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1. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author

Dent Earl, Jacob O. Kitzman, Iain MacCallum, James R. Knight, Jacques Corbeil, Elenie Godzaridis, Cristian Del Fabbro, Paul J. Kersey, Martin Hunt, Octávio S. Paulo, Joseph Fass, Isaac Ho, Michael C. Schatz, Erich D. Jarvis, Dominique Lavenier, Simone Scalabrin, Thomas D. Otto, Nicolas Maillet, Siu-Ming Yiu, Timothy I. Shaw, David B. Jaffe, Henry Song, Ruibang Luo, Steve Goldstein, David Haussler, Francisco Pina-Martins, Richard A. Gibbs, Adam M. Phillippy, Michael Bechner, Ganeshkumar Ganapathy, Stephen Richards, Riccardo Vicedomini, Shuangye Yin, François Laviolette, Yingrui Li, T. Roderick Docking, Binghang Liu, Carson Qu, Wen-Chi Chou, Hao Zhang, Nuno A. Fonseca, Dariusz Przybylski, Bruno Vieira, Yue Liu, Matthew D. MacManes, Sébastien Boisvert, Yujian Shi, Jared T. Simpson, Sergey Kazakov, Sergey Koren, Jarrod Chapman, Giles Hall, Paul Baranay, Sante Gnerre, Shiguo Zhou, Rayan Chikhi, Filipe J. Ribeiro, Jason T. Howard, Zhenyu Li, Pavel Fedotov, Jay Shendure, J. Graham Ruby, Joseph B. Hiatt, Benedict Paten, Ian F Korf, David C. Schwartz, Keith Bradnam, Jianying Yuan, Alexey Sergushichev, Jun Wang, Hamidreza Chitsaz, Daniel S. Rokhsar, Inanc Birol, Huaiyang Jiang, Kim C. Worley, Anton Alexandrov, Zemin Ning, Delphine Naquin, Michael Place, Matthias Haimel, Guojie Zhang, Guillaume Chapuis, Fedor Tsarev, Scott J. Emrich, Shaun D. Jackman, Sergey Melnikov, Xiang Qin, Ted Sharpe, Francesco Vezzi, Tak-Wah Lam, Richard Durbin, Genome Center [UC Davis], University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Computational Biology and Bioinformatics [New Haven], Yale University [New Haven], Laboratory for Molecular and Computational Genomics [Madison], University of Wisconsin-Madison, Genome Sciences Centre [Vancouver] (GSC), British Columbia Cancer Agency, Infectious Diseases Research Center [Québec], Université Laval [Québec] (ULaval), Faculté de médecine de l'Université Laval [Québec] (ULaval), DOE Joint Genome Institute [Walnut Creek], Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Dependability Interoperability and perfOrmance aNalYsiS Of networkS (DIONYSOS), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-RÉSEAUX, TÉLÉCOMMUNICATION ET SERVICES (IRISA-D2), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of computer science [Detroit], Wayne State University [Detroit], Institute of Bioinformatics [Athens], University of Georgia [USA], Institute of Aging Research [Boston], Hebrew SeniorLife [Boston], Department of Molecular Medicine [Québec], Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, The Wellcome Trust Sanger Institute [Cambridge], Howard Hughes Medical Institute [Santa Cruz] (HHMI), Howard Hughes Medical Institute (HHMI)-University of California [Santa Cruz] (UC Santa Cruz), Department of Computer Science and Engineering [South Bend], University of Notre Dame [Indiana] (UND), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, CRACS & Inesc TEC [Porto], Universidade do Porto = University of Porto, Medical Center [Durham], Duke University [Durham], Human Genome Sequencing Center [Houston] (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), Faculty of Medicine, Department of Genome Sciences [Seattle] (GS), University of Washington [Seattle], 454 Life Sciences [Branford], 454 Life Sciences, National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, Center for Bioinformatics and Computational Biology [Maryland] (CBCB), University of Maryland [College Park], University of Maryland System-University of Maryland System, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong], The University of Hong Kong (HKU), Invariant Preserving SOlvers (IPSO), Institut de Recherche Mathématique de Rennes (IRMAR), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Computer Science and Software Engineering [Québec], Beijing Genomics Institute [Shenzhen] (BGI), Berkeley California Institute for Quantitative Biosciences [Berkeley], University of California (UC), Computational Biology & Population Genomics Group [Lisboa], Centre for Environmental Biology, New York Genome Center [New York], New York Genome Center, Department of Molecular and Cell Biology, Department of Biochemistry and Biophysics, Howard Hughes Medical Institute (HHMI), Simons Center for Quantitative Biology [Cold Spring Harbor], Cold Spring Harbor Laboratory, Department of Epidemiology and Biostatistics [Athens], University of Georgia [USA]-College of Public Health, Science for Life Laboratory [Solna], Royal Institute of Technology [Stockholm] (KTH ), Department of Mathematics and Computer Science [Udine], Università degli Studi di Udine - University of Udine [Italie], University of California-University of California, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Howard Hughes Medical Institute (HHMI)-University of California [Santa Cruz] (UCSC), Universidade do Porto, Harvard University [Cambridge]-Massachusetts Institute of Technology (MIT), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-AGROCAMPUS OUEST, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Inria Rennes – Bretagne Atlantique, and University of California

Subjects
[INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Computer science, Sequence assembly, GENOMES, Health Informatics, Computational biology, Assessment, COMPASS, Genome, 03 medical and health sciences, 0302 clinical medicine, biology.animal, Quantitative Biology - Genomics, Gene, 030304 developmental biology, Sequence (medicine), Scaffolds, Genomics (q-bio.GN), Whole genome sequencing, 0303 health sciences, Genome assembly, Heterozygosity, biology, N50, Research, Vertebrate, De novo Assembly, Computer Science Applications, Fosmid, FOS: Biological sciences, Scalability, 030217 neurology & neurosurgery
Abstract

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets

Published
2013
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2. Detailed analysis of a contiguous 22-Mb region of the maize genome

Author

Cheng Ting Yeh, Lucinda Fulton, Phillip San Miguel, Srinivas Aluru, Shiran Pasternak, Stephanie Adams, Lori Spiegel, Fusheng Wei, Regina S. Baucom, Melissa Kramer, Patrick S. Schnable, Blake C. Meyers, Lixing Yang, Rod A. Wing, Pamela J. Green, Catrina Fronick, Robert S. Fulton, Kristi Collura, Cristian Chaparro, Scott Kruchowski, Gabriel Scara, Susan M. Rock, David Kudrna, Joshua C. Stein, Richard K. Wilson, Yeisoo Yu, Jianwei Zhang, Dawn H. Nagel, Hyeran Kim, Jinke Lin, Emanuele De Paoli, William Courtney, Marina Wissotski, Sandra W. Clifton, Lifang Zhang, Angelina Angelova, Lydia Nascimento, Apurva Narechania, Laura Courtney, Robert A. Martienssen, Wolfgang Golser, Kai Ying, Ananth Kalyanaraman, Chengzhi Liang, Doreen Ware, Ning Jiang, Shiguo Zhou, David C. Schwartz, Susan R. Wessler, Jennifer Currie, Jeffrey L. Bennetzen, W. Richard McCombie, Yujun Han, Tina Graves, Jean-Marc Deragon, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Cold Spring Harbor Laboratory (CSHL), Department of Genetics [Saint-Louis], Washington University in Saint Louis (WUSTL), Department of Genetics, University of Georgia [USA], Delaware Biotechnology Institute, University of Delaware [Newark], Laboratory for Molecular and Computational Genomics [Madison], University of Wisconsin-Madison, Department of Plant Biology [Athens], Center for Plant Genomics, Iowa State University (ISU), School of Electrical Engineering and Computer Science (EECS), Washington State University (WSU), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Horticulture and Landscape Architecture, Purdue University [West Lafayette], Department of Horticulture, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Department of Electrical and Computer Engineering, and Ecker, Joseph R

Subjects
0106 biological sciences, MESH: Zea mays, Sequence Homology, MESH: Base Sequence, MESH: RNA, Plant, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Gene Duplication, MESH: Genes, Plant, MESH: Chromosomes, Plant, Base Pairing, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Gene Duplication, food and beverages, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Physical Chromosome Mapping, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: DNA Transposable Elements, RNA, Plant, Genetics and Genomics/Comparative Genomics, Transposable element, Evolution, MESH: Gene Rearrangement, Molecular Sequence Data, Gene redundancy, MESH: Physical Chromosome Mapping, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Open Reading Frames, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Genetics and Genomics/Plant Genomes and Evolution, Synteny, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Molecular Sequence Data, Molecular, Oryza, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene rearrangement, Plant, MESH: Open Reading Frames, Genes, Genetic Loci, Mutation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Developmental Biology, MESH: Genome, Plant, Cancer Research, Sequence assembly, Retrotransposon, Genome, MESH: Sorghum, Genetics (clinical), MESH: Evolution, Molecular, 2. Zero hunger, Gene Rearrangement, MESH: Synteny, Genetics and Genomics/Bioinformatics, MESH: Oryza sativa, Genome, Plant, Research Article, Biotechnology, MESH: Mutation, lcsh:QH426-470, MESH: Base Pairing, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Genes, Plant, Zea mays, MESH: Sequence Homology, Nucleic Acid, MESH: Genetic Loci, Chromosomes, Plant, Chromosomes, Sequence Homology, Nucleic Acid, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genetics and Genomics/Genomics, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Gene, Sorghum, 030304 developmental biology, Base Sequence, Nucleic Acid, Human Genome, lcsh:Genetics, Genetics and Genomics/Genome Projects, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, DNA Transposable Elements, RNA, 010606 plant biology & botany
Abstract

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses., Author Summary Maize is a major cereal crop and key experimental system for eukaryotic biology. Previous investigations of the maize genome at the sequence level have primarily focused on analyses of genome survey sequences and BAC contigs. Here we used a comprehensive set of resources to construct an ordered and oriented 22-Mb sequence from chromosome 4 that represents 1% of the maize genome. Genome annotation revealed the presence of 544 genes that are interspersed with transposable elements (TEs), which occupy 83.8% of the sequence. Fifty-one genes were involved in 14 tandem gene clusters and most appear to have arisen after lineage divergence. TEs, especially helitrons, were found to contain gene fragments and were widely distributed in gene-rich regions. Large inversions and unequal gene deletion between the two homoeologous maize regions were the main contributors to synteny disruption among maize, sorghum, and rice. We also show that small RNAs are primarily associated with TEs across the region. Comparison of this ordered and oriented sequence with the corresponding uncurated region in the whole genome sequence of maize resulted in improvements in TE annotation that will ultimately enhance detection sensitivity and characterization of TEs. Doing so is likely to improve the specificity of gene annotations.

Published
2009
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