September 2020 Table of Contents

Investigations

• Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)

  James M. Pflug, Valerie Renee Holmes, Crystal Burrus, J. Spencer Johnston, David R. Maddison

  G3: Genes, Genomes, Genetics September 2020 10: 3047-3060; https://doi.org/10.1534/g3.120.401028
• Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History

  Marja E. Heikkinen, Minna Ruokonen, Thomas A. White, Michelle M. Alexander, İslam Gündüz, Keith M. Dobney, Jouni Aspi, Jeremy B. Searle, Tanja Pyhäjärvi

  G3: Genes, Genomes, Genetics September 2020 10: 3061-3070; https://doi.org/10.1534/g3.120.400886
• cnd-1/NeuroD1 Functions with the Homeobox Gene ceh-5/Vax2 and Hox Gene ceh-13/labial To Specify Aspects of RME and DD Neuron Fate in Caenorhabditis elegans

  Wendy Aquino-Nunez, Zachery E. Mielko, Trae Dunn, Elise M. Santorella, Ciara Hosea, Lauren Leitner, Derrica McCalla, Claire Simms, Wendy M. Verola, Sharanya Vijaykumar, Martin L. Hudson

  G3: Genes, Genomes, Genetics September 2020 10: 3071-3085; https://doi.org/10.1534/g3.120.401515
• The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions

  Anna Fijarczyk, Mathieu Hénault, Souhir Marsit, Guillaume Charron, Tobias Fischborn, Luc Nicole-Labrie, Christian R. Landry

  G3: Genes, Genomes, Genetics September 2020 10: 3087-3097; https://doi.org/10.1534/g3.120.401149
• Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets

  Oluwasegun Kuloyo, Ruan Fourie, Errol Cason, Jacobus Albertyn, Carolina H. Pohl

  G3: Genes, Genomes, Genetics September 2020 10: 3099-3108; https://doi.org/10.1534/g3.120.401340
• Loss of the Antimicrobial Peptide Metchnikowin Protects Against Traumatic Brain Injury Outcomes in Drosophila melanogaster

  Laura C. Swanson, Stacey A. Rimkus, Barry Ganetzky, David A. Wassarman

  G3: Genes, Genomes, Genetics September 2020 10: 3109-3119; https://doi.org/10.1534/g3.120.401377
• Protein Interactions of the Mechanosensory Proteins Wsc2 and Wsc3 for Stress Resistance in Saccharomyces cerevisiae

  Vladimir Vélez-Segarra, Sahily González-Crespo, Ednalise Santiago-Cartagena, Luis E. Vázquez-Quiñones, Nelson Martínez-Matías, Yamirelis Otero, Julián J. Zayas, Rafael Siaca, Jeanmadi del Rosario, Inoushka Mejías, José J. Aponte, Noelani C. Collazo, Francisco J. Lasso, Jamie Snider, Matthew Jessulat, Hiroyuki Aoki, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina

  G3: Genes, Genomes, Genetics September 2020 10: 3121-3135; https://doi.org/10.1534/g3.120.401468
• Phantom Epistasis in Genomic Selection: On the Predictive Ability of Epistatic Models

  Matías F. Schrauf, Johannes W. R. Martini, Henner Simianer, Gustavo de los Campos, Rodolfo Cantet, Jan Freudenthal, Arthur Korte, Sebastián Munilla

  G3: Genes, Genomes, Genetics September 2020 10: 3137-3145; https://doi.org/10.1534/g3.120.401300
• The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes (Zosterops lateralis)

  Ashley T. Sendell-Price, Kristen C. Ruegg, Eric C. Anderson, Claudio S. Quilodrán, Benjamin M. Van Doren, Vinh L. Underwood, Tim Coulson, Sonya M. Clegg

  G3: Genes, Genomes, Genetics September 2020 10: 3147-3163; https://doi.org/10.1534/g3.120.401352
• Antipsychotic Behavioral Phenotypes in the Mouse Collaborative Cross Recombinant Inbred Inter-Crosses (RIX)

  Paola Giusti-Rodríguez, James G. Xenakis, James J. Crowley, Randal J. Nonneman, Daniela M. DeCristo, Allison Ryan, Corey R. Quackenbush, Darla R. Miller, Ginger D. Shaw, Vasyl Zhabotynsky, Patrick F. Sullivan, Fernando Pardo Manuel de Villena, Fei Zou

  G3: Genes, Genomes, Genetics September 2020 10: 3165-3177; https://doi.org/10.1534/g3.120.400975
• Low Oxygen Stress During Early Development Influences Regulation of Hypoxia-Response Genes in Farmed Atlantic Salmon (Salmo salar)

  Tara Kelly, Hanne Johnsen, Erik Burgerhout, Helge Tveiten, Tina Thesslund, Øivind Andersen, Nicholas Robinson

  G3: Genes, Genomes, Genetics September 2020 10: 3179-3188; https://doi.org/10.1534/g3.120.401459
• Precise Replacement of Saccharomyces cerevisiae Proteasome Genes with Human Orthologs by an Integrative Targeting Method

  Christopher M. Yellman

  G3: Genes, Genomes, Genetics September 2020 10: 3189-3200; https://doi.org/10.1534/g3.120.401526
• Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus

  Chuanji Zhao, Lijiang Liu, Luqman Bin Safdar, Meili Xie, Xiaohui Cheng, Yueying Liu, Yang Xiang, Chaobo Tong, Jinxing Tu, Junyan Huang, Shengyi Liu

  G3: Genes, Genomes, Genetics September 2020 10: 3201-3211; https://doi.org/10.1534/g3.120.401460
• The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments

  R. Nicolas Lou, Nina O. Therkildsen, Philipp W. Messer

  G3: Genes, Genomes, Genetics September 2020 10: 3213-3227; https://doi.org/10.1534/g3.120.401287
• Gene Transcription as a Limiting Factor in Protein Production and Cell Growth

  Eyal Metzl-Raz, Moshe Kafri, Gilad Yaakov, Naama Barkai

  G3: Genes, Genomes, Genetics September 2020 10: 3229-3242; https://doi.org/10.1534/g3.120.401303
• A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts

  Matthew Chung, Preston J. Basting, Rayanna S. Patkus, Alexandra Grote, Ashley N. Luck, Elodie Ghedin, Barton E. Slatko, Michelle Michalski, Jeremy M. Foster, Casey M. Bergman, Julie C. Dunning Hotopp

  G3: Genes, Genomes, Genetics September 2020 10: 3243-3260; https://doi.org/10.1534/g3.120.401534
• Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt

  Hannah C. Halpern, Peng Qi, Robert C. Kemerait, Marin T. Brewer

  G3: Genes, Genomes, Genetics September 2020 10: 3261-3269; https://doi.org/10.1534/g3.120.401187
• Regulation of Gliogenesis by lin-32/Atoh1 in Caenorhabditis elegans

  Albert Zhang, Kentaro Noma, Dong Yan

  G3: Genes, Genomes, Genetics September 2020 10: 3271-3278; https://doi.org/10.1534/g3.120.401547
• Genome-Wide Association Analysis Identified ANXA1 Associated with Shoulder Impingement Syndrome in UK Biobank Samples

  Bolun Cheng, Yujie Ning, Chujun Liang, Ping Li, Li Liu, Shiqiang Cheng, Mei Ma, Lu Zhang, Xin Qi, Yan Wen, Feng Zhang

  G3: Genes, Genomes, Genetics September 2020 10: 3279-3284; https://doi.org/10.1534/g3.120.401257
• Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Pyrus Collection

  Sara Montanari, Joseph Postman, Nahla V. Bassil, David B. Neale

  G3: Genes, Genomes, Genetics September 2020 10: 3285-3297; https://doi.org/10.1534/g3.120.401327
• Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms

  R. Rebecca Love, Marco Pombi, Moussa W. Guelbeogo, Nathan R. Campbell, Melissa T. Stephens, Roch K. Dabire, Carlo Costantini, Alessandra della Torre, Nora J. Besansky

  G3: Genes, Genomes, Genetics September 2020 10: 3299-3307; https://doi.org/10.1534/g3.120.401418
• Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

  Ajith V. Pankajam, Suman Dash, Asma Saifudeen, Abhishek Dutta, Koodali T. Nishant

  G3: Genes, Genomes, Genetics September 2020 10: 3309-3319; https://doi.org/10.1534/g3.120.401551
• Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR

  Arash Akbarzadeh, Aimee Lee S. Houde, Ben J. G. Sutherland, Oliver P. Günther, Kristina M. Miller

  G3: Genes, Genomes, Genetics September 2020 10: 3321-3336; https://doi.org/10.1534/g3.120.401487
• The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development

  Yijia Zhou, Funan He, Weilin Pu, Xun Gu, Jiucun Wang, Zhixi Su

  G3: Genes, Genomes, Genetics September 2020 10: 3337-3346; https://doi.org/10.1534/g3.120.401511
• High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (Lolium perenne L.)

  Thomas Keep, Jean-Paul Sampoux, José Luis Blanco-Pastor, Klaus J. Dehmer, Matthew J. Hegarty, Thomas Ledauphin, Isabelle Litrico, Hilde Muylle, Isabel Roldán-Ruiz, Anna M. Roschanski, Tom Ruttink, Fabien Surault, Evelin Willner, Philippe Barre

  G3: Genes, Genomes, Genetics September 2020 10: 3347-3364; https://doi.org/10.1534/g3.120.401491
• Genome Resequencing, Improvement of Variant Calling, and Population Genomic Analyses Provide Insights into the Seedlessness in the Genus Vitis

  Myung-Shin Kim, Youn Young Hur, Ji Hong Kim, Soon-Chun Jeong

  G3: Genes, Genomes, Genetics September 2020 10: 3365-3377; https://doi.org/10.1534/g3.120.401521
• The SEM-4 Transcription Factor Is Required for Regulation of the Oxidative Stress Response in Caenorhabditis elegans

  Adilya Rafikova, Queenie Hu, Terrance J. Kubiseski

  G3: Genes, Genomes, Genetics September 2020 10: 3379-3385; https://doi.org/10.1534/g3.120.401316
• speck, First Identified in Drosophila melanogaster in 1910, Is Encoded by the Arylalkalamine N-Acetyltransferase (AANAT1) Gene

  Eric P. Spana, Amanda B. Abrams, Katharine T. Ellis, Jason C. Klein, Brandon T. Ruderman, Alvin H. Shi, Daniel Zhu, Andrea Stewart, Susan May

  G3: Genes, Genomes, Genetics September 2020 10: 3387-3398; https://doi.org/10.1534/g3.120.401470
• A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions

  Dae-Kyum Kim, Jennifer J. Knapp, Da Kuang, Aditya Chawla, Patricia Cassonnet, Hunsang Lee, Dayag Sheykhkarimli, Payman Samavarchi-Tehrani, Hala Abdouni, Ashyad Rayhan, Roujia Li, Oxana Pogoutse, Étienne Coyaud, Sylvie van der Werf, Caroline Demeret, Anne-Claude Gingras, Mikko Taipale, Brian Raught, Yves Jacob, Frederick P. Roth

  G3: Genes, Genomes, Genetics September 2020 10: 3399-3402; https://doi.org/10.1534/g3.120.401554
• Can a Population Targeted by a CRISPR-Based Homing Gene Drive Be Rescued?

  Nicolas O. Rode, Virginie Courtier-Orgogozo, Florence Débarre

  G3: Genes, Genomes, Genetics September 2020 10: 3403-3415; https://doi.org/10.1534/g3.120.401484
• Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus

  Javier F. Tabima, Ian A. Trautman, Ying Chang, Yan Wang, Stephen Mondo, Alan Kuo, Asaf Salamov, Igor V. Grigoriev, Jason E. Stajich, Joseph W. Spatafora

  G3: Genes, Genomes, Genetics September 2020 10: 3417-3433; https://doi.org/10.1534/g3.120.401516
• SIR2 Expression Noise Can Generate Heterogeneity in Viability but Does Not Affect Cell-to-Cell Epigenetic Silencing of Subtelomeric URA3 in Yeast

  Jian Liu, Laureline Mosser, Catherine Botanch, Jean-Marie François, Jean-Pascal Capp

  G3: Genes, Genomes, Genetics September 2020 10: 3435-3443; https://doi.org/10.1534/g3.120.401589
• Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum

  Sibel Kucukyildirim, Megan Behringer, Way Sung, Debra A. Brock, Thomas G. Doak, Hatice Mergen, David C. Queller, Joan E. Strassmann, Michael Lynch

  G3: Genes, Genomes, Genetics September 2020 10: 3445-3452; https://doi.org/10.1534/g3.120.401578
• Genetic Basis of Natural Variation in Spontaneous Grooming in Drosophila melanogaster

  Aya Yanagawa, Wen Huang, Akihiko Yamamoto, Ayako Wada-Katsumata, Coby Schal, Trudy F. C. Mackay

  G3: Genes, Genomes, Genetics September 2020 10: 3453-3460; https://doi.org/10.1534/g3.120.401360