September 2017

Wild primates are now recognised as important reservoirs of malaria parasites that can infect humans. Diez Benavente et al. studied the macaque parasite Plasmodium knowlesi. They used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Their analysis reveals genetic regions that have been recently exchanged between long-tailed and pig-tailed macaques, which contain genes with signals indicative of rapid contemporary ecological change, including deforestation. The image shows a long-tailed macaque (Macaca fascicularis), one of two simian hosts known to carry the zoonotic malaria parasite P. knowlesi in Malaysia. See Diez Benavente et al.

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Image Credit: Shankar S. (flickr; CC BY 2.0)

Editorial

Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology

Leah E. Mechanic, Sara Lindström, Kenneth M. Daily, Solveig K. Sieberts, Christopher I. Amos, Huann-Sheng Chen, Nancy J. Cox, Marina Dathe, Eric J. Feuer, Michael J. Guertin, Joshua Hoffman, Yunxian Liu, Jason H. Moore, Chad L. Myers, Marylyn D. Ritchie, Joellen Schildkraut, Fredrick Schumacher, John S. Witte, Wen Wang, Scott M. Williams, U4C Challenge Participants, U4C Challenge Data Contributors, Elizabeth M. Gillanders

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1006945

Perspective

"T-bet"-ing on autoimmunity variants

Michelle L. T. Nguyen, Dimitre R. Simeonov, Alexander Marson

PLOS Genetics: published September 7, 2017 | https://doi.org/10.1371/journal.pgen.1006924

Review

Forensic genetics and genomics: Much more than just a human affair

Miguel Arenas, Filipe Pereira, Manuela Oliveira, Nadia Pinto, Alexandra M. Lopes, Veronica Gomes, Angel Carracedo, Antonio Amorim

PLOS Genetics: published September 21, 2017 | https://doi.org/10.1371/journal.pgen.1006960

Research Articles

Functional divergence of chloroplast Cpn60α subunits during Arabidopsis embryo development

Xiaolong Ke, Wenxuan Zou, Yafang Ren, Zhiqin Wang, Jin Li, Xuan Wu, Jie Zhao

PLOS Genetics: published September 29, 2017 | https://doi.org/10.1371/journal.pgen.1007036

Widespread epistasis regulates glucose homeostasis and gene expression

Anlu Chen, Yang Liu, Scott M. Williams, Nathan Morris, David A. Buchner

PLOS Genetics: published September 29, 2017 | https://doi.org/10.1371/journal.pgen.1007025

Estimation of kinship coefficient in structured and admixed populations using sparse sequencing data

Jinzhuang Dou, Baoluo Sun, Xueling Sim, Jason D. Hughes, Dermot F. Reilly, E. Shyong Tai, Jianjun Liu, Chaolong Wang

PLOS Genetics: published September 29, 2017 | https://doi.org/10.1371/journal.pgen.1007021

Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States

Le Shu, Kei Hang K. Chan, Guanglin Zhang, Tianxiao Huan, Zeyneb Kurt, Yuqi Zhao, Veronica Codoni, David-Alexandre Trégouët, Cardiogenics Consortium, Jun Yang, James G. Wilson, Xi Luo, Daniel Levy, Aldons J. Lusis, Simin Liu, Xia Yang

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1007040

Identification of genetic networks that act in the somatic cells of the testis to mediate the developmental program of spermatogenesis

Michael John Fairchild, Fayeza Islam, Guy Tanentzapf

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1007026

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

Emily R. Ebel, Natalie Telis, Sandeep Venkataram, Dmitri A. Petrov, David Enard

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1007023

Pathway-based discovery of genetic interactions in breast cancer

Wen Wang, Zack Z. Xu, Michael Costanzo, Charles Boone, Carol A. Lange, Chad L. Myers

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1006973

The population genetics of human disease: The case of recessive, lethal mutations

Carlos Eduardo G. Amorim, Ziyue Gao, Zachary Baker, José Francisco Diesel, Yuval B. Simons, Imran S. Haque, Joseph Pickrell, Molly Przeworski

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1006915

Identification of breast cancer associated variants that modulate transcription factor binding

Yunxian Liu, Ninad M. Walavalkar, Mikhail G. Dozmorov, Stephen S. Rich, Mete Civelek, Michael J. Guertin

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1006761

Trans-ethnic predicted expression genome-wide association analysis identifies a gene for estrogen receptor-negative breast cancer

Guimin Gao, Brandon L. Pierce, Olufunmilayo I. Olopade, Hae Kyung Im, Dezheng Huo

PLOS Genetics: published September 28, 2017 | https://doi.org/10.1371/journal.pgen.1006727

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

Jinliang Yang, Sofiane Mezmouk, Andy Baumgarten, Edward S. Buckler, Katherine E. Guill, Michael D. McMullen, Rita H. Mumm, Jeffrey Ross-Ibarra

PLOS Genetics: published September 27, 2017 | https://doi.org/10.1371/journal.pgen.1007019

Rescuing the aberrant sex development of H3K9 demethylase Jmjd1a-deficient mice by modulating H3K9 methylation balance

Shunsuke Kuroki, Naoki Okashita, Shoko Baba, Ryo Maeda, Shingo Miyawaki, Masashi Yano, Miyoko Yamaguchi, Satsuki Kitano, Hitoshi Miyachi, Akihiro Itoh, Minoru Yoshida, Makoto Tachibana

PLOS Genetics: published September 26, 2017 | https://doi.org/10.1371/journal.pgen.1007034

p53-dependent programmed necrosis controls germ cell homeostasis during spermatogenesis

Francesco Napoletano, Benjamin Gibert, Keren Yacobi-Sharon, Stéphane Vincent, Clémentine Favrot, Patrick Mehlen, Victor Girard, Margaux Teil, Gilles Chatelain, Ludivine Walter, Eli Arama, Bertrand Mollereau

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007024

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

Mario López-Pérez, Jose M. Haro-Moreno, Rafael Gonzalez-Serrano, Marcos Parras-Moltó, Francisco Rodriguez-Valera

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007018

The bacterial Sec system is required for the organization and function of the MreB cytoskeleton

Sutharsan Govindarajan, Orna Amster-Choder

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007017

A two-step transport pathway allows the mother cell to nurture the developing spore in Bacillus subtilis

Fernando H. Ramírez-Guadiana, Alexander J. Meeske, Christopher D. A. Rodrigues, Rocío del Carmen Barajas-Ornelas, Andrew C. Kruse, David Z. Rudner

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007015

Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences

Giulia Pilla, Gareth McVicker, Christoph M. Tang

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007014

Formation of a TBX20-CASZ1 protein complex is protective against dilated cardiomyopathy and critical for cardiac homeostasis

Leslie Kennedy, Erin Kaltenbrun, Todd M. Greco, Brenda Temple, Laura E. Herring, Ileana M. Cristea, Frank L. Conlon

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007011

Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model

Edward B. Li, Dawn Truong, Shawn A. Hallett, Kusumika Mukherjee, Brian C. Schutte, Eric C. Liao

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007009

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

Niedzica Camacho, Peter Van Loo, Sandra Edwards, Jonathan D. Kay, Lucy Matthews, Kerstin Haase, Jeremy Clark, Nening Dennis, Sarah Thomas, Barbara Kremeyer, Jorge Zamora, Adam P. Butler, Gunes Gundem, Sue Merson, Hayley Luxton, Steve Hawkins, Mohammed Ghori, Luke Marsden, Adam Lambert, Katalin Karaszi, Gill Pelvender, Charlie E. Massie, Zsofia Kote-Jarai, Keiran Raine, David Jones, William J. Howat, Steven Hazell, Naomi Livni, Cyril Fisher, Christopher Ogden, Pardeep Kumar, Alan Thompson, David Nicol, Erik Mayer, Tim Dudderidge, Yongwei Yu, Hongwei Zhang, Nimish C. Shah, Vincent J. Gnanapragasam, The CRUK-ICGC Prostate Group, William Isaacs, Tapio Visakorpi, Freddie Hamdy, Dan Berney, Clare Verrill, Anne Y. Warren, David C. Wedge, Andrew G. Lynch, Christopher S. Foster, Yong Jie Lu, G. Steven Bova, Hayley C. Whitaker, Ultan McDermott, David E. Neal, Rosalind Eeles, Colin S. Cooper, Daniel S. Brewer

PLOS Genetics: published September 25, 2017 | https://doi.org/10.1371/journal.pgen.1007001

Interference with plastome gene expression and Clp protease activity in Arabidopsis triggers a chloroplast unfolded protein response to restore protein homeostasis

Ernesto Llamas, Pablo Pulido, Manuel Rodriguez-Concepcion

PLOS Genetics: published September 22, 2017 | https://doi.org/10.1371/journal.pgen.1007022

A Rab5 GTPase module is important for autophagosome closure

Fan Zhou, Shenshen Zou, Yong Chen, Zhanna Lipatova, Dan Sun, Xiaolong Zhu, Rui Li, Zulin Wu, Weiming You, Xiaoxia Cong, Yiting Zhou, Zhiping Xie, Valeriya Gyurkovska, Yutao Liu, Qunli Li, Wenjing Li, Jie Cheng, Yongheng Liang, Nava Segev

PLOS Genetics: published September 21, 2017 | https://doi.org/10.1371/journal.pgen.1007020

CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB

Danielle M. Heller, Mrinalini Tavag, Ann Hochschild

PLOS Genetics: published September 20, 2017 | https://doi.org/10.1371/journal.pgen.1007007

Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis by modulating cell-extrinsic signaling pathways

Pawat Seritrakul, Jeffrey M. Gross

PLOS Genetics: published September 19, 2017 | https://doi.org/10.1371/journal.pgen.1006987

Lingering single-strand breaks trigger Rad51-independent homology-directed repair of collapsed replication forks in the polynucleotide kinase/phosphatase mutant of fission yeast

Arancha Sanchez, Mariana C. Gadaleta, Oliver Limbo, Paul Russell

PLOS Genetics: published September 18, 2017 | https://doi.org/10.1371/journal.pgen.1007013

Dynein light chain regulates adaptive and innate B cell development by distinctive genetic mechanisms

Ashleigh King, Lingli Li, David M. Wong, Rui Liu, Rebecca Bamford, Andreas Strasser, David M. Tarlinton, Jörg Heierhorst

PLOS Genetics: published September 18, 2017 | https://doi.org/10.1371/journal.pgen.1007010

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

Ernest Diez Benavente, Paola Florez de Sessions, Robert W. Moon, Anthony A. Holder, Michael J. Blackman, Cally Roper, Christopher J. Drakeley, Arnab Pain, Colin J. Sutherland, Martin L. Hibberd, Susana Campino, Taane G. Clark

PLOS Genetics: published September 18, 2017 | https://doi.org/10.1371/journal.pgen.1007008

DNA replication stress restricts ribosomal DNA copy number

Devika Salim, William D. Bradford, Amy Freeland, Gillian Cady, Jianmin Wang, Steven C. Pruitt, Jennifer L. Gerton

PLOS Genetics: published September 15, 2017 | https://doi.org/10.1371/journal.pgen.1007006

The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases

Muhammad Ahsan, Weronica E. Ek, Mathias Rask-Andersen, Torgny Karlsson, Allan Lind-Thomsen, Stefan Enroth, Ulf Gyllensten, Åsa Johansson

PLOS Genetics: published September 15, 2017 | https://doi.org/10.1371/journal.pgen.1007005

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

Emily L. Clark, Stephen J. Bush, Mary E. B. McCulloch, Iseabail L. Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu G. Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C. Bruce Whitelaw, Tom C. Freeman, Kim M. Summers, Alan L. Archibald, David A. Hume

PLOS Genetics: published September 15, 2017 | https://doi.org/10.1371/journal.pgen.1006997

Genomics-enabled analysis of the emergent disease cotton bacterial blight

Anne Z. Phillips, Jeffrey C. Berry, Mark C. Wilson, Anupama Vijayaraghavan, Jillian Burke, J. Imani Bunn, Tom W. Allen, Terry Wheeler, Rebecca S. Bart

PLOS Genetics: published September 14, 2017 | https://doi.org/10.1371/journal.pgen.1007003

Defective erythropoiesis caused by mutations of the thyroid hormone receptor α gene

Sunmi Park, Cho Rong Han, Jeong Won Park, Li Zhao, Xuguang Zhu, Mark Willingham, David M. Bodine, Sheue-yann Cheng

PLOS Genetics: published September 14, 2017 | https://doi.org/10.1371/journal.pgen.1006991

Interplay between microtubule bundling and sorting factors ensures acentriolar spindle stability during C. elegans oocyte meiosis

Timothy J. Mullen, Sarah M. Wignall

PLOS Genetics: published September 14, 2017 | https://doi.org/10.1371/journal.pgen.1006986

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis

Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret R. Crawford, Konrad Paszkiewicz, Nicholas A. Kent, James A. H. Murray

PLOS Genetics: published September 13, 2017 | https://doi.org/10.1371/journal.pgen.1006988

Glucosamine stimulates pheromone-independent dimorphic transition in Cryptococcus neoformans by promoting Crz1 nuclear translocation

Xinping Xu, Jianfeng Lin, Youbao Zhao, Elyssa Kirkman, Yee-Seul So, Yong-Sun Bahn, Xiaorong Lin

PLOS Genetics: published September 12, 2017 | https://doi.org/10.1371/journal.pgen.1006982

Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms

Ryosuke Yamamoto, Jagan M. Obbineni, Lea M. Alford, Takahiro Ide, Mikito Owa, Juyeon Hwang, Takahide Kon, Kazuo Inaba, Noliyanda James, Stephen M. King, Takashi Ishikawa, Winfield S. Sale, Susan K. Dutcher

PLOS Genetics: published September 11, 2017 | https://doi.org/10.1371/journal.pgen.1006996

Self-fertility in Chromocrea spinulosa is a consequence of direct repeat-mediated loss of MAT1-2, subsequent imbalance of nuclei differing in mating type, and recognition between unlike nuclei in a common cytoplasm

Sung-Hwan Yun, Hee-Kyoung Kim, Theresa Lee, B. Gillian Turgeon

PLOS Genetics: published September 11, 2017 | https://doi.org/10.1371/journal.pgen.1006981

Six1 is essential for differentiation and patterning of the mammalian auditory sensory epithelium

Ting Zhang, Jinshu Xu, Pascal Maire, Pin-Xian Xu

PLOS Genetics: published September 11, 2017 | https://doi.org/10.1371/journal.pgen.1006967

The adiponectin receptor AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 prevent membrane rigidification by exogenous saturated fatty acids

Ranjan Devkota, Emma Svensk, Mario Ruiz, Marcus Ståhlman, Jan Borén, Marc Pilon

PLOS Genetics: published September 8, 2017 | https://doi.org/10.1371/journal.pgen.1007004

FtsEX-mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus

Elizabeth L. Meier, Allison K. Daitch, Qing Yao, Anant Bhargava, Grant J. Jensen, Erin D. Goley

PLOS Genetics: published September 8, 2017 | https://doi.org/10.1371/journal.pgen.1006999

Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation

Meng Wang, Bernardo Lemos

PLOS Genetics: published September 7, 2017 | https://doi.org/10.1371/journal.pgen.1006994

Microtubule-actin crosslinking factor 1 (Macf1) domain function in Balbiani body dissociation and nuclear positioning

Matias Escobar-Aguirre, Hong Zhang, Allison Jamieson-Lucy, Mary C. Mullins

PLOS Genetics: published September 7, 2017 | https://doi.org/10.1371/journal.pgen.1006983

Gene-environment interaction study for BMI reveals interactions between genetic factors and physical activity, alcohol consumption and socioeconomic status

Mathias Rask-Andersen, Torgny Karlsson, Weronica E. Ek, Åsa Johansson

PLOS Genetics: published September 5, 2017 | https://doi.org/10.1371/journal.pgen.1006977

Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

David A. Turissini, Daniel R. Matute

PLOS Genetics: published September 5, 2017 | https://doi.org/10.1371/journal.pgen.1006971

Fibroblast growth factor signaling is required for early somatic gonad development in zebrafish

Dena M. Leerberg, Kaori Sano, Bruce W. Draper

PLOS Genetics: published September 5, 2017 | https://doi.org/10.1371/journal.pgen.1006993

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

Krzysztof Poterlowicz, Joanne L. Yarker, Igor Malashchuk, Brian R. Lajoie, Andrei N. Mardaryev, Michal R. Gdula, Andrey A. Sharov, Terumi Kohwi-Shigematsu, Vladimir A. Botchkarev, Michael Y. Fessing

PLOS Genetics: published September 1, 2017 | https://doi.org/10.1371/journal.pgen.1006966

Cover

Genomic diversity of Plasmodium knowlesi.

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**Genomic diversity of Plasmodium knowlesi.**