Full-length transcriptome assembly from RNA-Seq data without a reference genome

Nature Biotechnology
Manfred G GrabherrAviv Regev

Abstract

Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

References

Feb 15, 2001·Trends in Genetics : TIG·B R Graveley
Aug 16, 2001·Proceedings of the National Academy of Sciences of the United States of America·Pavel A PevznerM S Waterman
Apr 5, 2002·Genome Research·W James Kent
Dec 19, 2003·Nucleic Acids Research·Christiane Hertz-FowlerBart Barrell
Feb 25, 2005·Bioinformatics·Thomas D Wu, Colin K Watanabe
Jun 16, 2005·Nature Reviews. Molecular Cell Biology·Arianne J MatlinChristopher W J Smith
Jun 18, 2005·Bioinformatics·Alkes L PricePavel A Pevzner
Dec 8, 2005·Bioinformatics·Steven L Salzberg, James A Yorke
Dec 31, 2005·Nucleic Acids Research·Cathy H WuBaris Suzek
Mar 15, 2008·Genome Research·Jonathan ButlerDavid B Jaffe
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Jan 27, 2009·Nature·Zhenyu XuLars M Steinmetz
Feb 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Moran YassourAviv Regev
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Jun 6, 2009·Bioinformatics·Ruiqiang LiJun Wang
Jun 17, 2009·Bioinformatics·Inanc BirolSteven Jm Jones
Jul 22, 2009·Nucleic Acids Research·Dmitri ParkhomchukAlexey Soldatov
Mar 9, 2010·Bioinformatics·Manfred G GrabherrKerstin Lindblad-Toh
May 12, 2010·Nature Biotechnology·Brian J Haas, Michael C Zody
Aug 17, 2010·Nature Methods·Joshua Z LevinAviv Regev
Oct 12, 2010·Nature Methods·Gordon RobertsonInanc Birol
Apr 23, 2011·Science·Nicholas RhindChad Nusbaum

Citations

May 28, 2013·Molecules and Cells·Bo-Rahm LeeByung-Kwan Cho
Jul 27, 2012·Pharmaceutical Research·Jack A TuszynskiGane Ka-Shu Wong
Mar 15, 2013·Developmental and Comparative Immunology·Mylène ToubianaPhilippe Roch
Mar 19, 2013·Journal of Biotechnology·Subhash J JakhesaraChaitanya G Joshi
Oct 4, 2012·Animal : an International Journal of Animal Bioscience·D P MorgaviG T Attwood
Apr 20, 2013·Nature·Chris T AmemiyaKerstin Lindblad-Toh
Nov 10, 2011·Nature Biotechnology·Phillip E C CompeauGlenn Tesler
Jul 24, 2012·Nature Biotechnology·Andrea L HarperIan Bancroft
Jun 28, 2012·Nature Communications·Shilin ChenChao Sun
Aug 15, 2013·Nature Communications·Hiroshi SugaIñaki Ruiz-Trillo
Nov 26, 2013·Nature Genetics·Hyung-Soon YimJung-Hyun Lee
Aug 23, 2012·Nature Immunology·Weihua Zeng, Ali Mortazavi
Nov 5, 2013·Nature Methods·Tamara SteijgerPaul Bertone
Nov 30, 2011·Nature Reviews. Genetics·Todd J Treangen, Steven L Salzberg
Jul 19, 2012·Nature Reviews. Genetics·Ziv Bar-JosephItamar Simon
Apr 19, 2013·Nature Reviews. Genetics·Bonnie BergerMona Singh
Aug 13, 2013·Nature Structural & Molecular Biology·Liying YanFuchou Tang
Aug 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jason PellC Titus Brown
Nov 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Sangeet LamichhaneyLeif Andersson
Mar 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·Yuyu SongScott T Brady
May 23, 2013·Proceedings of the National Academy of Sciences of the United States of America·Stéphane HacquardEmiel Ver Loren van Themaat
Jul 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Henry C M LeungFrancis Y L Chin
Nov 10, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Stefano BerettaRaffaella Rizzi
Feb 7, 2012·Briefings in Functional Genomics·Yu-Bin WangJr-Kai Yu
Jul 27, 2012·Briefings in Bioinformatics·Chang F QuoGil Alterovitz
Sep 19, 2012·Briefings in Bioinformatics·Marie-Agnès DilliesFrench StatOmique Consortium
Mar 2, 2012·Bioinformatics·Aparna BhaduriPaul A Khavari
Mar 16, 2013·Bioinformatics·Ergude BaoThomas Girke
May 10, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideki NagasakiYasukazu Nakamura
Apr 25, 2013·Molecular Biology and Evolution·Fanwei MengJohn H Postlethwait
May 21, 2013·Molecular Biology and Evolution·Péter SzövényiAndreas Wagner
Dec 27, 2011·Nucleic Acids Research·Leslie Y ChenLeroy E Hood
Dec 21, 2012·Nucleic Acids Research·Yang LiJian Ma
Apr 6, 2013·Nucleic Acids Research·Hai-Son LeZiv Bar-Joseph
Feb 4, 2012·Genes & Development·Markus KretzPaul A Khavari
Aug 17, 2011·Genome Research·Lewis Z HongGregory S Barsh
Jun 19, 2012·Genome Research·Jin-Wu Nam, David P Bartel
Jan 10, 2013·Genome Research·Jonathon T HillH Joseph Yost
Apr 25, 2013·Plant Physiology·Philipp ZerbeJörg Bohlmann
Nov 19, 2011·Cancer Discovery·John R Prensner, Arul M Chinnaiyan
Oct 8, 2013·BMC Bioinformatics·Martin Jones, Mark Blaxter
Nov 21, 2013·BMC Bioinformatics·Casey W DunnFelipe Zapata
Aug 7, 2013·BMC Evolutionary Biology·Jian-Bo YuanJianhai Xiang
Sep 15, 2012·BMC Genomics·Xiao YangMatthew R Henn
Sep 20, 2012·BMC Genomics·Andreas W SchreiberUte Baumann
Mar 16, 2012·BMC Genomics·Nicole GruenheitPeter Lockhart
Feb 26, 2013·BMC Genomics·Eva Jiménez-GuriJohannes Jaeger
May 16, 2013·BMC Genomics·Ya Yang, Stephen A Smith
May 30, 2013·BMC Genomics·Nunzio D'AgostinoIvo Rieu
Jun 20, 2013·BMC Genomics·Zhangyong SongZhongkang Wang
Jun 27, 2013·BMC Genomics·Xin-Chao WangYa-Jun Yang
Jul 11, 2013·BMC Genomics·Shawn T O'Neil, Scott J Emrich
Jul 13, 2013·BMC Genomics·Juan J Gutierrez-GonzalezDavid F Garvin
Aug 10, 2013·BMC Genomics·Alberto PallaviciniGiuseppe Scapigliati
Aug 14, 2013·BMC Genomics·Shaadi F Pooyaei MehrDavid F Gruber
Sep 10, 2013·BMC Genomics·Wei XueXiao-Wen Sun
Oct 12, 2013·BMC Genomics·Vincent P RichardsMahmood S Shivji
Dec 18, 2013·BMC Genomics·Andrezza C ChagasJose M Ribeiro
Oct 8, 2013·BMC Plant Biology·Hui MaJianquan Liu
Dec 24, 2013·BMC Plant Biology·Sandra S A SoetaertDieter L D Deforce
Sep 18, 2013·Algorithms for Molecular Biology : AMB·Rayan Chikhi, Guillaume Rizk
Oct 22, 2011·Genome Biology·Harm van BakelJonathan E Page
Jul 4, 2012·Genome Biology·Elizabeth N KochChad L Myers
Jun 29, 2013·Genome Biology·Savio de Siqueira FerreiraGlaucia Mendes Souza
Jun 19, 2013·Genome Biology·Nicolas SierroNikolai V Ivanov
Oct 8, 2013·PLoS Computational Biology·Sven-Eric SchelhornFrank Berthold
Aug 31, 2013·PLoS Genetics·Scott E CampbellBryony A P Williams
May 17, 2014·PLoS Genetics·Josephine A ReinhardtGerald S Wilkinson
Sep 27, 2013·PLoS Neglected Tropical Diseases·Cinzia CantacessiAlex Loukas
Aug 23, 2012·PloS One·Yan FuGuangyou Yang
Nov 1, 2012·PloS One·Zi Long WangZhi Jiang Zeng
Mar 23, 2013·PloS One·Scott N PetersonWalter Bretz
Apr 5, 2013·PloS One·Esma OzhunerTurgay Unver
May 30, 2013·PloS One·Jeremy GoecksTodd A Schlenke
Jul 11, 2013·PloS One·Nicholas J KaplinskyRay Watson
Jul 12, 2013·PloS One·Andrew D FernandesGregory B Gloor
Aug 8, 2013·PloS One·Guilherme Toledo-SilvaAnete Pereira Souza
Jan 1, 2014·PloS One·Cristian Del FabbroFederico M Giorgi
Feb 14, 2014·PloS One·Claudio Benicio Cardoso-SilvaRenato Vicentini
Mar 25, 2014·PloS One·Yi Jin LiewChristian R Voolstra
Apr 25, 2014·PloS One·Jacqueline M DoyleJ Andrew DeWoody
Jul 18, 2014·PLoS Pathogens·Joël T van MierloRonald P van Rij
Dec 4, 2012·International Journal of Molecular Sciences·Huaizhi MuGuifeng Liu
Jul 28, 2013·International Journal of Molecular Sciences·Giovanni BussottiAnton J Enright
Nov 15, 2013·Viruses·Quan NguyenSteven Reid
Oct 24, 2012·International Journal of Biological Sciences·Wen XieYoujun Zhang
Jun 20, 2013·International Journal of Biological Sciences·Nicolas GlaserE Jacquin-Joly
May 16, 2014·PloS One·Jérôme MarietteChristophe Klopp
Jul 1, 2014·BMC Bioinformatics·Neda ZamaniManfred G Grabherr
Feb 22, 2014·Genome Biology and Evolution·Gilbert SmithAdriana D Briscoe
Feb 1, 2014·Science·Suomeng DongSophien Kamoun
Feb 4, 2014·BMC Research Notes·Keng-See ChowZainorlina Mohd-Zainuddin
Dec 18, 2013·Molecular Biology and Evolution·Daniel B SloanDouglas R Taylor
Jan 21, 2014·BMC Genomics·Gareth B GillardChris M Brown
Apr 13, 2013·Reproduction : the Official Journal of the Society for the Study of Fertility·Xiangyang Miao, Qingmiao Luo
Mar 20, 2014·International Journal of Molecular Sciences·Yanpeng DongMinjie Deng
Mar 7, 2014·Nature·K KunteM R Kronforst
Dec 18, 2013·Briefings in Functional Genomics·Håvard AanesPeter Aleström
Feb 26, 2014·Algorithms for Molecular Biology : AMB·Kamil SalikhovGregory Kucherov
Mar 26, 2014·International Journal of Molecular Sciences·Xiaoshen ZhangGuoqiang Fan
Dec 4, 2013·Proceedings of the National Academy of Sciences of the United States of America·Freek J VonkMichael K Richardson
Feb 22, 2014·BMC Genomics·Luis A Martínez-LópezOctavio Martínez
Jan 1, 2014·Developmental and Comparative Immunology·Chao LiEric Peatman
Mar 22, 2014·Functional & Integrative Genomics·Won Gi YooJae Sam Hwang
Feb 12, 2014·Plant Molecular Biology·M Kamran AzimYong Zhang
Apr 4, 2014·Proceedings. Biological Sciences·Zhe WangShuyi Zhang
May 17, 2014·Genome Announcements·Gilbert SmithAdriana D Briscoe
Apr 15, 2014·Insect Biochemistry and Molecular Biology·Marco Herde, Gregg A Howe
Apr 25, 2014·Nature Communications·Sateesh KagaleIsobel A P Parkin
Mar 29, 2014·Molecular Biology and Evolution·Rosa FernándezGonzalo Giribet
Apr 30, 2014·BMC Genomics·R Travis MorelandAndreas D Baxevanis
Jan 2, 2014·Omics : a Journal of Integrative Biology·Xi QianGuofang Zhong
Mar 29, 2014·Planta·Bhavisha P Sheth, Vrinda S Thaker
Jul 13, 2013·Bioinformatics·Laura H LeGault, Colin N Dewey
Apr 29, 2014·BMC Genomics·Haibao TangChristopher D Town
Apr 12, 2014·International Journal of Molecular Sciences·Xiasheng ZhengWeiwen Chen
Jan 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·Wangpeng ShiWeiguo Fang
May 9, 2014·Nature Communications·Nicolas SierroNikolai V Ivanov
Jun 1, 2014·Genome Biology and Evolution·Péter SzövényiAndreas Wagner
May 23, 2014·Proceedings. Biological Sciences·Maximilian J TelfordRichard R Copley
Feb 27, 2014·Nucleic Acids Research·Lukasz Jan Kielpinski, Jeppe Vinther
Sep 14, 2013·Journal of Microbiological Methods·Julia M Di BellaGregor Reid
Oct 3, 2013·Bioinformatics·Dror HibshOrit Shefi
Jul 31, 2013·Nucleic Acids Research·Kinga P OrlowskaAndrzej Dziembowski
Feb 12, 2013·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Xianggang GaoChongbo He
May 16, 2014·Gene Expression Patterns : GEP·Yi-Hsuan Wang, Caroline W Beck
Aug 27, 2013·Brain Imaging and Behavior·Ivo D DinovAlzheimer’s Disease Neuroimaging Initiative
Apr 16, 2014·Proceedings of the National Academy of Sciences of the United States of America·Fay-Wei LiKathleen M Pryer
Apr 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Xin-Cheng QinYong-Zhen Zhang
Aug 2, 2014·BMC Genomics·Serghei MangulAlex Zelikovsky
Jul 6, 2014·Database : the Journal of Biological Databases and Curation·Chuanlin YinFei Li
Jun 8, 2014·Integrative and Comparative Biology·Antje H L FischerJoel Smith
Feb 18, 2014·Bioinformatics·Yinlong XieJun Wang
Jun 28, 2014·Science·Jason R GallantMichael R Sussman
Jun 22, 2014·Genome Biology and Evolution·Ian A WarrenSeirian Sumner
Aug 15, 2014·Proceedings. Biological Sciences·Prashant P SharmaWard C Wheeler
Jun 18, 2014·Integrative and Comparative Biology·David C PlachetzkiRichard K Grosberg
Apr 29, 2014·Integrative and Comparative Biology·Leslie S Babonis, Mark Q Martindale
Jun 17, 2014·Developmental and Comparative Immunology·Angela Z Poole, Virginia M Weis
Aug 30, 2014·BMC Genomics·Panagiotis IoannidisJulie C Dunning Hotopp
Sep 7, 2014·Genome Biology and Evolution·Björn M von ReumontChristoph Bleidorn
Apr 9, 2014·Bioinformatics·Hervé Marie-NellyRomain Koszul
Jun 26, 2012·Annual Review of Phytopathology·Daniel J Kliebenstein
Sep 26, 2014·BMC Bioinformatics·Wazim Mohammed IsmailHaixu Tang
Apr 29, 2014·Biochemical and Biophysical Research Communications·Masa-aki YoshidaNoritaka Hirohashi
Jun 17, 2014·Bioinformatics·Zhaojun Zhang, Wei Wang
Aug 1, 2014·Genome Biology and Evolution·Adam D HargreavesJohn F Mulley
Jul 19, 2014·Science·International Wheat Genome Sequencing Consortium (IWGSC)
Sep 7, 2014·Molecular Biology and Evolution·Findley R FinsethRichard G Harrison
Nov 5, 2014·Genome Biology and Evolution·Dana J WohlbachAudrey P Gasch
Dec 4, 2014·PeerJ·Emanuel HeitlingerMark Blaxter
Sep 28, 2014·BMC Genomics·Alexey KutsenkoLars Wieslander
Oct 29, 2014·Nature Neuroscience·Ian MazeEric J Nestler
Jun 30, 2014·Bioinformatics·Ehsan Behnam, Andrew D Smith
Mar 19, 2014·Nature Biotechnology·Nathan BoleyJames B Brown
Jul 9, 2014·Archives of Virology·P MargariaM Turina
Oct 11, 2014·Genome Announcements·Mark D StengleinJoseph L DeRisi
Oct 11, 2014·Nature Communications·Wenquan WangMing Peng
Oct 7, 2014·Ecotoxicology and Environmental Safety·Srinithi MayilswamiRavi Naidu
Nov 11, 2014·Nature Communications·Andrew D W GeeringPierre-Yves Teycheney
Sep 17, 2014·Genome Biology and Evolution·Jainy ThomasEllen J Pritham
May 22, 2013·Proceedings of the National Academy of Sciences of the United States of America·Nathan T MortimerTodd A Schlenke
Sep 26, 2014·Genome Biology and Evolution·Finlay MaguireThomas A Richards
Nov 13, 2014·Database : the Journal of Biological Databases and Curation·Zan ZhangFei Li
Nov 12, 2014·Nature Communications·Yang Jae KangSuk-Ha Lee
Dec 18, 2014·International Journal for Parasitology. Drugs and Drug Resistance·Andrew C KotzeRoger K Prichard
Oct 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·M Sabrina PankeyTodd H Oakley
Oct 25, 2014·BMC Genomics·Nicholas J Marra, J Andrew DeWoody
Jul 30, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Meeta SunilSubhashini Srinivasan
Sep 26, 2014·Archives of Virology·I P AdamsN Boonham
Oct 17, 2014·Plant & Cell Physiology·Suk-Chae JungSun Chang Kim
Aug 26, 2014·The Journal of Heredity·Kristina M YimRosemary G Gillespie
Jan 16, 2015·Proceedings. Biological Sciences·Vanessa L GonzálezGonzalo Giribet
Oct 19, 2013·Nature Communications·Shengxiong HuangYongsheng Liu
Nov 28, 2013·Proceedings of the National Academy of Sciences of the United States of America·Alex de MendozaIñaki Ruiz-Trillo
Aug 1, 2014·International Journal of Biological Sciences·Depan CaoGui-Rong Wang
Jul 28, 2013·Statistics in Biosciences·David Hiller, Wing Hung Wong
Jan 10, 2016·Molecular Phylogenetics and Evolution·Jason R ComerJames H Leebens-Mack
Feb 2, 2016·Developmental and Comparative Immunology·Umberto RosaniPaola Venier
Feb 21, 2016·Marine Genomics·Manuela TruebanoJohn I Spicer
Feb 16, 2016·Scientific Reports·Matthew A CollinCheryl Y Hayashi
Mar 17, 2016·Genomics Data·Aliki XanthopoulouPanagiotis Madesis
Dec 31, 2015·Molecular Biology and Evolution·Peter A HosnerRebecca T Kimball
Feb 18, 2016·Molecular Phylogenetics and Evolution·Nicholas W PersonsRebecca T Kimball
Feb 18, 2016·The Journal of Allergy and Clinical Immunology·Luise WesternbergBjoern Peters
Dec 17, 2015·Marine Genomics·Tsvia GildorSmadar Ben-Tabou de-Leon
Jan 20, 2016·Molecular Biology and Evolution·Rebecca D TarvinDavid C Cannatella
Jun 4, 2014·Journal of Proteomics·Valérie CornetCéline Zatylny-Gaudin
May 27, 2015·International Journal of Molecular Sciences·Xiaodong ZhangQiu-Yang Yao
Jan 29, 2016·Journal of Invertebrate Pathology·Abul Farah Md HasanuzzamanPaulino Martínez
Sep 18, 2015·International Journal of Molecular Sciences·Micah D GearhartKaren Echeverri
Jun 13, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yong-Hua LiYong Li
Jun 26, 2015·Toxins·Quentin Kaas, David J Craik
Feb 13, 2015·Marine Drugs·Louisi Souza de OliveiraFabiano L Thompson