New in G3: halophilic yeast, cotton gene flow, and karyotypic evolution in icefish

Check out the July issue of G3!

Table of Contents

Genome Report

Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure

Sunita Sinha, Stephane Flibotte, Mauricio Neira, Sean Formby, Ana Plemenitaš, Nina Gunde Cimerman, Metka Lenassi, Cene Gostincar, Jason E. Stajich, Corey Nislow

G3: Genes, Genomes, Genetics July 2017 7: 2015-2022;

DOI: https://doi.org/10.1534/g3.117.040691

Mutant Screen Report

RNAi-Mediated Reverse Genetic Screen Identified Drosophila Chaperones Regulating Eye and Neuromuscular Junction Morphology

Sandeep Raut, Bhagaban Mallik, Arpan Parichha, Valsakumar Amrutha, Chandan Sahi, Vimlesh Kumar

G3: Genes, Genomes, Genetics July 2017 7: 2023-2038;

DOI: https://doi.org/10.1534/g3.117.041632

Investigations

Assessment of Single Cell RNA-Seq Normalization Methods

Bo Ding, Lina Zheng, Wei Wang

G3: Genes, Genomes, Genetics July 2017 7: 2039-2045;

DOI: https://doi.org/10.1534/g3.117.040683

Construction of a Recyclable Genetic Marker and Serial Gene Deletions in the Human Pathogenic Mucorales Mucor circinelloides

Alexis Garcia, Gloria Adedoyin, Joseph Heitman, Soo Chan Lee

G3: Genes, Genomes, Genetics July 2017 7: 2047-2054;

DOI: https://doi.org/10.1534/g3.117.041095

Novel Mutations in Synaptic Transmission Genes Suppress Neuronal Hyperexcitation in Caenorhabditis elegans

Katherine A. McCulloch, Yingchuan B. Qi, Seika Takayanagi-Kiya, Yishi Jin, Salvatore J. Cherra

G3: Genes, Genomes, Genetics July 2017 7: 2055-2063;

DOI: https://doi.org/10.1534/g3.117.042598

Manipulating the Mitochondrial Genome To Enhance Cattle Embryo Development

Kanokwan Srirattana, Justin C. St. John

G3: Genes, Genomes, Genetics July 2017 7: 2065-2080;

DOI: https://doi.org/10.1534/g3.117.042655

Validated Bayesian Differentiation of Causative and Passenger Mutations

Frederick R. Cross, Michal Breker, Kristi Lieberman

G3: Genes, Genomes, Genetics July 2017 7: 2081-2094;

DOI: https://doi.org/10.1534/g3.117.039016

Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

Zhangyi He, Mark Beaumont, Feng Yu

G3: Genes, Genomes, Genetics July 2017 7: 2095-2106;

DOI: https://doi.org/10.1534/g3.117.041038

Exploring the Impact of Cleavage and Polyadenylation Factors on Pre-mRNA Splicing Across Eukaryotes

Gildas Lepennetier, Francesco Catania

G3: Genes, Genomes, Genetics July 2017 7: 2107-2114;

DOI: https://doi.org/10.1534/g3.117.041483

Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation

Marta Niedzicka, Katarzyna Dudek, Anna Fijarczyk, Piotr Zielinski, Wieslaw Babik

G3: Genes, Genomes, Genetics July 2017 7: 2115-2124;

DOI: https://doi.org/10.1534/g3.117.041178

Comparative Transcriptomic Analysis of Race 1 and Race 4 of Fusarium oxysporum f. sp. cubense Induced with Different Carbon Sources

Shiwen Qin, Chunyan Ji, Yunfeng Li, Zhenzhong Wang

G3: Genes, Genomes, Genetics July 2017 7: 2125-2138;

DOI: https://doi.org/10.1534/g3.117.042226

The Immune Phenotype of Three Drosophila Leukemia Models

Badrul Arefin, Martin Kunc, Robert Krautz, Ulrich Theopold

G3: Genes, Genomes, Genetics July 2017 7: 2139-2149;

DOI: https://doi.org/10.1534/g3.117.039487

Two Loci Contribute Epistastically to Heterospecific Pollen Rejection, a Postmating Isolating Barrier Between Species

Jennafer A. P. Hamlin, Natasha A. Sherman, Leonie C. Moyle

G3: Genes, Genomes, Genetics July 2017 7: 2151-2159;

DOI: https://doi.org/10.1534/g3.117.041673

Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize

Heather Manching, Subhajit Sengupta, Keith R. Hopper, Shawn W. Polson, Yuan Ji, Randall J. Wisser

G3: Genes, Genomes, Genetics July 2017 7: 2161-2170;

DOI: https://doi.org/10.1534/g3.117.042036

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

Jordi Leno-Colorado, Nick J. Hudson, Antonio Reverter, Miguel Pérez-Enciso

G3: Genes, Genomes, Genetics July 2017 7: 2171-2184;

DOI: https://doi.org/10.1534/g3.117.042671

Assessment of Gene Flow Between Gossypium hirsutum and G. herbaceum: Evidence of Unreduced Gametes in the Diploid Progenitor

E. Montes, O. Coriton, F. Eber, V. Huteau, J. M. Lacape, C. Reinhardt, D. Marais, J. L. Hofs, A. M. Chèvre, C. Pannetier

G3: Genes, Genomes, Genetics July 2017 7: 2185-2193;

DOI: https://doi.org/10.1534/g3.117.041509

Cold Fusion: Massive Karyotype Evolution in the Antarctic Bullhead Notothen Notothenia coriiceps

Angel Amores, Catherine A. Wilson, Corey A. H. Allard, H. William Detrich, John H. Postlethwait

G3: Genes, Genomes, Genetics July 2017 7: 2195-2207;

DOI: https://doi.org/10.1534/g3.117.040063

Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis)

Alejandro P. Gutierrez, Frances Turner, Karim Gharbi, Richard Talbot, Natalie R. Lowe, Carolina Peñaloza, Mark McCullough, Paulo A. Prodöhl, Tim P. Bean, Ross D. Houston

G3: Genes, Genomes, Genetics July 2017 7: 2209-2218;

DOI: https://doi.org/10.1534/g3.117.041780

Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae

Kinnari Matheson, Lance Parsons, Alison Gammie

G3: Genes, Genomes, Genetics July 2017 7: 2219-2226;

DOI: https://doi.org/10.1534/g3.117.040022

A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

Yasuaki Takada, Ryutaro Miyagi, Aya Takahashi, Toshinori Endo, Naoki Osada

G3: Genes, Genomes, Genetics July 2017 7: 2227-2234;

DOI: https://doi.org/10.1534/g3.117.042895

Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae

Siwen Wang, Zheng Xing, Pete E. Pascuzzi, Elizabeth J. Tran

G3: Genes, Genomes, Genetics July 2017 7: 2235-2247;

DOI: https://doi.org/10.1534/g3.117.041814

Definition of a RACK1 Interaction Network in Drosophila melanogaster Using SWATH-MS

Lauriane Kuhn, Karim Majzoub, Evelyne Einhorn, Johana Chicher, Julien Pompon, Jean-Luc Imler, Philippe Hammann, Carine Meignin

G3: Genes, Genomes, Genetics July 2017 7: 2249-2258;

DOI: https://doi.org/10.1534/g3.117.042564

Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

R. J. Cody Markelz, Michael F. Covington, Marcus T. Brock, Upendra K. Devisetty, Daniel J. Kliebenstein, Cynthia Weinig, Julin N. Maloof

G3: Genes, Genomes, Genetics July 2017 7: 2259-2270;

DOI: https://doi.org/10.1534/g3.117.043000

A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease

Chao Xu, Ji-Gang Zhang, Dongdong Lin, Lan Zhang, Hui Shen, Hong-Wen Deng

G3: Genes, Genomes, Genetics July 2017 7: 2271-2279;

DOI: https://doi.org/10.1534/g3.117.042408

Genetic Subtraction Profiling Identifies Candidate miRNAs Involved in Rice Female Gametophyte Abortion

Liyu Yang, Ya Wu, Wenliang Wang, Bigang Mao, Bingran Zhao, Jianbo Wang

G3: Genes, Genomes, Genetics July 2017 7: 2281-2293;

DOI: https://doi.org/10.1534/g3.117.040808

The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes

Claude Pasquier, Sandra Agnel, Alain Robichon

G3: Genes, Genomes, Genetics July 2017 7: 2295-2304;

DOI: https://doi.org/10.1534/g3.117.042911

Essential Function of the Serine Hydroxymethyl Transferase (SHMT) Gene During Rapid Syncytial Cell Cycles in Drosophila

Franziska Winkler, Maria Kriebel, Michaela Clever, Stephanie Gröning, Jörg Großhans

G3: Genes, Genomes, Genetics July 2017 7: 2305-2314;

DOI: https://doi.org/10.1534/g3.117.043133

Rapid Cycling Genomic Selection in a Multiparental Tropical Maize Population

Xuecai Zhang, Paulino Pérez-Rodríguez, Juan Burgueño, Michael Olsen, Edward Buckler, Gary Atlin, Boddupalli M. Prasanna, Mateo Vargas, Félix San Vicente, José Crossa

G3: Genes, Genomes, Genetics July 2017 7: 2315-2326;

DOI: https://doi.org/10.1534/g3.117.043141

A Coding Variant in the Gene Bardet-Biedl Syndrome 4 (BBS4) Is Associated with a Novel Form of Canine Progressive Retinal Atrophy

Tracy Chew, Bianca Haase, Roslyn Bathgate, Cali E. Willet, Maria K. Kaukonen, Lisa J. Mascord, Hannes T. Lohi, Claire M. Wade

G3: Genes, Genomes, Genetics July 2017 7: 2327-2335;

DOI: https://doi.org/10.1534/g3.117.043109

Drosophila simulans: A Species with Improved Resolution in Evolve and Resequence Studies

Neda Barghi, Raymond Tobler, Viola Nolte, Christian Schlötterer

G3: Genes, Genomes, Genetics July 2017 7: 2337-2343;

DOI: https://doi.org/10.1534/g3.117.043349

Whole-Genome Resequencing Identifies the Molecular Genetic Cause for the Absence of a Gy5 Glycinin Protein in Soybean PI 603408

Jason D. Gillman, Won-Seok Kim, Bo Song, Nathan W. Oehrle, Nilesh R. Tawari, Shanshan Liu, Hari B. Krishnan

G3: Genes, Genomes, Genetics July 2017 7: 2345-2352;

DOI: https://doi.org/10.1534/g3.117.039347

A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata

Jacob A. Tennessen, Stephanie R. Bollmann, Michael S. Blouin

G3: Genes, Genomes, Genetics July 2017 7: 2353-2361;

DOI: https://doi.org/10.1534/g3.117.041319

The Evolutionary Basis of Translational Accuracy in Plants

Salvatore Camiolo, Gaurav Sablok, Andrea Porceddu

G3: Genes, Genomes, Genetics July 2017 7: 2363-2373;

DOI: https://doi.org/10.1534/g3.117.040626

Systematic Analysis of the DNA Damage Response Network in Telomere Defective Budding Yeast

Eva-Maria Holstein, Greg Ngo, Conor Lawless, Peter Banks, Matthew Greetham, Darren Wilkinson, David Lydall

G3: Genes, Genomes, Genetics July 2017 7: 2375-2389;

DOI: https://doi.org/10.1534/g3.117.042283

The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

Amanda S. Lobell, Rachel R. Kaspari, Yazmin L. Serrano Negron, Susan T. Harbison

G3: Genes, Genomes, Genetics July 2017 7: 2391-2403;

DOI: https://doi.org/10.1534/g3.117.042390

CORRIGENDUM

Corrigendum

G3: Genes, Genomes, Genetics July 2017 7: 2405;

DOI: https://doi.org/10.1534/g3.117.043190