January 2020

In addition to its culinary and cultural importance, Carolina Gold Select rice is resistant to strains of two important disease-causing bacteria. A high quality genome sequence was generated by combining long and short-read DNA sequencing technologies. All of the more than 400 disease resistance genes in Carolina Gold Select were identified and compared with those in other sequenced rice genomes. A candidate gene for the bacterial disease resistance was identified and discovered to have unusual features found in a small number of disease resistance genes across rice and several related species. The Carolina Gold Select genome is the first of a tropical japonica variety and represents a valuable resource for harnessing disease resistance as well as other useful traits. See Read et al.

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Image Credit: Kay Rentschler

Perspective

Loss of ferritin in developing wing cells: Apoptosis and ferroptosis coincide

Anna Karen Hernández-Gallardo, Fanis Missirlis

PLOS Genetics: published January 2, 2020 | https://doi.org/10.1371/journal.pgen.1008503

Research Articles

DNA double strand break repair in Escherichia coli perturbs cell division and chromosome dynamics

Martin A. White, Elise Darmon, Manuel A. Lopez-Vernaza, David R. F. Leach

PLOS Genetics: published January 2, 2020 | https://doi.org/10.1371/journal.pgen.1008473

ELF5 modulates the estrogen receptor cistrome in breast cancer

Catherine L. Piggin, Daniel L. Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha R. Oakes, David Gallego-Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartonicek, Christopher J. Ormandy

PLOS Genetics: published January 2, 2020 | https://doi.org/10.1371/journal.pgen.1008531

Ligand dependent gene regulation by transient ERα clustered enhancers

Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Sudeshna Majumdar, Rajat Mann, Sweety Meel, Umer Farooq, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani

PLOS Genetics: published January 6, 2020 | https://doi.org/10.1371/journal.pgen.1008516

Dynamic and regulated TAF gene expression during mouse embryonic germ cell development

Megan A. Gura, Maria M. Mikedis, Kimberly A. Seymour, Dirk G. de Rooij, David C. Page, Richard N. Freiman

PLOS Genetics: published January 8, 2020 | https://doi.org/10.1371/journal.pgen.1008515

Environmentally-relevant exposure to diethylhexyl phthalate (DEHP) alters regulation of double-strand break formation and crossover designation leading to germline dysfunction in Caenorhabditis elegans

Luciann Cuenca, Nara Shin, Laura I. Lascarez-Lagunas, Marina Martinez-Garcia, Saravanapriah Nadarajan, Rajendiran Karthikraj, Kurunthachalam Kannan, Mónica P. Colaiácovo

PLOS Genetics: published January 9, 2020 | https://doi.org/10.1371/journal.pgen.1008529

Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases

Sylvia T. Nurnberg, Marie A. Guerraty, Robert C. Wirka, H. Shanker Rao, Milos Pjanic, Scott Norton, Felipe Serrano, Ljubica Perisic, Susannah Elwyn, John Pluta, Wei Zhao, Stephanie Testa, YoSon Park, Trieu Nguyen, Yi-An Ko, Ting Wang, Ulf Hedin, Sanjay Sinha, Yoseph Barash, Christopher D. Brown, Thomas Quertermous, Daniel J. Rader

PLOS Genetics: published January 9, 2020 | https://doi.org/10.1371/journal.pgen.1008538

Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumors

Joe R. Delaney, Chandni B. Patel, Jaidev Bapat, Christian M. Jones, Maria Ramos-Zapatero, Katherine K. Ortell, Ralph Tanios, Mina Haghighiabyaneh, Joshua Axelrod, John W. DeStefano, Isabelle Tancioni, David D. Schlaepfer, Olivier Harismendy, Albert R. La Spada, Dwayne G. Stupack

PLOS Genetics: published January 10, 2020 | https://doi.org/10.1371/journal.pgen.1008558

Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice

Hui Zhang, Ming Li, Dongli He, Kun Wang, Pingfang Yang

PLOS Genetics: published January 10, 2020 | https://doi.org/10.1371/journal.pgen.1008562

Loss of androgen signaling in mesenchymal sonic hedgehog responsive cells diminishes prostate development, growth, and regeneration

Vien Le, Yongfeng He, Joseph Aldahl, Erika Hooker, Eun-Jeong Yu, Adam Olson, Won Kyung Kim, Dong-Hoon Lee, Monica Wong, Ruoyu Sheng, Jiaqi Mi, Joseph Geradts, Gerald R. Cunha, Zijie Sun

PLOS Genetics: published January 13, 2020 | https://doi.org/10.1371/journal.pgen.1008588

Dysfunction of Oskyddad causes Harlequin-type ichthyosis-like defects in Drosophila melanogaster

Yiwen Wang, Michaela Norum, Kathrin Oehl, Yang Yang, Renata Zuber, Jing Yang, Jean-Pierre Farine, Nicole Gehring, Matthias Flötenmeyer, Jean-François Ferveur, Bernard Moussian

PLOS Genetics: published January 13, 2020 | https://doi.org/10.1371/journal.pgen.1008363

High-throughput discovery of genetic determinants of circadian misalignment

Tao Zhang, Pancheng Xie, Yingying Dong, Zhiwei Liu, Fei Zhou, Dejing Pan, Zhengyun Huang, Qiaocheng Zhai, Yue Gu, Qingyu Wu, Nobuhiko Tanaka, Yuichi Obata, Allan Bradley, Christopher J. Lelliott, Sanger Institute Mouse Genetics Project, Lauryl M. J. Nutter, Colin McKerlie, Ann M. Flenniken, Marie-France Champy, Tania Sorg, Yann Herault, Martin Hrabe De Angelis, Valerie Gailus Durner, Ann-Marie Mallon, Steve D. M. Brown, Terry Meehan, Helen E. Parkinson, Damian Smedley, K. C. Kent Lloyd, Jun Yan, Xiang Gao, Je Kyung Seong, Chi-Kuang Leo Wang, Radislav Sedlacek, Yi Liu, Jan Rozman, Ling Yang, Ying Xu

PLOS Genetics: published January 13, 2020 | https://doi.org/10.1371/journal.pgen.1008577

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

Máté Pálfy, Gunnar Schulze, Eivind Valen, Nadine L. Vastenhouw

PLOS Genetics: published January 15, 2020 | https://doi.org/10.1371/journal.pgen.1008546

RNA binding protein FXR1-miR301a-3p axis contributes to p21^WAF1 degradation in oral cancer

Mrinmoyee Majumder, Viswanathan Palanisamy

PLOS Genetics: published January 15, 2020 | https://doi.org/10.1371/journal.pgen.1008580

Low dose ionizing radiation strongly stimulates insertional mutagenesis in a γH2AX dependent manner

Alex N. Zelensky, Mascha Schoonakker, Inger Brandsma, Marcel Tijsterman, Dik C. van Gent, Jeroen Essers, Roland Kanaar

PLOS Genetics: published January 16, 2020 | https://doi.org/10.1371/journal.pgen.1008550

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey

PLOS Genetics: published January 21, 2020 | https://doi.org/10.1371/journal.pgen.1008537

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality

Katherine Lagree, Carol A. Woolford, Manning Y. Huang, Gemma May, C. Joel McManus, Norma V. Solis, Scott G. Filler, Aaron P. Mitchell

PLOS Genetics: published January 21, 2020 | https://doi.org/10.1371/journal.pgen.1008582

The Arabidopsis receptor kinase STRUBBELIG regulates the response to cellulose deficiency

Ajeet Chaudhary, Xia Chen, Jin Gao, Barbara Leśniewska, Richard Hammerl, Corinna Dawid, Kay Schneitz

PLOS Genetics: published January 21, 2020 | https://doi.org/10.1371/journal.pgen.1008433

The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter

Selamawit Abi Woldemeskel, Allison K. Daitch, Laura Alvarez, Gaël Panis, Rilee Zeinert, Diego Gonzalez, Erika Smith, Justine Collier, Peter Chien, Felipe Cava, Patrick H. Viollier, Erin D. Goley

PLOS Genetics: published January 21, 2020 | https://doi.org/10.1371/journal.pgen.1008591

Nexin-Dynein regulatory complex component DRC7 but not FBXL13 is required for sperm flagellum formation and male fertility in mice

Akane Morohoshi, Haruhiko Miyata, Keisuke Shimada, Kaori Nozawa, Takafumi Matsumura, Ryuji Yanase, Kogiku Shiba, Kazuo Inaba, Masahito Ikawa

PLOS Genetics: published January 21, 2020 | https://doi.org/10.1371/journal.pgen.1008585

Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation

Annabelle Dold, Hong Han, Niankun Liu, Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Heike Hänel, Anke Busch, Petra Beli, Kathi Zarnack, Julian König, Jean-Yves Roignant, Paul Lasko

PLOS Genetics: published January 24, 2020 | https://doi.org/10.1371/journal.pgen.1008581

The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders

Mette K. Andersen, Emil Jørsboe, Line Skotte, Kristian Hanghøj, Camilla H. Sandholt, Ida Moltke, Niels Grarup, Timo Kern, Yuvaraj Mahendran, Bolette Søborg, Peter Bjerregaard, Christina V. L. Larsen, Inger K. Dahl-Petersen, Hemant K. Tiwari, Bjarke Feenstra, Anders Koch, Howard W. Wiener, Scarlett E. Hopkins, Oluf Pedersen, Mads Melbye, Bert B. Boyer, Marit E. Jørgensen, Anders Albrechtsen, Torben Hansen

PLOS Genetics: published January 24, 2020 | https://doi.org/10.1371/journal.pgen.1008544

Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis

Alfredo Rago, John H. Werren, John K. Colbourne

PLOS Genetics: published January 27, 2020 | https://doi.org/10.1371/journal.pgen.1008518

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Andrew C. Read, Matthew J. Moscou, Aleksey V. Zimin, Geo Pertea, Rachel S. Meyer, Michael D. Purugganan, Jan E. Leach, Lindsay R. Triplett, Steven L. Salzberg, Adam J. Bogdanove

PLOS Genetics: published January 27, 2020 | https://doi.org/10.1371/journal.pgen.1008571

Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping

Eleanor Young, Heba Z. Abid, Pui-Yan Kwok, Harold Riethman, Ming Xiao

PLOS Genetics: published January 27, 2020 | https://doi.org/10.1371/journal.pgen.1008347

Characterisation of canine KCNIP4: A novel gene for cerebellar ataxia identified by whole-genome sequencing two affected Norwegian Buhund dogs

Christopher A. Jenkins, Lajos Kalmar, Kaspar Matiasek, Lorenzo Mari, Kaisa Kyöstilä, Hannes Lohi, Ellen C. Schofield, Cathryn S. Mellersh, Luisa De Risio, Sally L. Ricketts

PLOS Genetics: published January 30, 2020 | https://doi.org/10.1371/journal.pgen.1008527

The epilepsy and intellectual disability-associated protein TBC1D24 regulates the maintenance of excitatory synapses and animal behaviors

Lianfeng Lin, Quanwei Lyu, Pui-Yi Kwan, Junjun Zhao, Ruolin Fan, Anping Chai, Cora Sau Wan Lai, Ying-Shing Chan, Xuting Shen, Kwok-On Lai

PLOS Genetics: published January 31, 2020 | https://doi.org/10.1371/journal.pgen.1008587

Cover

Golden hulled grains of heirloom rice cultivar Carolina Gold Select.