May 2020

The painted burrowing frog (Neobatrachus pictus) is one of six diploid species in an Australian diploid-tetraploid species complex. The three tetraploids tend to occupy harsher habitats. Strikingly, genomic analyses show that the tetraploids are not completely genetically isolated from each other or the diploids, which in contrast are genetically isolated. Modelling of ecologically suitable areas for each species through time and genomic estimates of demographic histories, indicate that the diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. See Novikova, Brennan et al.

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Image Credit: Vera Novikova.

Research Articles

Interplay between axonal Wnt5-Vang and dendritic Wnt5-Drl/Ryk signaling controls glomerular patterning in the Drosophila antennal lobe

Huey Hing, Noah Reger, Jennifer Snyder, Lee G. Fradkin

PLOS Genetics: published May 1, 2020 | https://doi.org/10.1371/journal.pgen.1008767

An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages

Roberto F. Nespolo, Carlos A. Villarroel, Christian I. Oporto, Sebastián M. Tapia, Franco Vega-Macaya, Kamila Urbina, Matteo De Chiara, Simone Mozzachiodi, Ekaterina Mikhalev, Dawn Thompson, Luis F. Larrondo, Pablo Saenz-Agudelo, Gianni Liti, Francisco A. Cubillos

PLOS Genetics: published May 1, 2020 | https://doi.org/10.1371/journal.pgen.1008777

A new neuropeptide insect parathyroid hormone iPTH in the red flour beetle Tribolium castaneum

Jia Xie, Ming Sang, Xiaowen Song, Sisi Zhang, Donghun Kim, Jan A. Veenstra, Yoonseong Park, Bin Li

PLOS Genetics: published May 4, 2020 | https://doi.org/10.1371/journal.pgen.1008772

Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models

Sahir R. Bhatnagar, Yi Yang, Tianyuan Lu, Erwin Schurr, JC Loredo-Osti, Marie Forest, Karim Oualkacha, Celia M. T. Greenwood

PLOS Genetics: published May 4, 2020 | https://doi.org/10.1371/journal.pgen.1008766

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

Shan Jiang, Katherine Williams, Xiangduo Kong, Weihua Zeng, Nam Viet Nguyen, Xinyi Ma, Rabi Tawil, Kyoko Yokomori, Ali Mortazavi

PLOS Genetics: published May 4, 2020 | https://doi.org/10.1371/journal.pgen.1008754

Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma

Yosuke Tanigawa, Michael Wainberg, Juha Karjalainen, Tuomo Kiiskinen, Guhan Venkataraman, Susanna Lemmelä, Joni A. Turunen, Robert R. Graham, Aki S. Havulinna, Markus Perola, Aarno Palotie, FinnGen, Mark J. Daly, Manuel A. Rivas

PLOS Genetics: published May 5, 2020 | https://doi.org/10.1371/journal.pgen.1008682

Accounting for long-range correlations in genome-wide simulations of large cohorts

Dominic Nelson, Jerome Kelleher, Aaron P. Ragsdale, Claudia Moreau, Gil McVean, Simon Gravel

PLOS Genetics: published May 5, 2020 | https://doi.org/10.1371/journal.pgen.1008619

Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum

Eva L. Koch, Frédéric Guillaume

PLOS Genetics: published May 7, 2020 | https://doi.org/10.1371/journal.pgen.1008768

Bidirectional crosstalk between Hypoxia-Inducible Factor and glucocorticoid signalling in zebrafish larvae

Davide Marchi, Kirankumar Santhakumar, Eleanor Markham, Nan Li, Karl-Heinz Storbeck, Nils Krone, Vincent T. Cunliffe, Fredericus J. M. van Eeden

PLOS Genetics: published May 7, 2020 | https://doi.org/10.1371/journal.pgen.1008757

Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation

Sarina Y. Porcella, Natasha C. Koussa, Colin P. Tang, Daphne N. Kramer, Priyanka Srivastava, Duncan J. Smith

PLOS Genetics: published May 7, 2020 | https://doi.org/10.1371/journal.pgen.1008755

An EHBP-1-SID-3-DYN-1 axis promotes membranous tubule fission during endocytic recycling

Jinghu Gao, Linyue Zhao, Qian Luo, Shuyao Liu, Ziyang Lin, Peixiang Wang, Xin Fu, Juan Chen, Hongjie Zhang, Long Lin, Anbing Shi

PLOS Genetics: published May 8, 2020 | https://doi.org/10.1371/journal.pgen.1008763

ALC1/eIF4A1-mediated regulation of CtIP mRNA stability controls DNA end resection

Fernando Mejías-Navarro, Guillermo Rodríguez-Real, Javier Ramón, Rosa Camarillo, Pablo Huertas

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008787

Depletion of Ric-8B leads to reduced mTORC2 activity

Maíra H. Nagai, Victor P. S. Xavier, Luciana M. Gutiyama, Cleiton F. Machado, Alice H. Reis, Elisa R. Donnard, Pedro A. F. Galante, Jose G. Abreu, William T. Festuccia, Bettina Malnic

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008255

A cross-disorder PRS-pheWAS of 5 major psychiatric disorders in UK Biobank

Beate Leppert, Louise A. C. Millard, Lucy Riglin, George Davey Smith, Anita Thapar, Kate Tilling, Esther Walton, Evie Stergiakouli

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008185

ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing

Jiaxin Fan, Jian Hu, Chenyi Xue, Hanrui Zhang, Katalin Susztak, Muredach P. Reilly, Rui Xiao, Mingyao Li

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008786

The phosphorelay BarA/SirA activates the non-cognate regulator RcsB in Salmonella enterica

Hubert Salvail, Eduardo A. Groisman

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008722

Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta)

Marina Brasó-Vives, Inna S. Povolotskaya, Diego A. Hartasánchez, Xavier Farré, Marcos Fernandez-Callejo, Muthuswamy Raveendran, R. Alan Harris, Douglas L. Rosene, Belen Lorente-Galdos, Arcadi Navarro, Tomas Marques-Bonet, Jeffrey Rogers, David Juan

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008742

UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis

Eleni Tavridou, Emanuel Schmid-Siegert, Christian Fankhauser, Roman Ulm

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008797

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polina Yu. Novikova, Ian G. Brennan, William Booker, Michael Mahony, Paul Doughty, Alan R. Lemmon, Emily Moriarty Lemmon, J. Dale Roberts, Levi Yant, Yves Van de Peer, J. Scott Keogh, Stephen C. Donnellan

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008769

Dynamic genetic architecture of yeast response to environmental perturbation shed light on origin of cryptic genetic variation

Yanjun Zan, Örjan Carlborg

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008801

The temporal regulation of TEK contributes to pollen wall exine patterning

Shuang-Xi Xiong, Qiu-Ye Zeng, Jian-Qiao Hou, Ling-Li Hou, Jun Zhu, Min Yang, Zhong-Nan Yang, Yue Lou

PLOS Genetics: published May 14, 2020 | https://doi.org/10.1371/journal.pgen.1008807

The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication

Qiuyue Chen, Luis Fernando Samayoa, Chin Jian Yang, Peter J. Bradbury, Bode A. Olukolu, Michael A. Neumeyer, Maria Cinta Romay, Qi Sun, Anne Lorant, Edward S. Buckler, Jeffrey Ross-Ibarra, James B. Holland, John F. Doebley

PLOS Genetics: published May 14, 2020 | https://doi.org/10.1371/journal.pgen.1008791

Trans-ethnic meta-analysis of genome-wide association studies identifies maternal ITPR1 as a novel locus influencing fetal growth during sensitive periods in pregnancy

Fasil Tekola-Ayele, Cuilin Zhang, Jing Wu, Katherine L. Grantz, Mohammad L. Rahman, Deepika Shrestha, Marion Ouidir, Tsegaselassie Workalemahu, Michael Y. Tsai

PLOS Genetics: published May 14, 2020 | https://doi.org/10.1371/journal.pgen.1008747

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility

Maya Hiltpold, Guanglin Niu, Naveen Kumar Kadri, Danang Crysnanto, Zih-Hua Fang, Mirjam Spengeler, Fritz Schmitz-Hsu, Christian Fuerst, Hermann Schwarzenbacher, Franz R. Seefried, Frauke Seehusen, Ulrich Witschi, Angelika Schnieke, Ruedi Fries, Heinrich Bollwein, Krzysztof Flisikowski, Hubert Pausch

PLOS Genetics: published May 14, 2020 | https://doi.org/10.1371/journal.pgen.1008804

Alternative splicing of jnk1a in zebrafish determines first heart field ventricular cardiomyocyte numbers through modulation of hand2 expression

Adrian Santos-Ledo, Sam Washer, Tamil Dhanaseelan, Lorraine Eley, Ahlam Alqatani, Paul W. Chrystal, Tania Papoutsi, Deborah J. Henderson, Bill Chaudhry

PLOS Genetics: published May 18, 2020 | https://doi.org/10.1371/journal.pgen.1008782

Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2

Dana Lau-Corona, Woo Kyun Bae, Lothar Hennighausen, David J. Waxman

PLOS Genetics: published May 19, 2020 | https://doi.org/10.1371/journal.pgen.1008796

Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model

Dominic Holland, Oleksandr Frei, Rahul Desikan, Chun-Chieh Fan, Alexey A. Shadrin, Olav B. Smeland, V. S. Sundar, Paul Thompson, Ole A. Andreassen, Anders M. Dale

PLOS Genetics: published May 19, 2020 | https://doi.org/10.1371/journal.pgen.1008612

A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)

Rebecca Bruders, Hannah Van Hollebeke, Edward J. Osborne, Zev Kronenberg, Emily Maclary, Mark Yandell, Michael D. Shapiro

PLOS Genetics: published May 20, 2020 | https://doi.org/10.1371/journal.pgen.1008274

A high-fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine

Jakob von Frieling, Muhammed Naeem Faisal, Femke Sporn, Roxana Pfefferkorn, Stella Solveig Nolte, Felix Sommer, Philip Rosenstiel, Thomas Roeder

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008789

Glucose transporter 10 modulates adipogenesis via an ascorbic acid-mediated pathway to protect mice against diet-induced metabolic dysregulation

Chung-Lin Jiang, Wei-Ping Jen, Chang-Yu Tsao, Li-Ching Chang, Chien-Hsiun Chen, Yi-Ching Lee

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008823

Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone

Stine M. Præstholm, Majken S. Siersbæk, Ronni Nielsen, Xuguang Zhu, Anthony N. Hollenberg, Sheue-yann Cheng, Lars Grøntved

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008770

Novel frameshift variant in MYL2 reveals molecular differences between dominant and recessive forms of hypertrophic cardiomyopathy

Sathiya N. Manivannan, Sihem Darouich, Aida Masmoudi, David Gordon, Gloria Zender, Zhe Han, Sara Fitzgerald-Butt, Peter White, Kim L. McBride, Maher Kharrat, Vidu Garg

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008639

Intimate functional interactions between TGS1 and the Smn complex revealed by an analysis of the Drosophila eye development

Paolo Maccallini, Francesca Bavasso, Livia Scatolini, Elisabetta Bucciarelli, Gemma Noviello, Veronica Lisi, Valeria Palumbo, Simone D'Angeli, Stefano Cacchione, Giovanni Cenci, Laura Ciapponi, James G. Wakefield, Maurizio Gatti, Grazia Daniela Raffa

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008815

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

Heini M. Natri, Katalina S. Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S. Jacobs, Georgi Hudjashov, J. Stephen Lansing, Herawati Sudoyo, Nicholas E. Banovich, Murray P. Cox, Irene Gallego Romero

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008749

Congenital hearing impairment associated with peripheral cochlear nerve dysmyelination in glycosylation-deficient muscular dystrophy

Shigefumi Morioka, Hirofumi Sakaguchi, Hiroaki Mohri, Mariko Taniguchi-Ikeda, Motoi Kanagawa, Toshiaki Suzuki, Yuko Miyagoe-Suzuki, Tatsushi Toda, Naoaki Saito, Takehiko Ueyama

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008826

Osteocalcin is necessary for the alignment of apatite crystallites, but not glucose metabolism, testosterone synthesis, or muscle mass

Takeshi Moriishi, Ryosuke Ozasa, Takuya Ishimoto, Takayoshi Nakano, Tomoka Hasegawa, Toshihiro Miyazaki, Wenguang Liu, Ryo Fukuyama, Yuying Wang, Hisato Komori, Xin Qin, Norio Amizuka, Toshihisa Komori

PLOS Genetics: published May 28, 2020 | https://doi.org/10.1371/journal.pgen.1008586

An osteocalcin-deficient mouse strain without endocrine abnormalities

Cassandra R. Diegel, Steven Hann, Ugur M. Ayturk, Jennifer C. W. Hu, Kyung-eun Lim, Casey J. Droscha, Zachary B. Madaj, Gabrielle E. Foxa, Isaac Izaguirre, VAI Vivarium and Transgenics Core, Noorulain Paracha, Bohdan Pidhaynyy, Terry L. Dowd, Alexander G. Robling, Matthew L. Warman, Bart O. Williams

PLOS Genetics: published May 28, 2020 | https://doi.org/10.1371/journal.pgen.1008361

The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)

Christos N. Velanis, Pumi Perera, Bennett Thomson, Erica de Leau, Shih Chieh Liang, Ben Hartwig, Alexander Förderer, Harry Thornton, Pedro Arede, Jiawen Chen, Kimberly M. Webb, Serin Gümüs, Geert De Jaeger, Clinton A. Page, C. Nathan Hancock, Christos Spanos, Juri Rappsilber, Philipp Voigt, Franziska Turck, Frank Wellmer, Justin Goodrich

PLOS Genetics: published May 28, 2020 | https://doi.org/10.1371/journal.pgen.1008681

The genomic landscape of metastasis in treatment-naïve breast cancer models

Christina Ross, Karol Szczepanek, Maxwell Lee, Howard Yang, Tinghu Qiu, Jack D. Sanford, Kent Hunter

PLOS Genetics: published May 28, 2020 | https://doi.org/10.1371/journal.pgen.1008743

Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti

Laura B. Dickson, Sarah H. Merkling, Mathieu Gautier, Amine Ghozlane, Davy Jiolle, Christophe Paupy, Diego Ayala, Isabelle Moltini-Conclois, Albin Fontaine, Louis Lambrechts

PLOS Genetics: published May 28, 2020 | https://doi.org/10.1371/journal.pgen.1008794

The Mediator CDK8-Cyclin C complex modulates Dpp signaling in Drosophila by stimulating Mad-dependent transcription

Xiao Li, Mengmeng Liu, Xingjie Ren, Nicolas Loncle, Qun Wang, Rajitha-Udakara-Sampath Hemba-Waduge, Stephen H. Yu, Muriel Boube, Henri-Marc G. Bourbon, Jian-Quan Ni, Jun-Yuan Ji

PLOS Genetics: published May 28, 2020 | https://doi.org/10.1371/journal.pgen.1008832

Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes

Marco Gründl, Susanne Walz, Laura Hauf, Melissa Schwab, Kerstin Marcela Werner, Susanne Spahr, Clemens Schulte, Hans Michael Maric, Carsten P. Ade, Stefan Gaubatz

PLOS Genetics: published May 29, 2020 | https://doi.org/10.1371/journal.pgen.1008818

Saccharomyces cerevisiae Mus81-Mms4 prevents accelerated senescence in telomerase-deficient cells

Erin K. Schwartz, Shih-Hsun Hung, Damon Meyer, Aurèle Piazza, Kevin Yan, Becky Xu Hua Fu, Wolf-Dietrich Heyer

PLOS Genetics: published May 29, 2020 | https://doi.org/10.1371/journal.pgen.1008816

Yeast mismatch repair components are required for stable inheritance of gene silencing

Qian Liu, Xuefeng Zhu, Michelle Lindström, Yonghong Shi, Ju Zheng, Xinxin Hao, Claes M. Gustafsson, Beidong Liu

PLOS Genetics: published May 29, 2020 | https://doi.org/10.1371/journal.pgen.1008798

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution

Christian D. Huber, Bernard Y. Kim, Kirk E. Lohmueller

PLOS Genetics: published May 29, 2020 | https://doi.org/10.1371/journal.pgen.1008827

Scalable probabilistic PCA for large-scale genetic variation data

Aman Agrawal, Alec M. Chiu, Minh Le, Eran Halperin, Sriram Sankararaman

PLOS Genetics: published May 29, 2020 | https://doi.org/10.1371/journal.pgen.1008773

Corrections

Correction: Regulation of ATG4B Stability by RNF5 Limits Basal Levels of Autophagy and Influences Susceptibility to Bacterial Infection

Ersheng Kuang, Cheryl Y. M. Okumura, Sharon Sheffy-Levin, Tal Varsano, Vincent Chih-Wen Shu, Jianfei Qi, Ingrid R. Niesman, Huei-Jiun Yang, Carlos López-Otín, Wei Yuan Yang, John C. Reed, Limor Broday, Victor Nizet, Ze'ev A. Ronai

PLOS Genetics: published May 11, 2020 | https://doi.org/10.1371/journal.pgen.1008795

Correction: The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants

Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle M. Henry

PLOS Genetics: published May 26, 2020 | https://doi.org/10.1371/journal.pgen.1008845

Correction: Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome

Jason Talkish, Haller Igel, Rhonda J. Perriman, Lily Shiue, Sol Katzman, Elizabeth M. Munding, Robert Shelansky, John Paul Donohue, Manuel Ares Jr.

PLOS Genetics: published May 27, 2020 | https://doi.org/10.1371/journal.pgen.1008854

Cover

Neobatrachus pictus, common name - painted burrowing frog.

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