Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Martin Mascher,Gary J. Muehlbauer,Daniel S. Rokhsar,Daniel S. Rokhsar,Jarrod Chapman,Jeremy Schmutz,Kerrie Barry,María Muñoz-Amatriaín,Timothy J. Close,Roger P. Wise,Alan H. Schulman,Axel Himmelbach,Klaus F. X. Mayer,Uwe Scholz,Jesse Poland,Nils Stein,Robbie Waugh +16 more
TLDR
A strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism is introduced, which will enable rapid and cost-efficient establishment of powerful genomic information for many species.Abstract:
Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.read more
Citations
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Journal ArticleDOI
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
Klaus F. X. Mayer,Jane Rogers,Jaroslav Doležel,Curtis J. Pozniak,Kellye Eversole,Catherine Feuillet,Bikram S. Gill,Bernd Friebe,Adam J. Lukaszewski,Pierre Sourdille,Takashi R. Endo,M. Kubaláková,Jarmila Číhalíková,Zdeňka Dubská,Jan Vrána,Romana Šperková,Hana Šimková,Melanie Febrer,Leah Clissold,Kirsten McLay,Kuldeep Singh,Parveen Chhuneja,Nagendra K. Singh,Jitendra P. Khurana,Eduard Akhunov,Frédéric Choulet,Adriana Alberti,Valérie Barbe,Patrick Wincker,Hiroyuki Kanamori,Fuminori Kobayashi,Takeshi Itoh,Takashi Matsumoto,Hiroaki Sakai,Tsuyoshi Tanaka,Jianzhong Wu,Yasunari Ogihara,Hirokazu Handa,P. Ron Maclachlan,Andrew G. Sharpe,Darrin Klassen,David Edwards,Jacqueline Batley,Odd-Arne Olsen,Simen Rød Sandve,Sigbjørn Lien,Burkhard Steuernagel,Brande B. H. Wulff,Mario Caccamo,Sarah Ayling,Ricardo H. Ramirez-Gonzalez,Bernardo J. Clavijo,Jonathan M. Wright,Matthias Pfeifer,Manuel Spannagl,Mihaela Martis,Martin Mascher,Jarrod Chapman,Jesse Poland,Uwe Scholz,Kerrie Barry,Robbie Waugh,Daniel S. Rokhsar,Gary J. Muehlbauer,Nils Stein,Heidrun Gundlach,Matthias Zytnicki,Véronique Jamilloux,Hadi Quesneville,Thomas Wicker,Primetta Faccioli,Moreno Colaiacovo,Antonio Michele Stanca,Hikmet Budak,Luigi Cattivelli,Natasha Glover,Lise Pingault,Etienne Paux,Sapna Sharma,Rudi Appels,Matthew I. Bellgard,Brett Chapman,Thomas Nussbaumer,Kai Christian Bader,Hélène Rimbert,Shichen Wang,Ron Knox,Andrzej Kilian,Michael Alaux,Françoise Alfama,Loïc Couderc,Nicolas Guilhot,Claire Viseux,Mikaël Loaec,Beat Keller,Sébastien Praud +95 more
TL;DR: Insight into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Journal ArticleDOI
A chromosome conformation capture ordered sequence of the barley genome
Martin Mascher,Heidrun Gundlach,Axel Himmelbach,Sebastian Beier,Sven Twardziok,Thomas Wicker,Volodymyr Radchuk,Christoph Dockter,Pete E. Hedley,Joanne Russell,Micha Bayer,Luke Ramsay,Hui Liu,Georg Haberer,Xiao-Qi Zhang,Qisen Zhang,Roberto A. Barrero,Lin Li,Stefan Taudien,Marco Groth,Marius Felder,Alex Hastie,Hana Šimková,Helena Staňková,Jan Vrána,Saki Chan,María Muñoz-Amatriaín,Rachid Ounit,Steve Wanamaker,Dan Bolser,Christian Colmsee,Thomas Schmutzer,Lala Aliyeva-Schnorr,Stefano Grasso,Jaakko Tanskanen,Anna Chailyan,Dharanya Sampath,Darren Heavens,Leah Clissold,Sujie Cao,Brett Chapman,Fei Dai,Yong Han,Hua Li,Xuan Li,Chongyun Lin,John K. McCooke,Cong Tan,Penghao Wang,Songbo Wang,Shuya Yin,Gaofeng Zhou,Jesse Poland,Matthew I. Bellgard,Ljudmilla Borisjuk,Andreas Houben,Jaroslav Doležel,Sarah Ayling,Stefano Lonardi,Paul J. Kersey,Peter Langridge,Gary J. Muehlbauer,Matthew D. Clark,Matthew D. Clark,Mario Caccamo,Mario Caccamo,Alan H. Schulman,Klaus F. X. Mayer,Matthias Platzer,Timothy J. Close,Uwe Scholz,Mats Hansson,Guoping Zhang,Ilka Braumann,Manuel Spannagl,Chengdao Li,Chengdao Li,Chengdao Li,Robbie Waugh,Robbie Waugh,Nils Stein,Nils Stein +81 more
TL;DR: The importance of the barley reference sequence for breeding is demonstrated by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Journal ArticleDOI
Ensembl Genomes 2016: more genomes, more complexity
Paul J. Kersey,James E. Allen,Irina M. Armean,Sanjay Boddu,Bruce J. Bolt,Denise Carvalho-Silva,Mikkel B. Christensen,Paul Davis,Lee J. Falin,Christoph Grabmueller,Jay C. Humphrey,Arnaud Kerhornou,Julia Khobova,Naveen K. Aranganathan,Nicholas Langridge,Ernesto Lowy,Mark D. McDowall,Uma Maheswari,Michael Nuhn,Chuang Kee Ong,Bert Overduin,Michael Paulini,Helder Pedro,Emily Perry,Giulietta Spudich,Electra Tapanari,Brandon Walts,Gareth Williams,Marcela K. Tello-Ruiz,Joshua C. Stein,Sharon Wei,Doreen Ware,Dan Bolser,Kevin L. Howe,Eugene Kulesha,Daniel Lawson,Gareth Maslen,Daniel M. Staines +37 more
TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes, with a focus on recent developments, including the development of new analyses and views to represent polyploid genomes and the continued up-scaling of the resource.
Journal ArticleDOI
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
TL;DR: Clark is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications, and it is significantly faster than any of its competitors.
Book ChapterDOI
Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data
TL;DR: Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species, including those of plant pathogens, pests, and pollinators.
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
TL;DR: This work presents a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation and demonstrates that this method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping.
Journal ArticleDOI
A greedy algorithm for aligning DNA sequences.
TL;DR: A new greedy alignment algorithm is introduced with particularly good performance and it is shown that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data.
Journal ArticleDOI
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable,Doreen Ware,Robert S. Fulton,Joshua C. Stein,Fusheng Wei,Shiran Pasternak,Chengzhi Liang,Jianwei Zhang,Lucinda Fulton,Tina Graves,Patrick Minx,Amy Denise Reily,Laura Courtney,Scott Kruchowski,Chad Tomlinson,Cindy Strong,Kim D. Delehaunty,Catrina Fronick,Bill Courtney,Susan M. Rock,Eddie Belter,Feiyu Du,Kyung Kim,Rachel Abbott,Marc Cotton,Andrew Levy,Pamela Marchetto,Kerri Ochoa,Stephanie M. Jackson,Barbara Gillam,Weizu Chen,Le Yan,Jamey Higginbotham,Marco Cardenas,Jason Waligorski,Elizabeth Applebaum,Lindsey Phelps,Jason Falcone,Krishna L. Kanchi,T. K. Thane,Adam Scimone,Nay Thane,Jessica Henke,Thomas J. Wang,Jessica Ruppert,Neha Shah,Kelsi Rotter,Jennifer S. Hodges,Elizabeth Ingenthron,Matt Cordes,Sara Kohlberg,Jennifer Sgro,Brandon Delgado,Kelly Mead,Asif T. Chinwalla,Shawn Leonard,Kevin Crouse,Kristi Collura,Dave Kudrna,Jennifer Currie,Ruifeng He,Angelina Angelova,Shanmugam Rajasekar,Teri Mueller,Rene Lomeli,Gabriel Scara,Ara Ko,Krista Delaney,Marina Wissotski,Georgina Lopez,David Campos,Michele Braidotti,Elizabeth Ashley,Wolfgang Golser,Hyeran Kim,Seunghee Lee,Jinke Lin,Zeljko Dujmic,Woojin Kim,Jayson Talag,Andrea Zuccolo,Chuanzhu Fan,Aswathy Sebastian,Melissa Kramer,Lori Spiegel,Lidia Nascimento,Theresa Zutavern,Beth Miller,Claude Ambroise,Stephanie Muller,William Spooner,Apurva Narechania,Liya Ren,Sharon Wei,Sunita Kumari,Ben Faga,Michael J. Levy,Linda McMahan,Peter Van Buren,Matthew W. Vaughn,Kai Ying,Cheng Ting Yeh,Scott J. Emrich,Scott J. Emrich,Yi Jia,Ananth Kalyanaraman,Ananth Kalyanaraman,An-Ping Hsia,W. Brad Barbazuk,Regina S. Baucom,Thomas P. Brutnell,Nicholas C. Carpita,Cristian Chaparro,Jer Ming Chia,Jean-Marc Deragon,James C. Estill,Yan Fu,Jeffrey A. Jeddeloh,Yujun Han,Hye-Ran Lee,Pinghua Li,Damon Lisch,Sanzhen Liu,Zhijie Liu,Dawn H. Nagel,Maureen C. McCann,Phillip SanMiguel,Alan M. Myers,Dan Nettleton,John D. Nguyen,Bryan W. Penning,Lalit Ponnala,Kevin L. Schneider,David C. Schwartz,Anupma Sharma,Carol Soderlund,Nathan M. Springer,Qi Sun,Hao Wang,Michael S. Waterman,Richard P. Westerman,Thomas K. Wolfgruber,Lixing Yang,Yeisoo Yu,Lifang Zhang,Shiguo Zhou,Qihui Zhu,Jeffrey L. Bennetzen,R. Kelly Dawe,Jiming Jiang,Ning Jiang,Gernot G. Presting,Susan R. Wessler,Srinivas Aluru,Srinivas Aluru,Robert A. Martienssen,Sandra W. Clifton,W. Richard McCombie,Rod A. Wing,Richard K. Wilson +159 more
TL;DR: The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported.
Journal ArticleDOI
Genome-wide association studies of 14 agronomic traits in rice landraces
Xuehui Huang,Xinghua Wei,Tao Sang,Qiang Zhao,Qiang Zhao,Qi Feng,Yan Zhao,Canyang Li,Chuanrang Zhu,Tingting Lu,Zhiwu Zhang,Meng Li,Meng Li,Danlin Fan,Yunli Guo,Ahong Wang,Lu Wang,Liuwei Deng,Wenjun Li,Yiqi Lu,Qijun Weng,Kunyan Liu,Tao Huang,Taoying Zhou,Yufeng Jing,Wei Li,Zhang Lin,Edward S. Buckler,Edward S. Buckler,Qian Qian,Qifa Zhang,Jiayang Li,Bin Han,Bin Han +33 more
TL;DR: This study identifies ∼3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method, demonstrating that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.
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A chromosome conformation capture ordered sequence of the barley genome
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A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
Klaus F. X. Mayer,Jane Rogers,Jaroslav Doležel,Curtis J. Pozniak,Kellye Eversole,Catherine Feuillet,Bikram S. Gill,Bernd Friebe,Adam J. Lukaszewski,Pierre Sourdille,Takashi R. Endo,M. Kubaláková,Jarmila Číhalíková,Zdeňka Dubská,Jan Vrána,Romana Šperková,Hana Šimková,Melanie Febrer,Leah Clissold,Kirsten McLay,Kuldeep Singh,Parveen Chhuneja,Nagendra K. Singh,Jitendra P. Khurana,Eduard Akhunov,Frédéric Choulet,Adriana Alberti,Valérie Barbe,Patrick Wincker,Hiroyuki Kanamori,Fuminori Kobayashi,Takeshi Itoh,Takashi Matsumoto,Hiroaki Sakai,Tsuyoshi Tanaka,Jianzhong Wu,Yasunari Ogihara,Hirokazu Handa,P. Ron Maclachlan,Andrew G. Sharpe,Darrin Klassen,David Edwards,Jacqueline Batley,Odd-Arne Olsen,Simen Rød Sandve,Sigbjørn Lien,Burkhard Steuernagel,Brande B. H. Wulff,Mario Caccamo,Sarah Ayling,Ricardo H. Ramirez-Gonzalez,Bernardo J. Clavijo,Jonathan M. Wright,Matthias Pfeifer,Manuel Spannagl,Mihaela Martis,Martin Mascher,Jarrod Chapman,Jesse Poland,Uwe Scholz,Kerrie Barry,Robbie Waugh,Daniel S. Rokhsar,Gary J. Muehlbauer,Nils Stein,Heidrun Gundlach,Matthias Zytnicki,Véronique Jamilloux,Hadi Quesneville,Thomas Wicker,Primetta Faccioli,Moreno Colaiacovo,Antonio Michele Stanca,Hikmet Budak,Luigi Cattivelli,Natasha Glover,Lise Pingault,Etienne Paux,Sapna Sharma,Rudi Appels,Matthew I. Bellgard,Brett Chapman,Thomas Nussbaumer,Kai Christian Bader,Hélène Rimbert,Shichen Wang,Ron Knox,Andrzej Kilian,Michael Alaux,Françoise Alfama,Loïc Couderc,Nicolas Guilhot,Claire Viseux,Mikaël Loaec,Beat Keller,Sébastien Praud +95 more