Genomics

  • Article
    | Open Access

    Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.

    • Mark Pinese
    • , Paul Lacaze
    • , Emma M. Rath
    • , Andrew Stone
    • , Marie-Jo Brion
    • , Adam Ameur
    • , Sini Nagpal
    • , Clare Puttick
    • , Shane Husson
    • , Dmitry Degrave
    • , Tina Navin Cristina
    • , Vivian F. S. Kahl
    • , Aaron L. Statham
    • , Robyn L. Woods
    • , John J. McNeil
    • , Moeen Riaz
    • , Margo Barr
    • , Mark R. Nelson
    • , Christopher M. Reid
    • , Anne M. Murray
    • , Raj C. Shah
    • , Rory Wolfe
    • , Joshua R. Atkins
    • , Chantel Fitzsimmons
    • , Heath M. Cairns
    • , Melissa J. Green
    • , Vaughan J. Carr
    • , Mark J. Cowley
    • , Hilda A. Pickett
    • , Paul A. James
    • , Joseph E. Powell
    • , Warren Kaplan
    • , Greg Gibson
    • , Ulf Gyllensten
    • , Murray J. Cairns
    • , Martin McNamara
    • , Marcel E. Dinger
    •  & David M. Thomas
  • Article
    | Open Access

    Mikania micrantha is an extremely fast-growing invasive plant species that can cause serious damage to natural ecosystems. Here, the authors assemble its chromosome-scale reference genome and explore possible mechanisms that contribute to its rapid growth.

    • Bo Liu
    • , Jian Yan
    • , Weihua Li
    • , Lijuan Yin
    • , Ping Li
    • , Hanxia Yu
    • , Longsheng Xing
    • , Minling Cai
    • , Hengchao Wang
    • , Mengxin Zhao
    • , Jin Zheng
    • , Feng Sun
    • , Zhenzhen Wang
    • , Zhaoyang Jiang
    • , Qiaojing Ou
    • , Shubin Li
    • , Lu Qu
    • , Qilei Zhang
    • , Yaping Zheng
    • , Xi Qiao
    • , Yu Xi
    • , Yan Zhang
    • , Fan Jiang
    • , Cong Huang
    • , Conghui Liu
    • , Yuwei Ren
    • , Sen Wang
    • , Hangwei Liu
    • , Jianyang Guo
    • , Haihong Wang
    • , Hui Dong
    • , Changlian Peng
    • , Wanqiang Qian
    • , Wei Fan
    •  & Fanghao Wan
  • Article
    | Open Access

    The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.

    • Changsheng Li
    • , Xiaoli Xiang
    • , Yongcai Huang
    • , Yong Zhou
    • , Dong An
    • , Jiaqiang Dong
    • , Chenxi Zhao
    • , Hongjun Liu
    • , Yubin Li
    • , Qiong Wang
    • , Chunguang Du
    • , Joachim Messing
    • , Brian A. Larkins
    • , Yongrui Wu
    •  & Wenqin Wang
  • Article
    | Open Access

    DNA methylation is associated with complex traits and the expression of genes and proteins. Here, Zaghlool et al. perform epigenome-wide association studies for 1,123 plasma proteins, replicate obtained protein (p)QTMs in an independent cohort and find overlap of pQTMs with expression QTMs and previously reported disease associations.

    • Shaza B. Zaghlool
    • , Brigitte Kühnel
    • , Mohamed A. Elhadad
    • , Sara Kader
    • , Anna Halama
    • , Gaurav Thareja
    • , Rudolf Engelke
    • , Hina Sarwath
    • , Eman K. Al-Dous
    • , Yasmin A. Mohamoud
    • , Thomas Meitinger
    • , Rory Wilson
    • , Konstantin Strauch
    • , Annette Peters
    • , Dennis O. Mook-Kanamori
    • , Johannes Graumann
    • , Joel A. Malek
    • , Christian Gieger
    • , Melanie Waldenberger
    •  & Karsten Suhre
  • Article
    | Open Access

    Single strand breaks represent the most common form of DNA damage yet no methods to map them in a genome-wide fashion at single nucleotide resolution exist. Here the authors develop such a method and apply to uncover patterns of single-strand DNA “breakome” in different biological conditions.

    • Huifen Cao
    • , Lorena Salazar-García
    • , Fan Gao
    • , Thor Wahlestedt
    • , Chun-Lin Wu
    • , Xueer Han
    • , Ye Cai
    • , Dongyang Xu
    • , Fang Wang
    • , Lu Tang
    • , Natalie Ricciardi
    • , DingDing Cai
    • , Huifang Wang
    • , Mario P. S. Chin
    • , James A. Timmons
    • , Claes Wahlestedt
    •  & Philipp Kapranov
  • Article
    | Open Access

    Stroke risk is influenced by genetic and lifestyle factors and previously a genomic risk score (GRS) for stroke was proposed, albeit with limited predictive power. Here, Abraham et al. develop a metaGRS that is composed of several stroke-related GRSs and demonstrate improved predictive power compared with individual GRS or classic risk factors.

    • Gad Abraham
    • , Rainer Malik
    • , Ekaterina Yonova-Doing
    • , Agus Salim
    • , Tingting Wang
    • , John Danesh
    • , Adam S. Butterworth
    • , Joanna M. M. Howson
    • , Michael Inouye
    •  & Martin Dichgans
  • Article
    | Open Access

    Newly acquired plasmids are frequently lost due to fitness costs. Here, Zhang et al. show that the evolution of satellite plasmids with gene deletions can reduce fitness costs by driving down the copy number of full plasmids and thus favor maintenance of the full plasmid and its novel accessory genes.

    • Xue Zhang
    • , Daniel E. Deatherage
    • , Hao Zheng
    • , Stratton J. Georgoulis
    •  & Jeffrey E. Barrick
  • Article
    | Open Access

    Why transposable elements (TEs) accumulate in polyploids and the evolutionary implications remain unclear. Here, the authors show that following whole genome duplication, relaxed purifying selection is the main driver of TE over-accumulation, which provides variants for rapid local adaptation.

    • Pierre Baduel
    • , Leandro Quadrana
    • , Ben Hunter
    • , Kirsten Bomblies
    •  & Vincent Colot
  • Article
    | Open Access

    The edematous form of severe acute childhood malnutrition (ESAM) presents with more severe multi-organ dysfunction than non-edematous SAM (NESAM). Here the authors assess genome-wide DNA methylation in buccal cells of SAM children and find that ESAM is characterized by hypomethylation at genes associated with disorders of nutrition and metabolism, including fatty liver and diabetes.

    • Katharina V. Schulze
    • , Shanker Swaminathan
    • , Sharon Howell
    • , Aarti Jajoo
    • , Natasha C. Lie
    • , Orgen Brown
    • , Roa Sadat
    • , Nancy Hall
    • , Liang Zhao
    • , Kwesi Marshall
    • , Thaddaeus May
    • , Marvin E. Reid
    • , Carolyn Taylor-Bryan
    • , Xueqing Wang
    • , John W. Belmont
    • , Yongtao Guan
    • , Mark J. Manary
    • , Indi Trehan
    • , Colin A. McKenzie
    •  & Neil A. Hanchard
  • Article
    | Open Access

    Uterine adenomyosis often co-occurs with endometriosis or leiomyoma, but little is known about its molecular underpinnings. Here, the authors show that KRAS mutations are frequent in this disease, which might reduce sensitivity to progestin treatment via epigenetic silencing of the progesterone receptor.

    • Satoshi Inoue
    • , Yasushi Hirota
    • , Toshihide Ueno
    • , Yamato Fukui
    • , Emiko Yoshida
    • , Takuo Hayashi
    • , Shinya Kojima
    • , Reina Takeyama
    • , Taiki Hashimoto
    • , Tohru Kiyono
    • , Masako Ikemura
    • , Ayumi Taguchi
    • , Tomoki Tanaka
    • , Yosuke Tanaka
    • , Seiji Sakata
    • , Kengo Takeuchi
    • , Ayako Muraoka
    • , Satoko Osuka
    • , Tsuyoshi Saito
    • , Katsutoshi Oda
    • , Yutaka Osuga
    • , Yasuhisa Terao
    • , Masahito Kawazu
    •  & Hiroyuki Mano
  • Article
    | Open Access

    Birch pitch is thought to have been used in prehistoric times as hafting material or antiseptic and tooth imprints suggest that it was chewed. Here, the authors report a 5,700 year-old piece of chewed birch pitch from Denmark from which they successfully recovered a complete ancient human genome and oral microbiome DNA.

    • Theis Z. T. Jensen
    • , Jonas Niemann
    • , Katrine Højholt Iversen
    • , Anna K. Fotakis
    • , Shyam Gopalakrishnan
    • , Åshild J. Vågene
    • , Mikkel Winther Pedersen
    • , Mikkel-Holger S. Sinding
    • , Martin R. Ellegaard
    • , Morten E. Allentoft
    • , Liam T. Lanigan
    • , Alberto J. Taurozzi
    • , Sofie Holtsmark Nielsen
    • , Michael W. Dee
    • , Martin N. Mortensen
    • , Mads C. Christensen
    • , Søren A. Sørensen
    • , Matthew J. Collins
    • , M. Thomas P. Gilbert
    • , Martin Sikora
    • , Simon Rasmussen
    •  & Hannes Schroeder
  • Article
    | Open Access

    Four genome-wide associated loci are currently known for malaria susceptibility. Here, the authors expand on earlier work by combining data from 11 malaria-endemic countries and additional population sequencing informing an African-enriched imputation reference panel, with findings including a previously unreported association on chromosome 6.

    • Gavin Band
    • , Quang Si Le
    • , Geraldine M. Clarke
    • , Katja Kivinen
    • , Christina Hubbart
    • , Anna E. Jeffreys
    • , Kate Rowlands
    • , Ellen M. Leffler
    • , Muminatou Jallow
    • , David J. Conway
    • , Fatoumatta Sisay-Joof
    • , Giorgio Sirugo
    • , Umberto d’Alessandro
    • , Ousmane B. Toure
    • , Mahamadou A. Thera
    • , Salimata Konate
    • , Sibiri Sissoko
    • , Valentina D. Mangano
    • , Edith C. Bougouma
    • , Sodiomon B. Sirima
    • , Lucas N. Amenga-Etego
    • , Anita K. Ghansah
    • , Abraham V. O. Hodgson
    • , Michael D. Wilson
    • , Anthony Enimil
    • , Daniel Ansong
    • , Jennifer Evans
    • , Subulade A. Ademola
    • , Tobias O. Apinjoh
    • , Carolyne M. Ndila
    • , Alphaxard Manjurano
    • , Chris Drakeley
    • , Hugh Reyburn
    • , Nguyen Hoan Phu
    • , Nguyen Thi Ngoc Quyen
    • , Cao Quang Thai
    • , Tran Tinh Hien
    • , Yik Ying Teo
    • , Laurens Manning
    • , Moses Laman
    • , Pascal Michon
    • , Harin Karunajeewa
    • , Peter Siba
    • , Steve Allen
    • , Angela Allen
    • , Melanie Bahlo
    • , Timothy M. E. Davis
    • , Victoria Simpson
    • , Jennifer Shelton
    • , Chris C. A. Spencer
    • , George B. J. Busby
    • , Angeliki Kerasidou
    • , Eleanor Drury
    • , Jim Stalker
    • , Alexander Dilthey
    • , Alexander J. Mentzer
    • , Gil McVean
    • , Kalifa A. Bojang
    • , Ogobara Doumbo
    • , David Modiano
    • , Kwadwo A. Koram
    • , Tsiri Agbenyega
    • , Olukemi K. Amodu
    • , Eric Achidi
    • , Thomas N. Williams
    • , Kevin Marsh
    • , Eleanor M. Riley
    • , Malcolm Molyneux
    • , Terrie Taylor
    • , Sarah J. Dunstan
    • , Jeremy Farrar
    • , Ivo Mueller
    • , Kirk A. Rockett
    •  & Dominic P. Kwiatkowski
  • Article
    | Open Access

    The kidney is vascularized with highly specialized and zonated endothelial cells that are essential for its filtration function. Here, Barry et al. provide a single-cell RNA sequencing analysis of the kidney vasculature that highlights its transcriptional heterogeneity and uncovers pathways important for its development and function.

    • David M. Barry
    • , Elizabeth A. McMillan
    • , Balvir Kunar
    • , Raphael Lis
    • , Tuo Zhang
    • , Tyler Lu
    • , Edward Daniel
    • , Masataka Yokoyama
    • , Jesus M. Gomez-Salinero
    • , Angara Sureshbabu
    • , Ondine Cleaver
    • , Annarita Di Lorenzo
    • , Mary E. Choi
    • , Jenny Xiang
    • , David Redmond
    • , Sina Y. Rabbany
    • , Thangamani Muthukumar
    •  & Shahin Rafii
  • Article
    | Open Access

    Cell senescence involves stable arrest of cell proliferation and changes in gene expression and 3D genome reorganization. Here, the authors show that human condensin II complex participates in reorganization of the chromatin compartments, primarily through switching from heterochromatic B to euchromatic A compartments.

    • Osamu Iwasaki
    • , Hideki Tanizawa
    • , Kyoung-Dong Kim
    • , Andrew Kossenkov
    • , Timothy Nacarelli
    • , Sanki Tashiro
    • , Sonali Majumdar
    • , Louise C. Showe
    • , Rugang Zhang
    •  & Ken-ichi Noma
  • Article
    | Open Access

    N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are eukaryotic mRNA modifications. Here the authors develop m6A-Crosslinking-Exonuclease-sequencing to map quantitative methylome changes at single-base-resolution after individually knocking out each known methyltransferase or demethylase.

    • Casslynn W. Q. Koh
    • , Yeek Teck Goh
    •  & W. S. Sho Goh
  • Article
    | Open Access

    Although most are silenced, certain transposable elements (TEs) have been co-opted by the host. Here, the authors quantify the epigenomic status of TEs using data from the Roadmap Epigenomics Project, provide a systematic profile of TE activity across normal human tissues and development, finding that TEs encompass a quarter of the human regulatory epigenome, with 47% of TEs in regulatory states.

    • Erica C. Pehrsson
    • , Mayank N. K. Choudhary
    • , Vasavi Sundaram
    •  & Ting Wang
  • Article
    | Open Access

    The basis of sexual dimorphism in non-model species may be elusive, in part due to a lack of genomic and molecular resources. Here, Li et al. report a high-quality anuran genome and reveal candidate genes and pathways associated with shaping sexually dimorphic nuptial spines in a moustache toad.

    • Jun Li
    • , Haiyan Yu
    • , Wenxia Wang
    • , Chao Fu
    • , Wei Zhang
    • , Fengming Han
    •  & Hua Wu
  • Article
    | Open Access

    Urinary tract infections (UTIs) are associated with changes in the gut microbiome. Here, the authors evaluate the relationship between the gut microbiome and development of UTI in kidney transplant patients and show that uropathogenic gut abundance might represent a risk factor for development of bacteriuria and UTI.

    • Matthew Magruder
    • , Adam N. Sholi
    • , Catherine Gong
    • , Lisa Zhang
    • , Emmanuel Edusei
    • , Jennifer Huang
    • , Shady Albakry
    • , Michael J. Satlin
    • , Lars F. Westblade
    • , Carl Crawford
    • , Darshana M. Dadhania
    • , Michelle Lubetzky
    • , Ying Taur
    • , Eric Littman
    • , Lilan Ling
    • , Philip Burnham
    • , Iwijn De Vlaminck
    • , Eric Pamer
    • , Manikkam Suthanthiran
    •  & John Richard Lee
  • Article
    | Open Access

    The off-target effects and on-target mutations of CRISPR editing in higher non-human primates are complex. Here the authors perform whole genome trio sequencing of rhesus monkeys and see no unexpected mutations.

    • Xin Luo
    • , Yaoxi He
    • , Chao Zhang
    • , Xiechao He
    • , Lanzhen Yan
    • , Min Li
    • , Ting Hu
    • , Yan Hu
    • , Jin Jiang
    • , Xiaoyu Meng
    • , Weizhi Ji
    • , Xudong Zhao
    • , Ping Zheng
    • , Shuhua Xu
    •  & Bing Su
  • Article
    | Open Access

    Thymic epithelial cells (TEC) are essential for the maturation of functional T cells, while thymus size is proportional to the overall output efficiency. Here the authors show, using transcriptome analyses, that mouse fetal TEC maintain a Myc-dependent genetic program to ensure a rapid increase in thymus size, and thereby expedited T cell generation.

    • Jennifer E. Cowan
    • , Justin Malin
    • , Yongge Zhao
    • , Mina O. Seedhom
    • , Christelle Harly
    • , Izumi Ohigashi
    • , Michael Kelly
    • , Yousuke Takahama
    • , Jonathan W. Yewdell
    • , Maggie Cam
    •  & Avinash Bhandoola
  • Article
    | Open Access

    Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.

    • Cormac M. Kinsella
    • , Francisco J. Ruiz-Ruano
    • , Anne-Marie Dion-Côté
    • , Alexander J. Charles
    • , Toni I. Gossmann
    • , Josefa Cabrero
    • , Dennis Kappei
    • , Nicola Hemmings
    • , Mirre J. P. Simons
    • , Juan Pedro M. Camacho
    • , Wolfgang Forstmeier
    •  & Alexander Suh
  • Article
    | Open Access

    The neural tissues of coleoids have a greater fraction of nonsynonymous sites than synonymous sites subject to high levels of A-to-I RNA editing, a pattern thought to indicate widespread adaptive editing. Here the authors propose and provide evidence for an alternative, nonadaptive explanation.

    • Daohan Jiang
    •  & Jianzhi Zhang
  • Article
    | Open Access

    A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.

    • Jaime Iranzo
    • , Yuri I. Wolf
    • , Eugene V. Koonin
    •  & Itamar Sela
  • Article
    | Open Access

    The nematode Halicephalobus mephisto has been found more than 1 km underground and can tolerate high heat and low oxygen. Here Weinstein et al. report the genome and transcriptome of H. mephisto and identify genomic innovations that likely are responsible for its tolerance to heat.

    • Deborah J. Weinstein
    • , Sarah E. Allen
    • , Maggie C. Y. Lau
    • , Mariana Erasmus
    • , Kathryn C. Asalone
    • , Kathryn Walters-Conte
    • , Gintaras Deikus
    • , Robert Sebra
    • , Gaetan Borgonie
    • , Esta van Heerden
    • , Tullis C. Onstott
    •  & John R. Bracht
  • Article
    | Open Access

    Whole genome sequencing (WGS) holds promise to solve a subset of Mendelian disease cases for which exome sequencing did not provide a genetic diagnosis. Here, Wells et al. report a supervised machine learning model trained on functional, mutational and structural features for rank-scoring and interpreting variants in non-coding regions from WGS.

    • Alex Wells
    • , David Heckerman
    • , Ali Torkamani
    • , Li Yin
    • , Jonathan Sebat
    • , Bing Ren
    • , Amalio Telenti
    •  & Julia di Iulio
  • Article
    | Open Access

    Parkinson’s disease (PD) is characterized by neurodegeneration associated with loss of dopaminergic (DA) neurons and deposition of Lewy bodies. Here, Wang et al. use co-expression network analysis to pinpoint disease pathways and propose reduced expression of STMN2 as a cause of presynaptic function loss in PD.

    • Qian Wang
    • , Yuanxi Zhang
    • , Minghui Wang
    • , Won-Min Song
    • , Qi Shen
    • , Andrew McKenzie
    • , Insup Choi
    • , Xianxiao Zhou
    • , Ping-Yue Pan
    • , Zhenyu Yue
    •  & Bin Zhang
  • Article
    | Open Access

    Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

    • Jia-hui Chen
    • , Yuan Huang
    • , Benjamin Brachi
    • , Quan-zheng Yun
    • , Wei Zhang
    • , Wei Lu
    • , Hong-na Li
    • , Wen-qing Li
    • , Xu-dong Sun
    • , Guang-yan Wang
    • , Jun He
    • , Zhuo Zhou
    • , Kai-yun Chen
    • , Yun-heng Ji
    • , Ming-ming Shi
    • , Wen-guang Sun
    • , Yong-ping Yang
    • , Ren-gang Zhang
    • , Richard J. Abbott
    •  & Hang Sun
  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    • , Jinpeng Wang
    • , Wenrui Liu
    • , Qian Zhou
    • , Shaobo Luo
    • , Wu Huang
    • , Xiaoming He
    • , Qing Li
    • , Qingwu Peng
    • , Xueyong Yang
    • , Jiaqing Yuan
    • , Jigao Yu
    • , Xiyin Wang
    • , William J. Lucas
    • , Sanwen Huang
    • , Biao Jiang
    •  & Zhonghua Zhang
  • Article
    | Open Access

    The ‘parliament of genes’ hypothesis suggests that selfish genetic elements will be counteracted by suppressors that maintain equal transmission of the rest of the genome. Here, the authors find support for this hypothesis using mathematical models to explore a range of different scenarios.

    • Thomas W. Scott
    •  & Stuart A. West
  • Article
    | Open Access

    Strain Ug99 of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici, is a major threat to global food security. Here, the authors present genomic analyses supporting that Ug99 arose as a result of non-sexual genetic exchange between dikaryotic ancestors.

    • Feng Li
    • , Narayana M. Upadhyaya
    • , Jana Sperschneider
    • , Oadi Matny
    • , Hoa Nguyen-Phuc
    • , Rohit Mago
    • , Castle Raley
    • , Marisa E. Miller
    • , Kevin A. T. Silverstein
    • , Eva Henningsen
    • , Cory D. Hirsch
    • , Botma Visser
    • , Zacharias A. Pretorius
    • , Brian J. Steffenson
    • , Benjamin Schwessinger
    • , Peter N. Dodds
    •  & Melania Figueroa
  • Article
    | Open Access

    It is challenging to characterize diverse transcript isoforms by short-read sequencing. Here the authors report full-length transcriptomes in rat hippocampus by hybrid-sequencing, predict isoform-specific translational status, and reconstruct open reading frames validated by mass spectrometry.

    • Xi Wang
    • , Xintian You
    • , Julian D. Langer
    • , Jingyi Hou
    • , Fiona Rupprecht
    • , Irena Vlatkovic
    • , Claudia Quedenau
    • , Georgi Tushev
    • , Irina Epstein
    • , Bernhard Schaefke
    • , Wei Sun
    • , Liang Fang
    • , Guipeng Li
    • , Yuhui Hu
    • , Erin M. Schuman
    •  & Wei Chen
  • Article
    | Open Access

    Here, the authors report transcriptomes and proteomes of oocyst sporozoite and salivary gland sporozoite stages in rodent-infectious Plasmodium yoelii parasites and human infectious Plasmodium falciparum parasites and define two waves of translational repression during sporozoite maturation.

    • Scott E. Lindner
    • , Kristian E. Swearingen
    • , Melanie J. Shears
    • , Michael P. Walker
    • , Erin N. Vrana
    • , Kevin J. Hart
    • , Allen M. Minns
    • , Photini Sinnis
    • , Robert L. Moritz
    •  & Stefan H. I. Kappe
  • Article
    | Open Access

    Herpes simplex virus 1 (HSV-1) induces major reprogramming of the host cell environment. Here, the authors profile the transcriptomes of individual HSV-1-infected human fibroblasts and provide evidence of an antiviral program mediated by the activation of the host transcription factor NRF2.

    • Emanuel Wyler
    • , Vedran Franke
    • , Jennifer Menegatti
    • , Christine Kocks
    • , Anastasiya Boltengagen
    • , Samantha Praktiknjo
    • , Barbara Walch-Rückheim
    • , Jens Bosse
    • , Nikolaus Rajewsky
    • , Friedrich Grässer
    • , Altuna Akalin
    •  & Markus Landthaler
  • Article
    | Open Access

    Widely distributed red algae have experienced massive genome reduction during evolution. Here, using an improved genome assembly of Porphyridium purpureum, Lee et al. show the role of endosymbiotic gene transfer in plastid evolution and the correlation between phycobilisome linker diversification and the red algal radiation.

    • JunMo Lee
    • , Dongseok Kim
    • , Debashish Bhattacharya
    •  & Hwan Su Yoon
  • Article
    | Open Access

    Pumas are experiencing increased isolation as human persecution and habitat loss fragment the populations of this once widespread species. Here, the authors estimate the genomic consequences of this isolation by analyzing the genomes of ten pumas from across North and South America.

    • Nedda F. Saremi
    • , Megan A. Supple
    • , Ashley Byrne
    • , James A. Cahill
    • , Luiz Lehmann Coutinho
    • , Love Dalén
    • , Henrique V. Figueiró
    • , Warren E. Johnson
    • , Heather J. Milne
    • , Stephen J. O’Brien
    • , Brendan O’Connell
    • , David P. Onorato
    • , Seth P. D. Riley
    • , Jeff A. Sikich
    • , Daniel R. Stahler
    • , Priscilla Marqui Schmidt Villela
    • , Christopher Vollmers
    • , Robert K. Wayne
    • , Eduardo Eizirik
    • , Russell B. Corbett-Detig
    • , Richard E. Green
    • , Christopher C. Wilmers
    •  & Beth Shapiro
  • Article
    | Open Access

    In-depth functional characterization of genomes relies on comprehensive transcriptome data. Here, the authors employ four complementary RNA sequencing technologies to explore the transcription landscape across 16 tissues or different organ types in diploid A genome cotton using a newly developed computational pipeline.

    • Kun Wang
    • , Dehe Wang
    • , Xiaomin Zheng
    • , Ai Qin
    • , Jie Zhou
    • , Boyu Guo
    • , Yanjun Chen
    • , Xingpeng Wen
    • , Wen Ye
    • , Yu Zhou
    •  & Yuxian Zhu
  • Article
    | Open Access

    An understanding of the ancestral state of the neural crest (NC) gene regulatory network (GRN) gives insight into vertebrate evolution. Here, the authors use transcriptomic and chromatin accessibility analyses of the lamprey NC, as well as cross-species enhancer assays, to identify GRN elements conserved throughout vertebrates.

    • Dorit Hockman
    • , Vanessa Chong-Morrison
    • , Stephen A. Green
    • , Daria Gavriouchkina
    • , Ivan Candido-Ferreira
    • , Irving T. C. Ling
    • , Ruth M. Williams
    • , Chris T. Amemiya
    • , Jeramiah J. Smith
    • , Marianne E. Bronner
    •  & Tatjana Sauka-Spengler
  • Article
    | Open Access

    Black pepper (Piper nigrum) belongs to the long-isolated lineage of basal angiosperm and its fruit has been used for food spice and phytomedicines for thousands of years. Here, the authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis.

    • Lisong Hu
    • , Zhongping Xu
    • , Maojun Wang
    • , Rui Fan
    • , Daojun Yuan
    • , Baoduo Wu
    • , Huasong Wu
    • , Xiaowei Qin
    • , Lin Yan
    • , Lehe Tan
    • , Soonliang Sim
    • , Wen Li
    • , Christopher A Saski
    • , Henry Daniell
    • , Jonathan F. Wendel
    • , Keith Lindsey
    • , Xianlong Zhang
    • , Chaoyun Hao
    •  & Shuangxia Jin
  • Article
    | Open Access

    Retrotransposition events have been linked to some human disorders. Here, Gardner et al. systematically search for mobile genetic elements (ME) in trio whole exome-sequencing datasets and ascertain 9 de novo MEs and further estimate genome-wide germline ME burden and constraint.

    • Eugene J. Gardner
    • , Elena Prigmore
    • , Giuseppe Gallone
    • , Petr Danecek
    • , Kaitlin E. Samocha
    • , Juliet Handsaker
    • , Sebastian S. Gerety
    • , Holly Ironfield
    • , Patrick J. Short
    • , Alejandro Sifrim
    • , Tarjinder Singh
    • , Kate E. Chandler
    • , Emma Clement
    • , Katherine L. Lachlan
    • , Katrina Prescott
    • , Elisabeth Rosser
    • , David R. FitzPatrick
    • , Helen V. Firth
    •  & Matthew E. Hurles
  • Article
    | Open Access

    There has been a rapid rise in single cell RNA-seq methods and associated pipelines. Here the authors use simulated data to systematically evaluate the performance of 3000 possible pipelines to derive recommendations for data processing and analysis of different types of scRNA-seq experiments.

    • Beate Vieth
    • , Swati Parekh
    • , Christoph Ziegenhain
    • , Wolfgang Enard
    •  & Ines Hellmann
  • Article
    | Open Access

    The common carp is derived from recent whole genome duplication and represents a model for polyploid genome evolution, rare in vertebrates. Here, the authors generate and analyse chromosome-level reference genomes for common carp, and describe subgenome gene expression changes.

    • Peng Xu
    • , Jian Xu
    • , Guangjian Liu
    • , Lin Chen
    • , Zhixiong Zhou
    • , Wenzhu Peng
    • , Yanliang Jiang
    • , Zixia Zhao
    • , Zhiying Jia
    • , Yonghua Sun
    • , Yidi Wu
    • , Baohua Chen
    • , Fei Pu
    • , Jianxin Feng
    • , Jing Luo
    • , Jing Chai
    • , Hanyuan Zhang
    • , Hui Wang
    • , Chuanju Dong
    • , Wenkai Jiang
    •  & Xiaowen Sun
  • Article
    | Open Access

    Evolution of optimal gene expression in females is expected to be constrained by sexually-antagonistic selection on males. Here, Parker and colleagues show that gene expression has in fact become masculinized in female stick insects across five independent transitions to asexual reproduction.

    • Darren J. Parker
    • , Jens Bast
    • , Kirsten Jalvingh
    • , Zoé Dumas
    • , Marc Robinson-Rechavi
    •  & Tanja Schwander
  • Article
    | Open Access

    Single-cell ATAC-seq data is challenging to analyse for reasons such as high dimensionality and sparsity. Here, the authors develop SCALE, a deep learning method that leverages latent feature extraction for various tasks of scATACseq data analysis.

    • Lei Xiong
    • , Kui Xu
    • , Kang Tian
    • , Yanqiu Shao
    • , Lei Tang
    • , Ge Gao
    • , Michael Zhang
    • , Tao Jiang
    •  & Qiangfeng Cliff Zhang
  • Article
    | Open Access

    Here, the authors study the interplay between the microbiome and faecal and blood metabolome, and how the microbiome interacts in the dialogue between these metabolic compartments, identifying a key role for microbial functions and underscoring their relevance for microbiome therapeutic strategies.

    • Alessia Visconti
    • , Caroline I. Le Roy
    • , Fabio Rosa
    • , Niccolò Rossi
    • , Tiphaine C. Martin
    • , Robert P. Mohney
    • , Weizhong Li
    • , Emanuele de Rinaldis
    • , Jordana T. Bell
    • , J. Craig Venter
    • , Karen E. Nelson
    • , Tim D. Spector
    •  & Mario Falchi
  • Article
    | Open Access

    Interactions between metabolites and transcription factors are known to control gene expression but analyzing these events at genome-scale is challenging. Here, the authors integrate dynamic metabolome and transcriptome data from E.coli to predict regulatory metabolite-transcription factor interactions.

    • Martin Lempp
    • , Niklas Farke
    • , Michelle Kuntz
    • , Sven Andreas Freibert
    • , Roland Lill
    •  & Hannes Link
  • Article
    | Open Access

    A recent GWAS reported 12 genetic loci for attention deficit/hyperactivity disorder (ADHD). Here, Liao et al. perform transcriptomic imputation using these data and 12 brain-relevant tissues from GTEx and CMC to identify 9 genes associated with ADHD by TWAS, 3 of which had not yet been reported for ADHD.

    • Calwing Liao
    • , Alexandre D. Laporte
    • , Dan Spiegelman
    • , Fulya Akçimen
    • , Ridha Joober
    • , Patrick A. Dion
    •  & Guy A. Rouleau