Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements
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{"title"=>"Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements", "type"=>"journal", "authors"=>[{"first_name"=>"Rajiv C.", "last_name"=>"McCoy", "scopus_author_id"=>"55947815700"}, {"first_name"=>"Ryan W.", "last_name"=>"Taylor", "scopus_author_id"=>"56358883800"}, {"first_name"=>"Timothy A.", "last_name"=>"Blauwkamp", "scopus_author_id"=>"57189087115"}, {"first_name"=>"Joanna L.", "last_name"=>"Kelley", "scopus_author_id"=>"8234514200"}, {"first_name"=>"Michael", "last_name"=>"Kertesz", "scopus_author_id"=>"56212051200"}, {"first_name"=>"Dmitry", "last_name"=>"Pushkarev", "scopus_author_id"=>"55190079900"}, {"first_name"=>"Dmitri A.", "last_name"=>"Petrov", "scopus_author_id"=>"7103238750"}, {"first_name"=>"Anna Sophie", "last_name"=>"Fiston-Lavier", "scopus_author_id"=>"22234267900"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0106689", "sgr"=>"84907087679", "issn"=>"19326203", "pui"=>"600018084", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "pmid"=>"25188499", "scopus"=>"2-s2.0-84907087679"}, "id"=>"bac95aa9-3384-3d66-8f8f-63b14027baca", "abstract"=>"High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or complex genomic arrangements. While TEs strongly affect genome function and evolution, most current de novo assembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly-parallel library preparation and local assembly of short read data and which achieve lengths of 1.5–18.5 Kbp with an extremely low error rate (0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organism Drosophila melanogaster (reference genome strain y; cn, bw, sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long-reads, and likely other methods that generate long-reads, offer a powerful approach to improve de novo assemblies of whole genomes.", "link"=>"http://www.mendeley.com/research/illumina-truseq-synthetic-longreads-empower-novo-assembly-resolve-complex-highlyrepetitive-transposa", "reader_count"=>269, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>21, "Librarian"=>1, "Researcher"=>81, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>58, "Student > Postgraduate"=>13, "Other"=>15, "Student > Master"=>39, "Student > Bachelor"=>22, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>21, "Librarian"=>1, "Researcher"=>81, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>58, "Student > Postgraduate"=>13, "Other"=>15, "Student > Master"=>39, "Student > Bachelor"=>22, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Agricultural and Biological Sciences"=>172, "Arts and Humanities"=>1, "Chemistry"=>4, "Computer Science"=>19, "Earth and Planetary Sciences"=>1, "Engineering"=>4, "Environmental Science"=>7, "Biochemistry, Genetics and Molecular Biology"=>42, "Materials Science"=>1, "Medicine and Dentistry"=>9, "Neuroscience"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>7}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>4}, "Chemistry"=>{"Chemistry"=>4}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>172}, "Computer Science"=>{"Computer Science"=>19}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>42}}, "reader_count_by_country"=>{"Argentina"=>2, "United States"=>11, "Japan"=>1, "United Kingdom"=>1, "India"=>1, "New Zealand"=>1, "Canada"=>2, "Netherlands"=>2, "Austria"=>1, "Czech Republic"=>1, "South Korea"=>1, "Sweden"=>2, "Korea (South)"=>1, "China"=>2, "Taiwan"=>1, "Brazil"=>5, "Mexico"=>1, "France"=>1, "Australia"=>1, "Germany"=>5}, "group_count"=>9}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1662434"], "description"=>"<p><b>A</b>: NG(X) contig length for full and down-sampled coverage data sets. This metric represents the size of the contig for which X% of the genome length (180 Mbp) lies in contigs of that size or longer. <b>B</b>: The proportion of genes and transposable elements accurately assembled (100% length and sequence identity) for full and down-sampled coverage data sets.</p>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161933, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689.g004", "stats"=>{"downloads"=>1, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assembly_metrics_as_a_function_of_depth_of_coverage_of_TruSeq_synthetic_long_reads_/1161933", "title"=>"Assembly metrics as a function of depth of coverage of TruSeq synthetic long-reads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-04 04:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1662433"], "description"=>"<p>Predictor variables include: TE length (, , ), GC content (, , ), divergence (, , ), and number of high-identity (0.01 substitutions per base compared to the canonical sequence) copies within family (, , ). Black lines represent predicted values from the GLMM fit to the binary data (colored points). The upper sets of points represent TEs which were perfectly assembled, while the lower set of points represent TEs which are absent from the assembly or were mis-assembled with respect to the reference. The exact positions of the colored points along the Y-axis should therefore be disregarded. Colors indicate different TE families (122 total). To visualize the interaction between divergence and the number of high-identity copies (, , ), we plotted predicted values for both families with low numbers of high-identity copies (dashed line) as well as families with high numbers of high-identity copies (solid line).</p>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161932, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689.g003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_generalized_linear_mixed_model_describing_probability_of_accurate_TE_assembly_/1161932", "title"=>"Results of generalized linear mixed model describing probability of accurate TE assembly.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-04 04:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1662438"], "description"=>"<div><p>High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the <i>de novo</i> assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or complex genomic arrangements. While TEs strongly affect genome function and evolution, most current <i>de novo</i> assembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly-parallel library preparation and local assembly of short read data and which achieve lengths of 1.5–18.5 Kbp with an extremely low error rate (0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organism <i>Drosophila melanogaster</i> (reference genome strain <i>y; cn, bw, sp</i>) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long-reads, and likely other methods that generate long-reads, offer a powerful approach to improve <i>de novo</i> assemblies of whole genomes.</p></div>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161937, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Illumina_TruSeq_Synthetic_Long_Reads_Empower_De_Novo_Assembly_and_Resolve_Complex_Highly_Repetitive_Transposable_Elements/1161937", "title"=>"Illumina TruSeq Synthetic Long-Reads Empower <i>De Novo</i> Assembly and Resolve Complex, Highly-Repetitive Transposable Elements", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-09-04 04:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1662436"], "description"=>"<p>Alignment was performed with NUCmer <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106689#pone.0106689-Delcher1\" target=\"_blank\">[36]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106689#pone.0106689-Kurtz1\" target=\"_blank\">[37]</a>, filtering to extract only the optimal placement of each draft contig on the reference (see Supplemental Materials in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106689#pone.0106689.s001\" target=\"_blank\">File S1</a>). Note that the number of gaps can be substantially fewer than the number of aligned contigs because alignments may partially overlap or be perfectly adjacent with respect to the reference. The number of gaps can also exceed the number of aligned contigs due to multiple partial alignments of contigs to the reference sequence.</p><p>Alignment statistics for Celera Assembler contigs aligned to the reference genome.</p>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161935, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689.t002", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_statistics_for_Celera_Assembler_contigs_aligned_to_the_reference_genome_/1161935", "title"=>"Alignment statistics for Celera Assembler contigs aligned to the reference genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-09-04 04:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1662435"], "description"=>"<p>The N50 length metric measures the length of the contig for which 50% of the total assembly length is contained in contigs of that size or larger, while the L50 metric is the rank order of that contig if all contigs are ordered from longest to shortest. NG50 and LG50 are similar, but based on the expected genome size of 180 Mbp rather than the assembly length. QUAST <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106689#pone.0106689-Gurevich1\" target=\"_blank\">[39]</a> metrics are based on alignment of contigs to the euchromatic reference chromosome arms (which also contain most of the centric heterochromatin). NA50 and LA50 are analogous to N50 and L50, respectively, but in this case the lengths of aligned blocks rather than contigs are considered.</p><p>Values in parentheses represent metrics calculated upon inclusion of the heterochromatic reference scaffolds (XHet, 2LHet, 2RHet, 3LHet, 3RHet, YHet, and U), which contain gaps of arbitrary size and are in some cases not oriented with respect to one another <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0106689#pone.0106689-BDGP1\" target=\"_blank\">[72]</a>. Values outside of parentheses represent comparison of the assembly only to high-quality reference scaffolds X, 2L, 2R, 3L, 3R, and 4.</p><p>Size and correctness metrics for <i>de novo</i> assembly.</p>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161934, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689.t001", "stats"=>{"downloads"=>1, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Size_and_correctness_metrics_for_de_novo_assembly_/1161934", "title"=>"Size and correctness metrics for <i>de novo</i> assembly.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-09-04 04:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1662432"], "description"=>"<p>The suffix “Het” indicates the heterochromatic portion of the corresponding chromosome. M refers to the mitochondrial genome of the <i>y; cn, bw, sp</i> strain. U and Uextra are additional scaffolds in the reference assembly that could not be mapped to chromosomes.</p>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161931, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689.g002", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Depth_of_synthetic_long_read_coverage_per_chromosome_arm_/1161931", "title"=>"Depth of synthetic long-read coverage per chromosome arm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-04 04:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1662431"], "description"=>"<p><b>A</b>: Read length distribution. <b>B, C, & D</b>: Position-dependent profiles of <b>B</b>: mismatches, <b>C</b>: insertions, and <b>D</b>: deletions compared to the reference genome. Error rates presented in these figures represent all differences with the reference genome, and can be due to errors in the reads, mapping errors, errors in the reference genome, or accurate sequencing of residual polymorphism.</p>", "links"=>[], "tags"=>["euchromatic chromosome arms", "N 50 contig size", "assembly", "truseq", "dna", "novel Illumina technology", "reference genome strain y", "te", "reference genome", "model organism Drosophila melanogaster"], "article_id"=>1161930, "categories"=>["Biological Sciences"], "users"=>["Rajiv C. McCoy", "Ryan W. Taylor", "Timothy A. Blauwkamp", "Joanna L. Kelley", "Michael Kertesz", "Dmitry Pushkarev", "Dmitri A. Petrov", "Anna-Sophie Fiston-Lavier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106689.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_TruSeq_synthetic_long_reads_/1161930", "title"=>"Characteristics of TruSeq synthetic long-reads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-04 04:05:19"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"31", "full-text"=>"53", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[341, 529]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[333]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}]}
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