Volume 50 Issue 6, June 2018

Volume 50 Issue 6

Rose varieties

Clockwise from top: Rosa gallica ‘Versicolor’ (Rosa Mundi), Mme. Isaac Pereire, Maiden’s Blush, Rosa gallica ‘Officinalis’ (Apothecary’s Rose); center: Baron Girod de l’Ain.

See Raymond et al.

Image: Benjamin Perkins. Cover Design: Erin Dewalt.

Editorial

  • Editorial |

    To celebrate the Rosa genomes, we invite you to imagine ways to make rosy data as well loved as the roses themselves. This is an opportunity for data modeling and new discoveries from reanalysis, as well as for data display to feed public interest in the science and culture of flowers.

News & Views

  • News & Views |

    Roses have held an attraction for people all over the world as ornamental plants. Now genome sequencing of the highly heterozygous Rosa chinensis and resequencing of major genotypes open the door to a greater understanding of rose evolutionary history and the regulatory mechanisms determining rose flower color and scent.

    • Qing Xu
    •  & Zhong-Jian Liu

Letters

  • Letter | | Open Access

    High-quality genome assembly of diploid Rosa chinensis and resequencing of major genotypes highlights the origin of modern rose cultivars and provides insights into color biosynthesis and scent pathways.

    • Olivier Raymond
    • , Jérôme Gouzy
    • , Jérémy Just
    • , Hélène Badouin
    • , Marion Verdenaud
    • , Arnaud Lemainque
    • , Philippe Vergne
    • , Sandrine Moja
    • , Nathalie Choisne
    • , Caroline Pont
    • , Sébastien Carrère
    • , Jean-Claude Caissard
    • , Arnaud Couloux
    • , Ludovic Cottret
    • , Jean-Marc Aury
    • , Judit Szécsi
    • , David Latrasse
    • , Mohammed-Amin Madoui
    • , Léa François
    • , Xiaopeng Fu
    • , Shu-Hua Yang
    • , Annick Dubois
    • , Florence Piola
    • , Antoine Larrieu
    • , Magali Perez
    • , Karine Labadie
    • , Lauriane Perrier
    • , Benjamin Govetto
    • , Yoan Labrousse
    • , Priscilla Villand
    • , Claudia Bardoux
    • , Véronique Boltz
    • , Céline Lopez-Roques
    • , Pascal Heitzler
    • , Teva Vernoux
    • , Michiel Vandenbussche
    • , Hadi Quesneville
    • , Adnane Boualem
    • , Abdelhafid Bendahmane
    • , Chang Liu
    • , Manuel Le Bris
    • , Jérôme Salse
    • , Sylvie Baudino
    • , Moussa Benhamed
    • , Patrick Wincker
    •  & Mohammed Bendahmane
  • Letter |

    A meta-analysis of 139,555 Europeans identifies 68 new genomic loci associated with intraocular pressure. Incorporating these new findings into genetic models improves risk prediction for primary open-angle glaucoma.

    • Anthony P. Khawaja
    • , Jessica N. Cooke Bailey
    • , Nicholas J. Wareham
    • , Robert A. Scott
    • , Mark Simcoe
    • , Robert P. Igo Jr
    • , Yeunjoo E. Song
    • , Robert Wojciechowski
    • , Ching-Yu Cheng
    • , Peng T. Khaw
    • , Louis R. Pasquale
    • , Jonathan L. Haines
    • , Paul J. Foster
    • , Janey L. Wiggs
    • , Chris J. Hammond
    •  & Pirro G. Hysi
  • Letter |

    Shortening of mRNA 3′ UTRs is often observed in cancer. A combination of model-based analysis and experiments suggests that 3′ UTR shortening disrupts competing endogenous RNA crosstalk, thus influencing tumor-suppressor expression in trans.

    • Hyun Jung Park
    • , Ping Ji
    • , Soyeon Kim
    • , Zheng Xia
    • , Benjamin Rodriguez
    • , Lei Li
    • , Jianzhong Su
    • , Kaifu Chen
    • , Chioniso P. Masamha
    • , David Baillat
    • , Camila R. Fontes-Garfias
    • , Ann-Bin Shyu
    • , Joel R. Neilson
    • , Eric J. Wagner
    •  & Wei Li
  • Letter |

    Comprehensive fecal metabolic profiling in 786 individuals from TwinsUK provides insights into the influence of host genetics and gut microbial composition on metabolites that may mediate microbiome-associated phenotypes.

    • Jonas Zierer
    • , Matthew A. Jackson
    • , Gabi Kastenmüller
    • , Massimo Mangino
    • , Tao Long
    • , Amalio Telenti
    • , Robert P. Mohney
    • , Kerrin S. Small
    • , Jordana T. Bell
    • , Claire J. Steves
    • , Ana M. Valdes
    • , Tim D. Spector
    •  & Cristina Menni

    Collection:

  • Letter |

    The authors report an improved genome assembly of G. arboretum and resequencing of 243 diploid cotton accessions. GWAS and QTL-seq identify a number of candidate loci that associate with seed oil content, disease resistance and yield traits in cotton.

    • Xiongming Du
    • , Gai Huang
    • , Shoupu He
    • , Zhaoen Yang
    • , Gaofei Sun
    • , Xiongfeng Ma
    • , Nan Li
    • , Xueyan Zhang
    • , Junling Sun
    • , Min Liu
    • , Yinhua Jia
    • , Zhaoe Pan
    • , Wenfang Gong
    • , Zhaohui Liu
    • , Heqin Zhu
    • , Lei Ma
    • , Fuyan Liu
    • , Daigang Yang
    • , Fan Wang
    • , Wei Fan
    • , Qian Gong
    • , Zhen Peng
    • , Liru Wang
    • , Xiaoyang Wang
    • , Shuangjiao Xu
    • , Haihong Shang
    • , Cairui Lu
    • , Hongkun Zheng
    • , Sanwen Huang
    • , Tao Lin
    • , Yuxian Zhu
    •  & Fuguang Li

Articles

  • Article |

    The authors resequence a core collection of upland cotton (Gossypium hirsutum) comprising 419 accessions. They analyze genomic variation and conduct a genome-wide association study for 13 fiber quality and yield traits in 12 different environments.

    • Zhiying Ma
    • , Shoupu He
    • , Xingfen Wang
    • , Junling Sun
    • , Yan Zhang
    • , Guiyin Zhang
    • , Liqiang Wu
    • , Zhikun Li
    • , Zhihao Liu
    • , Gaofei Sun
    • , Yuanyuan Yan
    • , Yinhua Jia
    • , Jun Yang
    • , Zhaoe Pan
    • , Qishen Gu
    • , Xueyuan Li
    • , Zhengwen Sun
    • , Panhong Dai
    • , Zhengwen Liu
    • , Wenfang Gong
    • , Jinhua Wu
    • , Mi Wang
    • , Hengwei Liu
    • , Keyun Feng
    • , Huifeng Ke
    • , Junduo Wang
    • , Hongyu Lan
    • , Guoning Wang
    • , Jun Peng
    • , Nan Wang
    • , Liru Wang
    • , Baoyin Pang
    • , Zhen Peng
    • , Ruiqiang Li
    • , Shilin Tian
    •  & Xiongming Du
  • Article |

    ARLNC1 is a newly discovered lncRNA that is induced by androgen receptor (AR) and maintains AR signaling by stabilizing the AR transcript. Knockdown of ARLNC1 suppresses AR expression, AR signaling and prostate cancer growth in vitro and in vivo.

    • Yajia Zhang
    • , Sethuramasundaram Pitchiaya
    • , Marcin Cieślik
    • , Yashar S. Niknafs
    • , Jean C.-Y. Tien
    • , Yasuyuki Hosono
    • , Matthew K. Iyer
    • , Sahr Yazdani
    • , Shruthi Subramaniam
    • , Sudhanshu K. Shukla
    • , Xia Jiang
    • , Lisha Wang
    • , Tzu-Ying Liu
    • , Michael Uhl
    • , Alexander R. Gawronski
    • , Yuanyuan Qiao
    • , Lanbo Xiao
    • , Saravana M. Dhanasekaran
    • , Kristin M. Juckette
    • , Lakshmi P. Kunju
    • , Xuhong Cao
    • , Utsav Patel
    • , Mona Batish
    • , Girish C. Shukla
    • , Michelle T. Paulsen
    • , Mats Ljungman
    • , Hui Jiang
    • , Rohit Mehra
    • , Rolf Backofen
    • , Cenk S. Sahinalp
    • , Susan M. Freier
    • , Andrew T. Watt
    • , Shuling Guo
    • , John T. Wei
    • , Felix Y. Feng
    • , Rohit Malik
    •  & Arul M. Chinnaiyan
  • Article |

    Integration of single-cell RNA sequencing with genome-wide association data implicates specific brain cell types in schizophrenia. Gene sets previously associated with schizophrenia implicate the same cell types, which include pyramidal cells and medium spiny neurons.

    • Nathan G. Skene
    • , Julien Bryois
    • , Trygve E. Bakken
    • , Gerome Breen
    • , James J. Crowley
    • , Héléna A. Gaspar
    • , Paola Giusti-Rodriguez
    • , Rebecca D. Hodge
    • , Jeremy A. Miller
    • , Ana B. Muñoz-Manchado
    • , Michael C. O’Donovan
    • , Michael J. Owen
    • , Antonio F. Pardiñas
    • , Jesper Ryge
    • , James T. R. Walters
    • , Sten Linnarsson
    • , Ed S. Lein
    • , Patrick F. Sullivan
    •  & Jens Hjerling-Leffler
  • Article |

    Transancestral GWAS meta-analysis in 160,420 individuals identifies 139 loci associated with refractive error, including myopia. Newly identified genes implicate pathways involved in eye growth and light signaling cascades.

    • Milly S. Tedja
    • , Robert Wojciechowski
    • , Pirro G. Hysi
    • , Nicholas Eriksson
    • , Nicholas A. Furlotte
    • , Virginie J. M. Verhoeven
    • , Adriana I. Iglesias
    • , Magda A. Meester-Smoor
    • , Stuart W. Tompson
    • , Qiao Fan
    • , Anthony P. Khawaja
    • , Ching-Yu Cheng
    • , René Höhn
    • , Kenji Yamashiro
    • , Adam Wenocur
    • , Clare Grazal
    • , Toomas Haller
    • , Andres Metspalu
    • , Juho Wedenoja
    • , Jost B. Jonas
    • , Ya Xing Wang
    • , Jing Xie
    • , Paul Mitchell
    • , Paul J. Foster
    • , Barbara E. K. Klein
    • , Ronald Klein
    • , Andrew D. Paterson
    • , S. Mohsen Hosseini
    • , Rupal L. Shah
    • , Cathy Williams
    • , Yik Ying Teo
    • , Yih Chung Tham
    • , Preeti Gupta
    • , Wanting Zhao
    • , Yuan Shi
    • , Woei-Yuh Saw
    • , E-Shyong Tai
    • , Xue Ling Sim
    • , Jennifer E. Huffman
    • , Ozren Polašek
    • , Caroline Hayward
    • , Goran Bencic
    • , Igor Rudan
    • , James F. Wilson
    • , Tin Aung
    • , Amutha B. Veluchamy
    • , Kathryn P. Burdon
    • , Harry Campbell
    • , Li Jia Chen
    • , Peng Chen
    • , Wei Chen
    • , Emily Chew
    • , Margaret M. Deangelis
    • , Xiaohu Ding
    • , Angela Döring
    • , David M. Evans
    • , Sheng Feng
    • , Brian Fleck
    • , Rhys D. Fogarty
    • , Jeremy R. Fondran
    • , Maurizio Fossarello
    • , Xiaobo Guo
    • , Annet E. G. Haarman
    • , Mingguang He
    • , Laura D. Howe
    • , Sarayut Janmahasatian
    • , Vishal Jhanji
    • , Mika Kähönen
    • , Jaakko Kaprio
    • , John P. Kemp
    • , Kay-Tee Khaw
    • , Chiea-Chuen Khor
    • , Eva Krapohl
    • , Jean-François Korobelnik
    • , Kris Lee
    • , Shi-Ming Li
    • , Yi Lu
    • , Robert N. Luben
    • , Kari-Matti Mäkelä
    • , George McMahon
    • , Akira Meguro
    • , Evelin Mihailov
    • , Masahiro Miyake
    • , Nobuhisa Mizuki
    • , Margaux Morrison
    • , Vinay Nangia
    • , Konrad Oexle
    • , Songhomitra Panda-Jonas
    • , Chi Pui Pang
    • , Mario Pirastu
    • , Robert Plomin
    • , Taina Rantanen
    • , Maria Schache
    • , Ilkka Seppälä
    • , George D. Smith
    • , Beate St Pourcain
    • , Pancy O. Tam
    • , J. Willem L. Tideman
    • , Nicholas J. Timpson
    • , Simona Vaccargiu
    • , Zoran Vatavuk
    • , Jie Jin Wang
    • , Ningli Wang
    • , Nick J. Wareham
    • , Alan F. Wright
    • , Liang Xu
    • , Maurice K. H. Yap
    • , Seyhan Yazar
    • , Shea Ping Yip
    • , Nagahisa Yoshimura
    • , Alvin L. Young
    • , Jing Hua Zhao
    • , Xiangtian Zhou
    • , Michelle Agee
    • , Babak Alipanahi
    • , Adam Auton
    • , Robert K. Bell
    • , Katarzyna Bryc
    • , Sarah L. Elson
    • , Pierre Fontanillas
    • , David A. Hinds
    • , Jennifer C. McCreight
    • , Karen E. Huber
    • , Aaron Kleinman
    • , Nadia K. Litterman
    • , Matthew H. McIntyre
    • , Joanna L. Mountain
    • , Elizabeth S. Noblin
    • , Carrie A. M. Northover
    • , Steven J. Pitts
    • , J. Fah Sathirapongsasuti
    • , Olga V. Sazonova
    • , Janie F. Shelton
    • , Suyash Shringarpure
    • , Chao Tian
    • , Vladimir Vacic
    • , Catherine H. Wilson
    • , Tariq M. Aslam
    • , Sarah A. Barman
    • , Jenny H. Barrett
    • , Paul N. Bishop
    • , Peter Blows
    • , Catey Bunce
    • , Roxana O. Carare
    • , Usha Chakravarthy
    • , Michelle Chan
    • , Sharon Chua
    • , David Crabb
    • , Alexander Day
    • , Parul Desai
    • , Bal Dhillon
    • , Andrew D. Dick
    • , Cathy A. Egan
    • , Sarah Ennis
    • , Marcus Fruttiger
    • , John Gallacher
    • , David F. Garway-Heath
    • , Jane Gibson
    • , Dan M. Gore
    • , Alison Hardcastle
    • , Simon P. Harding
    • , Ruth E. Hogg
    • , Pearse A. Keane
    • , Peng Tee Khaw
    • , Gerassimos Lascaratos
    • , Andrew Lotery
    • , Phil J. Luthert
    • , Tom J. MacGillivray
    • , Sarah L. Mackie
    • , Keith R. Martin
    • , Michelle McGaughey
    • , Bernadette McGuinness
    • , Gareth J. McKay
    • , Martin McKibbin
    • , Danny Mitry
    • , Tony Moore
    • , James E. Morgan
    • , Zaynah A. Muthy
    • , Eoin O’Sullivan
    • , Chris Owen
    • , Praveen J. Patel
    • , Euan N. Paterson
    • , Tunde Peto
    • , Axel Petzold
    • , Alicja R. Rudnicka
    • , Jay E. Self
    • , Sobha Sivaprasad
    • , David H. W. Steel
    • , Irene M. Stratton
    • , Nicholas Strouthidis
    • , Cathie L. M. Sudlow
    • , Caroline Thaung
    • , Dhanes Thomas
    • , Emanuele Trucco
    • , Adnan Tufail
    • , Stephen A. Vernon
    • , Ananth C. Viswanathan
    • , Jayne V. Woodside
    • , Max Yates
    • , Jennifer L. Y. Yip
    • , Yalin Zheng
    • , Peter K. Joshi
    • , Akitaka Tsujikawa
    • , Fumihiko Matsuda
    • , Kristina N. Whisenhunt
    • , Tanja Zeller
    • , Peter J. van der Spek
    • , Roxanna Haak
    • , Hanne Meijers-Heijboer
    • , Elisabeth M. van Leeuwen
    • , Sudha K. Iyengar
    • , Jonathan H. Lass
    • , Albert Hofman
    • , Fernando Rivadeneira
    • , André G. Uitterlinden
    • , Johannes R. Vingerling
    • , Terho Lehtimäki
    • , Olli T. Raitakari
    • , Ginevra Biino
    • , Maria Pina Concas
    • , Tae-Hwi Schwantes-An
    • , Robert P. Igo Jr
    • , Gabriel Cuellar-Partida
    • , Nicholas G. Martin
    • , Jamie E. Craig
    • , Puya Gharahkhani
    • , Katie M. Williams
    • , Abhishek Nag
    • , Jugnoo S. Rahi
    • , Phillippa M. Cumberland
    • , Cécile Delcourt
    • , Céline Bellenguez
    • , Janina S. Ried
    • , Arthur A. Bergen
    • , Thomas Meitinger
    • , Christian Gieger
    • , Tien Yin Wong
    • , Alex W. Hewitt
    • , David A. Mackey
    • , Claire L. Simpson
    • , Norbert Pfeiffer
    • , Olavi Pärssinen
    • , Paul N. Baird
    • , Veronique Vitart
    • , Najaf Amin
    • , Cornelia M. van Duijn
    • , Joan E. Bailey-Wilson
    • , Terri L. Young
    • , Seang-Mei Saw
    • , Dwight Stambolian
    • , Stuart MacGregor
    • , Jeremy A. Guggenheim
    • , Joyce Y. Tung
    • , Christopher J. Hammond
    •  & Caroline C. W. Klaver
  • Article |

    Genomic analysis of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients identifies the transmission dynamics of Mtb in Vietnam including frequent transmission of Beijing lineage and positive selection for EsxW Beijing variant.

    • Kathryn E. Holt
    • , Paul McAdam
    • , Phan Vuong Khac Thai
    • , Nguyen Thuy Thuong Thuong
    • , Dang Thi Minh Ha
    • , Nguyen Ngoc Lan
    • , Nguyen Huu Lan
    • , Nguyen Thi Quynh Nhu
    • , Hoang Thanh Hai
    • , Vu Thi Ngoc Ha
    • , Guy Thwaites
    • , David J. Edwards
    • , Artika P. Nath
    • , Kym Pham
    • , David B. Ascher
    • , Jeremy Farrar
    • , Chiea Chuen Khor
    • , Yik Ying Teo
    • , Michael Inouye
    • , Maxine Caws
    •  & Sarah J. Dunstan
  • Article |

    Genome-wide cross-trait analysis shows a strong genetic correlation between asthma and allergic diseases. Shared susceptibility loci are enriched for genes involved in immune and inflammatory responses and genes expressed in epithelial tissues.

    • Zhaozhong Zhu
    • , Phil H. Lee
    • , Mark D. Chaffin
    • , Wonil Chung
    • , Po-Ru Loh
    • , Quan Lu
    • , David C. Christiani
    •  & Liming Liang
  • Article |

    VAMP-seq is a scalable assay that measures the effects of missense variants on intracellular protein abundance. Applying VAMP-seq to thousands of PTEN and TPMT variants helps to classify them as pathogenic or benign.

    • Kenneth A. Matreyek
    • , Lea M. Starita
    • , Jason J. Stephany
    • , Beth Martin
    • , Melissa A. Chiasson
    • , Vanessa E. Gray
    • , Martin Kircher
    • , Arineh Khechaduri
    • , Jennifer N. Dines
    • , Ronald J. Hause
    • , Smita Bhatia
    • , William E. Evans
    • , Mary V. Relling
    • , Wenjian Yang
    • , Jay Shendure
    •  & Douglas M. Fowler
  • Article |

    This study shows that UTX (KDM6A) suppresses myeloid leukemogenesis through noncatalytic functions. UTX loss leads to alterations in H3K27ac, H3K4me1 and chromatin accessibility, and in gene-regulatory programs mediated by ETS and GATA transcription factors.

    • Malgorzata Gozdecka
    • , Eshwar Meduri
    • , Milena Mazan
    • , Konstantinos Tzelepis
    • , Monika Dudek
    • , Andrew J. Knights
    • , Mercedes Pardo
    • , Lu Yu
    • , Jyoti S. Choudhary
    • , Emmanouil Metzakopian
    • , Vivek Iyer
    • , Haiyang Yun
    • , Naomi Park
    • , Ignacio Varela
    • , Ruben Bautista
    • , Grace Collord
    • , Oliver Dovey
    • , Dimitrios A. Garyfallos
    • , Etienne De Braekeleer
    • , Saki Kondo
    • , Jonathan Cooper
    • , Berthold Göttgens
    • , Lars Bullinger
    • , Paul A. Northcott
    • , David Adams
    • , George S. Vassiliou
    •  & Brian J. P. Huntly
  • Article |

    This analysis uses computational modeling of clonal selection to measure evolutionary dynamics in primary human cancers. The method employs high-throughput sequencing data and simultaneously measures the selective advantage and time of appearance of subclones.

    • Marc J. Williams
    • , Benjamin Werner
    • , Timon Heide
    • , Christina Curtis
    • , Chris P. Barnes
    • , Andrea Sottoriva
    •  & Trevor A. Graham