Literature DB >> 25000971

Timber! Felling the loblolly pine genome.

John P Hamilton, C Robin Buell.   

Abstract

Conventional short read sequences derived from haploid DNA were extended into long super-reads enabling assembly of the massive 22 Gbp loblolly pine, Pinus taeda, genome.

Entities:  

Mesh：

Year:  2014        PMID： 25000971      PMCID： PMC4053979          DOI： 10.1186/gb4170

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  10 in total

1.  The genome of woodland strawberry (Fragaria vesca).

Authors:  Vladimir Shulaev; Daniel J Sargent; Ross N Crowhurst; Todd C Mockler; Otto Folkerts; Arthur L Delcher; Pankaj Jaiswal; Keithanne Mockaitis; Aaron Liston; Shrinivasrao P Mane; Paul Burns; Thomas M Davis; Janet P Slovin; Nahla Bassil; Roger P Hellens; Clive Evans; Tim Harkins; Chinnappa Kodira; Brian Desany; Oswald R Crasta; Roderick V Jensen; Andrew C Allan; Todd P Michael; Joao Carlos Setubal; Jean-Marc Celton; D Jasper G Rees; Kelly P Williams; Sarah H Holt; Juan Jairo Ruiz Rojas; Mithu Chatterjee; Bo Liu; Herman Silva; Lee Meisel; Avital Adato; Sergei A Filichkin; Michela Troggio; Roberto Viola; Tia-Lynn Ashman; Hao Wang; Palitha Dharmawardhana; Justin Elser; Rajani Raja; Henry D Priest; Douglas W Bryant; Samuel E Fox; Scott A Givan; Larry J Wilhelm; Sushma Naithani; Alan Christoffels; David Y Salama; Jade Carter; Elena Lopez Girona; Anna Zdepski; Wenqin Wang; Randall A Kerstetter; Wilfried Schwab; Schuyler S Korban; Jahn Davik; Amparo Monfort; Beatrice Denoyes-Rothan; Pere Arus; Ron Mittler; Barry Flinn; Asaph Aharoni; Jeffrey L Bennetzen; Steven L Salzberg; Allan W Dickerman; Riccardo Velasco; Mark Borodovsky; Richard E Veilleux; Kevin M Folta
Journal:  Nat Genet       Date:  2010-12-26       Impact factor: 38.330

2.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.

Authors:  Genis Parra; Keith Bradnam; Ian Korf
Journal:  Bioinformatics       Date:  2007-03-01       Impact factor: 6.937

3.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Authors:  Olivier Jaillon; Jean-Marc Aury; Benjamin Noel; Alberto Policriti; Christian Clepet; Alberto Casagrande; Nathalie Choisne; Sébastien Aubourg; Nicola Vitulo; Claire Jubin; Alessandro Vezzi; Fabrice Legeai; Philippe Hugueney; Corinne Dasilva; David Horner; Erica Mica; Delphine Jublot; Julie Poulain; Clémence Bruyère; Alain Billault; Béatrice Segurens; Michel Gouyvenoux; Edgardo Ugarte; Federica Cattonaro; Véronique Anthouard; Virginie Vico; Cristian Del Fabbro; Michaël Alaux; Gabriele Di Gaspero; Vincent Dumas; Nicoletta Felice; Sophie Paillard; Irena Juman; Marco Moroldo; Simone Scalabrin; Aurélie Canaguier; Isabelle Le Clainche; Giorgio Malacrida; Eléonore Durand; Graziano Pesole; Valérie Laucou; Philippe Chatelet; Didier Merdinoglu; Massimo Delledonne; Mario Pezzotti; Alain Lecharny; Claude Scarpelli; François Artiguenave; M Enrico Pè; Giorgio Valle; Michele Morgante; Michel Caboche; Anne-Françoise Adam-Blondon; Jean Weissenbach; Francis Quétier; Patrick Wincker
Journal:  Nature       Date:  2007-08-26       Impact factor: 49.962

4.  The MaSuRCA genome assembler.

Authors:  Aleksey V Zimin; Guillaume Marçais; Daniela Puiu; Michael Roberts; Steven L Salzberg; James A Yorke
Journal:  Bioinformatics       Date:  2013-08-29       Impact factor: 6.937

Review 5.  Tapping the promise of genomics in species with complex, nonmodel genomes.

Authors:  Candice N Hirsch; C Robin Buell
Journal:  Annu Rev Plant Biol       Date:  2013-02-06       Impact factor: 26.379

6.  Real-time DNA sequencing from single polymerase molecules.

Authors:  John Eid; Adrian Fehr; Jeremy Gray; Khai Luong; John Lyle; Geoff Otto; Paul Peluso; David Rank; Primo Baybayan; Brad Bettman; Arkadiusz Bibillo; Keith Bjornson; Bidhan Chaudhuri; Frederick Christians; Ronald Cicero; Sonya Clark; Ravindra Dalal; Alex Dewinter; John Dixon; Mathieu Foquet; Alfred Gaertner; Paul Hardenbol; Cheryl Heiner; Kevin Hester; David Holden; Gregory Kearns; Xiangxu Kong; Ronald Kuse; Yves Lacroix; Steven Lin; Paul Lundquist; Congcong Ma; Patrick Marks; Mark Maxham; Devon Murphy; Insil Park; Thang Pham; Michael Phillips; Joy Roy; Robert Sebra; Gene Shen; Jon Sorenson; Austin Tomaney; Kevin Travers; Mark Trulson; John Vieceli; Jeffrey Wegener; Dawn Wu; Alicia Yang; Denis Zaccarin; Peter Zhao; Frank Zhong; Jonas Korlach; Stephen Turner
Journal:  Science       Date:  2008-11-20       Impact factor: 47.728

7.  Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Authors:  Jill L Wegrzyn; John D Liechty; Kristian A Stevens; Le-Shin Wu; Carol A Loopstra; Hans A Vasquez-Gross; William M Dougherty; Brian Y Lin; Jacob J Zieve; Pedro J Martínez-García; Carson Holt; Mark Yandell; Aleksey V Zimin; James A Yorke; Marc W Crepeau; Daniela Puiu; Steven L Salzberg; Pieter J Dejong; Keithanne Mockaitis; Doreen Main; Charles H Langley; David B Neale
Journal:  Genetics       Date:  2014-03       Impact factor: 4.562

8.  Whole-genome haplotyping using long reads and statistical methods.

Authors:  Volodymyr Kuleshov; Dan Xie; Rui Chen; Dmitry Pushkarev; Zhihai Ma; Tim Blauwkamp; Michael Kertesz; Michael Snyder
Journal:  Nat Biotechnol       Date:  2014-02-23       Impact factor: 54.908

9.  Sequencing and assembly of the 22-gb loblolly pine genome.

Authors:  Aleksey Zimin; Kristian A Stevens; Marc W Crepeau; Ann Holtz-Morris; Maxim Koriabine; Guillaume Marçais; Daniela Puiu; Michael Roberts; Jill L Wegrzyn; Pieter J de Jong; David B Neale; Steven L Salzberg; James A Yorke; Charles H Langley
Journal:  Genetics       Date:  2014-03       Impact factor: 4.562

10.  Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Authors:  David B Neale; Jill L Wegrzyn; Kristian A Stevens; Aleksey V Zimin; Daniela Puiu; Marc W Crepeau; Charis Cardeno; Maxim Koriabine; Ann E Holtz-Morris; John D Liechty; Pedro J Martínez-García; Hans A Vasquez-Gross; Brian Y Lin; Jacob J Zieve; William M Dougherty; Sara Fuentes-Soriano; Le-Shin Wu; Don Gilbert; Guillaume Marçais; Michael Roberts; Carson Holt; Mark Yandell; John M Davis; Katherine E Smith; Jeffrey F D Dean; W Walter Lorenz; Ross W Whetten; Ronald Sederoff; Nicholas Wheeler; Patrick E McGuire; Doreen Main; Carol A Loopstra; Keithanne Mockaitis; Pieter J deJong; James A Yorke; Steven L Salzberg; Charles H Langley
Journal:  Genome Biol       Date:  2014-03-04       Impact factor: 13.583
  10 in total

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