica Enoch, Jesse J. Ensign, Mary E. Franks, Breanna Haiker, Judith A. Ingles, Lyndsay D. Kirkland, Joshua M. Lorenz-Guertin, Jordan Matthews, Cody M. Mittig, Nicholaus Monsma, Katherine J. Olson, Guillermo Perez-Aragon, Alen Ramic, Jordan R. Ramirez, Christopher Scheiber, Patrick A. Schneider, Devon E. Schultz, Matthew Simon, Eric Spencer, Adam C. Wernette, Maxine E. Wykle, Elizabeth Zavala-Arellano, Mitchell J. McDonald, Kristine Ostby, Peter Wendland, Justin R. DiAngelo, Alexis M. Ceasrine, Amanda H. Cox, James E.B. Docherty, Robert M. Gingras, Stephanie M. Grieb, Michael J. Pavia, Casey L. Personius, Grzegorz L. Polak, Dale L. Beach, Heaven L. Cerritos, Edward A. Horansky, Karim A. Sharif, Ryan Moran, Susan Parrish, Kirsten Bickford, Jennifer Bland, Juliana Broussard, Kerry Campbell, Katelynn E. Deibel, Richard Forka, Monika C. Lemke, Marlee B. Nelson, Catherine O’Keeffe, S. Mariel Ramey, Luke Schmidt, Paola Villegas, Christopher J. Jones, Stephanie L. Christ, Sami Mamari, Adam S. Rinaldi, Ghazal Stity, Amy T. Hark, Mark Scheuerman, S. Catherine Silver Key, Briana D. McRae, Adam S. Haberman, Sam Asinof, Harriette Carrington, Kelly Drumm, Terrance Embry, Richard McGuire, Drew Miller-Foreman, Stella Rosen, Nadia Safa, Darrin Schultz, Matt Segal, Yakov Shevin, Petros Svoronos, Tam Vuong, Gary Skuse, Don W. Paetkau, Rachael K. Bridgman, Charlotte M. Brown, Alicia R. Carroll, Francesca M. Gifford, Julie Beth Gillespie, Susan E. Herman, Krystal L. Holtcamp, Misha A. Host, Gabrielle Hussey, Danielle M. Kramer, Joan Q. Lawrence, Madeline M. Martin, Ellen N. Niemiec, Ashleigh P. O’Reilly, Olivia A. Pahl, Guadalupe Quintana, Elizabeth A.S. Rettie, Torie L. Richardson, Arianne E. Rodriguez, Mona O. Rodriguez, Laura Schiraldi, Joanna J. Smith, Kelsey F. Sugrue, Lindsey J. Suriano, Kaitlyn E. Takach, Arielle M. Vasquez, Ximena Velez, Elizabeth J. Villafuerte, Laura T. Vives, Victoria R. Zellmer, Jeanette Hauke, Charles R. Hauser, Karolyn Barker, Laurie Cannon, Perouza Parsamian, Samantha Parsons, Zachariah Wichman, Christopher W. Bazinet, Diana E. Johnson, Abubakarr Bangura, Jordan A. Black, Victoria Chevee, Sarah A. Einsteen, Sarah K. Hilton, Max Kollmer, Rahul Nadendla, Joyce Stamm, Antoinette E. Fafara-Thompson, Amber M. Gygi, Emmy E. Ogawa, Matt Van Camp, Zuzana Kocsisova, Judith L. Leatherman, Cassie M. Modahl, Michael R. Rubin, Susana S. Apiz-Saab, Suzette M. Arias-Mejias, Carlos F. Carrion-Ortiz, Patricia N. Claudio-Vazquez, Debbie M. Espada-Green, Marium Feliciano-Camacho, Karina M. Gonzalez-Bonilla, Mariela Taboas-Arroyo, Dorianmarie Vargas-Franco, Raquel Montañez-Gonzalez, Joseph Perez-Otero, Myrielis Rivera-Burgos, Francisco J. Rivera-Rosario, Heather L. Eisler, Jackie Alexander, Samatha K. Begley, Deana Gabbard, Robert J. Allen, Wint Yan Aung, William D. Barshop, Amanda Boozalis, Vanessa P. Chu, Jeremy S. Davis, Ryan N. Duggal, Robert Franklin, Katherine Gavinski, Heran Gebreyesus, Henry Z. Gong, Rachel A. Greenstein, Averill D. Guo, Casey Hanson, Kaitlin E. Homa, Simon C. Hsu, Yi Huang, Lucy Huo, Sarah Jacobs, Sasha Jia, Kyle L. Jung, Sarah Wai-Chee Kong, Matthew R. Kroll, Brandon M. Lee, Paul F. Lee, Kevin M. Levine, Amy S. Li, Chengyu Liu, Max Mian Liu, Adam P. Lousararian, Peter B. Lowery, Allyson P. Mallya, Joseph E. Marcus, Patrick C. Ng, Hien P. Nguyen, Ruchik Patel, Hashini Precht, Suchita Rastogi, Jonathan M. Sarezky, Adam Schefkind, Michael B. Schultz, Delia Shen, Tara Skorupa, Nicholas C. Spies, Gabriel Stancu, Hiu Man Vivian Tsang, Alice L. Turski, Rohit Venkat, Leah E. Waldman, Kaidi Wang, Tracy Wang, Jeffrey W. Wei, Dennis Y. Wu, David D. Xiong, Jack Yu, Karen Zhou, Gerard P. McNeil, Robert W. Fernandez, Patrick Gomez Menzies, Tingting Gu, Jeremy Buhler, Elaine R. Mardis, Sarah C.R. Elgin

G3: Genes, Genomes, Genetics August 2017 7: 2439-2460;

DOI: https://doi.org/10.1534/g3.117.040907