Male orchid bee Euglossa dilemma drinking nectar. Whole genome sequencing efforts by Brand et al. (2891–2898) published in this issue of G3 revealed that E. dilemma has one of the largest genomes known for insects. Image: Thomas Eltz.

Check out the September issue of G3!

Table of Contents

Genome Reports

Whole Genome Sequence of the Heterozygous Clinical Isolate Candida krusei 81-B-5

Christina A. Cuomo, Terrance Shea, Bo Yang, Reeta Rao, Anja Forche

G3: Genes, Genomes, Genetics September 2017 7: 2883-2889;

DOI: https://doi.org/10.1534/g3.117.043547

The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

Philipp Brand, Nicholas Saleh, Hailin Pan, Cai Li, Karen M. Kapheim, Santiago R. Ramírez

G3: Genes, Genomes, Genetics September 2017 7: 2891-2898;

DOI: https://doi.org/10.1534/g3.117.043687

Genome-Wide Analysis of the First Sequenced Mycoplasma capricolum subsp. capripneumoniae Strain M1601

Shengli Chen, Huafang Hao, Ping Zhao, François Thiaucourt, Ying He, Pengcheng Gao, Han Guo, Wenheng Ji, Zhanhui Wang, Zhongxin Lu, Yuefeng Chu, Yongsheng Liu

G3: Genes, Genomes, Genetics September 2017 7: 2899-2906;

DOI: https://doi.org/10.1534/g3.117.300085

Mutant Screen Report

Genome-Wide Screen for Genes Involved in Caenorhabditis elegans Developmentally Timed Sleep

Huiyan Huang, Chen-Tseh Zhu, Lukas L. Skuja, Dustin J. Hayden, Anne C. Hart

G3: Genes, Genomes, Genetics September 2017 7: 2907-2917;

DOI: https://doi.org/10.1534/g3.117.300071

Investigations

Habitat Predicts Levels of Genetic Admixture in Saccharomyces cerevisiae

Viranga Tilakaratna, Douda Bensasson

G3: Genes, Genomes, Genetics September 2017 7: 2919-2929;

DOI: https://doi.org/10.1534/g3.117.041806

ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy

Isha Monga, Abid Qureshi, Nishant Thakur, Amit Kumar Gupta, Manoj Kumar

G3: Genes, Genomes, Genetics September 2017 7: 2931-2943;

DOI: https://doi.org/10.1534/g3.117.044024

Functional Profiling of Transcription Factor Genes in Neurospora crassa

Alexander J. Carrillo, Patrick Schacht, Ilva E. Cabrera, Johnathon Blahut, Loren Prudhomme, Sarah Dietrich, Thomas Bekman, Jennifer Mei, Cristian Carrera, Vivian Chen, Isaiah Clark, Gerardo Fierro, Logan Ganzen, Jose Orellana, Shelby Wise, Kevin Yang, Hui Zhong, Katherine A. Borkovich

G3: Genes, Genomes, Genetics September 2017 7: 2945-2956;

DOI: https://doi.org/10.1534/g3.117.043331

Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization

Benjamin R. Jack, Daniel R. Boutz, Matthew L. Paff, Bartram L. Smith, James J. Bull, Claus O. Wilke

G3: Genes, Genomes, Genetics September 2017 7: 2957-2968;

DOI: https://doi.org/10.1534/g3.117.041020

The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status

David Angeles-Albores, Daniel H. W. Leighton, Tiffany Tsou, Tiffany H. Khaw, Igor Antoshechkin, Paul W. Sternberg

G3: Genes, Genomes, Genetics September 2017 7: 2969-2977;

DOI: https://doi.org/10.1534/g3.117.300080

The SEK-1 p38 MAP Kinase Pathway Modulates Gq Signaling in Caenorhabditis elegans

Jill M. Hoyt, Samuel K. Wilson, Madhuri Kasa, Jeremy S. Rise, Irini Topalidou, Michael Ailion

G3: Genes, Genomes, Genetics September 2017 7: 2979-2989;

DOI: https://doi.org/10.1534/g3.117.043273

Two Types of Etiological Mutation in the Limb-Specific Enhancer of Shh

Takanori Amano, Tomoko Sagai, Ryohei Seki, Toshihiko Shiroishi

G3: Genes, Genomes, Genetics September 2017 7: 2991-2998;

DOI: https://doi.org/10.1534/g3.117.044669

Gene Expression Networks in the Murine Pulmonary Myocardium Provide Insight into the Pathobiology of Atrial Fibrillation

Jordan K. Boutilier, Rhonda L. Taylor, Tracy Mann, Elyshia McNamara, Gary J. Hoffman, Jacob Kenny, Rodney J. Dilley, Peter Henry, Grant Morahan, Nigel G. Laing, Kristen J. Nowak

G3: Genes, Genomes, Genetics September 2017 7: 2999-3017;

DOI: https://doi.org/10.1534/g3.117.044651

Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat

Philippa Borrill, Sophie A. Harrington, Cristobal Uauy

G3: Genes, Genomes, Genetics September 2017 7: 3019-3029;

DOI: https://doi.org/10.1534/g3.117.043679

RNA-seq of Rice Yellow Stem Borer Scirpophaga incertulas Reveals Molecular Insights During Four Larval Developmental Stages

Pichili Renuka, Maganti S. Madhav, Ayyagari Phani Padmakumari, Kalyani M. Barbadikar, Satendra K. Mangrauthia, Kola Vijaya Sudhakara Rao, Soma S. Marla, Vemuri Ravindra Babu

G3: Genes, Genomes, Genetics September 2017 7: 3031-3045;

DOI: https://doi.org/10.1534/g3.117.043737

Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

David L. Oldeschulte, Yvette A. Halley, Miranda L. Wilson, Eric K. Bhattarai, Wesley Brashear, Joshua Hill, Richard P. Metz, Charles D. Johnson, Dale Rollins, Markus J. Peterson, Derek M. Bickhart, Jared E. Decker, John F. Sewell, Christopher M. Seabury

G3: Genes, Genomes, Genetics September 2017 7: 3047-3058;

DOI: https://doi.org/10.1534/g3.117.043083

Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease

Joseph R. Owen, Noelle Noyes, Amy E. Young, Daniel J. Prince, Patricia C. Blanchard, Terry W. Lehenbauer, Sharif S. Aly, Jessica H. Davis, Sean M. O’Rourke, Zaid Abdo, Keith Belk, Michael R. Miller, Paul Morley, Alison L. Van Eenennaam

G3: Genes, Genomes, Genetics September 2017 7: 3059-3071;

DOI: https://doi.org/10.1534/g3.117.1137

Genome-Wide Transcriptional Dynamics in the Companion Bacterial Symbionts of the Glassy-Winged Sharpshooter (Cicadellidae: Homalodisca vitripennis) Reveal Differential Gene Expression in Bacteria Occupying Multiple Host Organs

Gordon M. Bennett, Rebecca A. Chong

G3: Genes, Genomes, Genetics September 2017 7: 3073-3082;

DOI: https://doi.org/10.1534/g3.117.044255

Regulation of Small Mitochondrial DNA Replicative Advantage by Ribonucleotide Reductase in Saccharomyces cerevisiae

Elliot Bradshaw, Minoru Yoshida, Feng Ling

G3: Genes, Genomes, Genetics September 2017 7: 3083-3090;

DOI: https://doi.org/10.1534/g3.117.043851

3′-Terminated Overhangs Regulate DNA Double-Strand Break Processing in Escherichia coli

Edyta ðermic, Davor Zahradka, Dušica Vujaklija, Siniša Ivankovic, Damir ðermic

G3: Genes, Genomes, Genetics September 2017 7: 3091-3102;

DOI: https://doi.org/10.1534/g3.117.043521

Application of Response Surface Methods To Determine Conditions for Optimal Genomic Prediction

Réka Howard, Alicia L. Carriquiry, William D. Beavis

G3: Genes, Genomes, Genetics September 2017 7: 3103-3113;

DOI: https://doi.org/10.1534/g3.117.044453

A Large Deletion in the NSDHL Gene in Labrador Retrievers with a Congenital Cornification Disorder

Anina Bauer, Michela De Lucia, Vidhya Jagannathan, Giorgia Mezzalira, Margret L. Casal, Monika M. Welle, Tosso Leeb

G3: Genes, Genomes, Genetics September 2017 7: 3115-3121;

DOI: https://doi.org/10.1534/g3.117.1124

Sequence-Based Mapping and Genome Editing Reveal Mutations in Stickleback Hps5 Cause Oculocutaneous Albinism and the casper Phenotype

James C. Hart, Craig T. Miller

G3: Genes, Genomes, Genetics September 2017 7: 3123-3131;

DOI: https://doi.org/10.1534/g3.117.1125

Ankyrin-1 Gene Exhibits Allelic Heterogeneity in Conferring Protection Against Malaria

Hong Ming Huang, Denis C. Bauer, Patrick M. Lelliott, Matthew W. A. Dixon, Leann Tilley, Brendan J. McMorran, Simon J. Foote, Gaetan Burgio

G3: Genes, Genomes, Genetics September 2017 7: 3133-3144;

DOI: https://doi.org/10.1534/g3.117.300079

Evolutionary Dynamics of Male Reproductive Genes in the Drosophila virilis Subgroup

Yasir H. Ahmed-Braimah, Robert L. Unckless, Andrew G. Clark

G3: Genes, Genomes, Genetics September 2017 7: 3145-3155;

DOI: https://doi.org/10.1534/g3.117.1136

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

David B. Neale, Patrick E. McGuire, Nicholas C. Wheeler, Kristian A. Stevens, Marc W. Crepeau, Charis Cardeno, Aleksey V. Zimin, Daniela Puiu, Geo M. Pertea, U. Uzay Sezen, Claudio Casola, Tomasz E. Koralewski, Robin Paul, Daniel Gonzalez-Ibeas, Sumaira Zaman, Richard Cronn, Mark Yandell, Carson Holt, Charles H. Langley, James A. Yorke, Steven L. Salzberg, Jill L. Wegrzyn

G3: Genes, Genomes, Genetics September 2017 7: 3157-3167;

DOI: https://doi.org/10.1534/g3.117.300078

Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer (Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing

Hengxing Ba, Boyin Jia, Guiwu Wang, Yifeng Yang, Gilead Kedem, Chunyi Li

G3: Genes, Genomes, Genetics September 2017 7: 3169-3176;

DOI: https://doi.org/10.1534/g3.117.300082

The Stress-Inducible Peroxidase TSA2 Underlies a Conditionally Beneficial Chromosomal Duplication in Saccharomyces cerevisiae

Robert A. Linder, John P. Greco, Fabian Seidl, Takeshi Matsui, Ian M. Ehrenreich

G3: Genes, Genomes, Genetics September 2017 7: 3177-3184;

DOI: https://doi.org/10.1534/g3.117.300069

Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans

Mark G. Sterken, Linda van Bemmelen van der Plaat, Joost A. G. Riksen, Miriam Rodriguez, Tobias Schmid, Alex Hajnal, Jan E. Kammenga, Basten L. Snoek

G3: Genes, Genomes, Genetics September 2017 7: 3185-3193;

DOI: https://doi.org/10.1534/g3.117.1120

The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes (Haplochromis chilotes x H. nyererei)

C. Darrin Hulsey, Gonzalo Machado-Schiaffino, Lara Keicher, Diego Ellis-Soto, Frederico Henning, Axel Meyer

G3: Genes, Genomes, Genetics September 2017 7: 3195-3202;

DOI: https://doi.org/10.1534/g3.117.300083

A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis

Vasso Makrantoni, Adam Ciesiolka, Conor Lawless, Josefin Fernius, Adele Marston, David Lydall, Michael J. R. Stark

G3: Genes, Genomes, Genetics September 2017 7: 3203-3215;

DOI: https://doi.org/10.1534/g3.117.300089

Trans-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus

Maren E. Cannon, Qing Duan, Ying Wu, Monica Zeynalzadeh, Zheng Xu, Antti J. Kangas, Pasi Soininen, Mika Ala-Korpela, Mete Civelek, Aldons J. Lusis, Johanna Kuusisto, Francis S. Collins, Michael Boehnke, Hua Tang, Markku Laakso, Yun Li, Karen L. Mohlke

G3: Genes, Genomes, Genetics September 2017 7: 3217-3227;

DOI: https://doi.org/10.1534/g3.117.300088

Accelerating Wright–Fisher Forward Simulations on the Graphics Processing Unit

David S. Lawrie

G3: Genes, Genomes, Genetics September 2017 7: 3229-3236;

DOI: https://doi.org/10.1534/g3.117.300103

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