Genome-Wide Analysis of Repeat Diversity across the Family Musaceae
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{"title"=>"Genome-wide analysis of repeat diversity across the family musaceae", "type"=>"journal", "authors"=>[{"first_name"=>"Petr", "last_name"=>"Novák", "scopus_author_id"=>"55802370930"}, {"first_name"=>"Eva", "last_name"=>"Hřibová", "scopus_author_id"=>"24467719600"}, {"first_name"=>"Pavel", "last_name"=>"Neumann", "scopus_author_id"=>"8272139100"}, {"first_name"=>"Andrea", "last_name"=>"Koblížková", "scopus_author_id"=>"6506848040"}, {"first_name"=>"Jaroslav", "last_name"=>"Doležel", "scopus_author_id"=>"7006010156"}, {"first_name"=>"Jiří", "last_name"=>"Macas", "scopus_author_id"=>"7003387962"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84903304411", "doi"=>"10.1371/journal.pone.0098918", "pui"=>"373394557", "issn"=>"19326203", "pmid"=>"24932725", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "scopus"=>"2-s2.0-84903304411"}, "id"=>"8070c51d-98ef-33f5-b2e7-3b84e7089b51", "abstract"=>"BACKGROUND: The banana family (Musaceae) includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, Musa acuminata and M. balbisiana. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family.\\n\\nRESULTS: Low-pass sequencing of M. acuminata, M. ornata, M. textilis, M. beccarii, M. balbisiana, and Ensete gilletii genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of Ty1/copia long terminal repeat (LTR) retrotransposons and the chromovirus lineage of Ty3/gypsy elements were found to make up most of highly repetitive DNA in all species (14-34.5% of the genome). However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (M. acuminata/M. ornata and M. beccarii/M. textilis) shared similar populations of repetitive elements.\\n\\nCONCLUSIONS: This study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.", "link"=>"http://www.mendeley.com/research/genomewide-analysis-repeat-diversity-across-family-musaceae", "reader_count"=>68, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Researcher"=>16, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>3, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Researcher"=>16, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>17, "Student > Postgraduate"=>3, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>45, "Philosophy"=>1, "Chemistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Czech Republic"=>3, "United States"=>1, "Brazil"=>4, "United Kingdom"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1536137"], "description"=>"<p>Sequenced species.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics"], "article_id"=>1058432, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequenced_species_/1058432", "title"=>"Sequenced species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536135"], "description"=>"<p>(A) Sequence reads are represented by nodes of the graph and reads with identity of at least 90% with minimal overlap of 110 nt are connected by lines. Graph layout was calculated using the 3D version of the Fruchterman and Reingold algorithm <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098918#pone.0098918-Fruchterman1\" target=\"_blank\">[55]</a> from which a 2D projection is shown. Reads are colored based on their similarity to conserved coding domains of LTR retrotransposons. Reads from LTR regions are colored by light blue. (B) Nodes of the graph are colored based on their species of origin. The six identical graphs show reads derived from each species in red; remaining reads are gray to highlight species-specific parts of the graphs. The parts of the graphs that represent the most variable sequence regions in CRM CL18 element, which can differentiate between species, are labeled by black arrows. (C) Maximum-likelihood tree based on nucleotide alignment of sequences covering the reverse transcriptase protein domain of CRM CL18. Sequence read names are colored based on the species of origin.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "sequences"], "article_id"=>1058430, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variability_of_sequences_within_cluster_CL18_/1058430", "title"=>"Variability of sequences within cluster CL18.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536132"], "description"=>"<p>(A) Sequence composition of the largest clusters is shown. The size of the rectangle is proportional to the number of reads in a cluster for each species. Bar plot in the top row shows the size of the clusters as number of reads. Color of the rectangles correspond to the type of the repeat. Upper lines label groups of clusters discussed in the text. The percentage of reads included in the group is shown in parentheses. (B) The presence of mobile element protein domains in the contig assembled from sequences within the cluster. Only clusters that were annotated are shown. (C–E) Validation of clustering results by Southern blot. Genomic DNA from 15 species was probed with sequences derived from clusters CL16, CL51. and CL30. The lanes contain DNA from 1/<i>M. acuminata</i> ssp. <i>zebrina</i> (ITC 0728), 2/<i>M. acuminata</i> ssp. <i>malaccensis</i> (ITC 0250), 3/<i>M. acuminata</i> ssp. <i>burmannicoides</i> (ITC 0249), 4/<i>M. ornata</i> (ITC 0637), 5/<i>M. mannii</i> (ITC 1411), 6/<i>M. ornata</i> (ITC 0528), 7/<i>M. balbisiana</i> (ITC 1120), 8/<i>M. balbisiana</i> (‘Pisang Klutuk Wulung’), 9/<i>M. balbisiana</i> (ITC 0247), 10/<i>M. peekelii</i> (ITC 0917), 11/<i>M. maclayi</i> (ITC 0614), 12/<i>M. textilis</i> (ITC 0539), 13/<i>M. beccarii</i> (ITC 1070), 14/<i>E. ventricosum</i> (ITC 1387), and 15/<i>E. gilletii</i> (ITC 1389).</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "musaceae"], "article_id"=>1058427, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.g004", "stats"=>{"downloads"=>2, "page_views"=>86, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_analysis_of_Musaceae_species_based_on_the_cluster_composition_/1058427", "title"=>"Comparative analysis of Musaceae species based on the cluster composition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536123"], "description"=>"<p>Phylogeny estimated from ITS data using BioNJ. Six genomes selected for repeat analysis are highlighted.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "musaceae"], "article_id"=>1058421, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.g001", "stats"=>{"downloads"=>1, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationship_between_species_of_Musaceae_family_/1058421", "title"=>"Evolutionary relationship between species of Musaceae family.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536140", "https://ndownloader.figshare.com/files/1536141", "https://ndownloader.figshare.com/files/1536142", "https://ndownloader.figshare.com/files/1536143", "https://ndownloader.figshare.com/files/1536144", "https://ndownloader.figshare.com/files/1536145", "https://ndownloader.figshare.com/files/1536146"], "description"=>"<div><p>Background</p><p>The banana family (Musaceae) includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, <i>Musa acuminata</i> and <i>M. balbisiana</i>. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family.</p><p>Results</p><p>Low-pass sequencing of <i>M. acuminata</i>, <i>M. ornata</i>, <i>M. textilis</i>, <i>M. beccarii</i>, <i>M. balbisiana</i>, and <i>Ensete gilletii</i> genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of <i>Ty1/copia</i> long terminal repeat (LTR) retrotransposons and the chromovirus lineage of <i>Ty3/gypsy</i> elements were found to make up most of highly repetitive DNA in all species (14–34.5% of the genome). However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (<i>M. acuminata</i>/<i>M. ornata</i> and <i>M. beccarii</i>/<i>M. textilis</i>) shared similar populations of repetitive elements.</p><p>Conclusions</p><p>This study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.</p></div>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics"], "article_id"=>1058435, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0098918.s001", "https://dx.doi.org/10.1371/journal.pone.0098918.s002", "https://dx.doi.org/10.1371/journal.pone.0098918.s003", "https://dx.doi.org/10.1371/journal.pone.0098918.s004", "https://dx.doi.org/10.1371/journal.pone.0098918.s005", "https://dx.doi.org/10.1371/journal.pone.0098918.s006", "https://dx.doi.org/10.1371/journal.pone.0098918.s007"], "stats"=>{"downloads"=>8, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_Wide_Analysis_of_Repeat_Diversity_across_the_Family_Musaceae_/1058435", "title"=>"Genome-Wide Analysis of Repeat Diversity across the Family Musaceae", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536125"], "description"=>"<p>(A) The barplot shows the total number of reads with detected similarity hits which is proportional to size of repetitive fraction of the genome. As the number of similarity hits to each read is also proportional to its copy number, reads derived from repetitive elements can be divided into low, medium and high copy number fractions. (B) The total number of similarity hits that correspond to number of read pairs with similarity.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "reads", "musaceae"], "article_id"=>1058423, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_All_to_all_similarity_comparison_of_sequence_reads_from_six_Musaceae_species_/1058423", "title"=>"All-to-all similarity comparison of sequence reads from six Musaceae species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536129"], "description"=>"<p>(A–O) Scatter plots show pairwise comparisons of all analyzed sequences between pairs of species. Each spot corresponds to one sequence read. For each sequence read, the number of similarity hits in each species is displayed (this number is proportional to genomic representation of a particular sequence). Red diagonal line marks the position of sequences with equiproportional genomic representations. Sequences with differential genomic representation between species deviate from diagonal. The 45S rDNA sequences are shown in red. (P) Graph summarizing the number of identified read similarities between and within genomes. Width of the lines connecting nodes of the graph correspond to the number of identified similarity hits between sequence reads from different species (straight lines) and within the same species (loops).</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "genomic", "abundance", "reads"], "article_id"=>1058424, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_genomic_abundance_of_analyzed_reads_in_all_six_species_/1058424", "title"=>"Comparison of genomic abundance of analyzed reads in all six species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536138"], "description"=>"<p>*Repeat proportion estimates from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098918#pone.0098918-DHont1\" target=\"_blank\">[20]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098918#pone.0098918-Davey1\" target=\"_blank\">[26]</a>.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "proportions", "repetitive"], "article_id"=>1058433, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_proportions_of_repetitive_sequences_/1058433", "title"=>"Genome proportions of repetitive sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-16 03:06:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536136"], "description"=>"<p>Genomic sequence Chr9:20,150,000–20,250,000 together with repeat annotation was obtained from the Banana Genome Hub (<a href=\"http://banana-genome.cirad.fr/\" target=\"_blank\">http://banana-genome.cirad.fr/</a>) and analyzed using the Profrep tool against our Musaceae repetitive sequence databases. (A) Six tracks show the numbers of similarity hits against reads from six Musaceae genomes as calculated by Profrep. (B) Annotation of genomic region based on our <i>M. acuminata</i> repeat annotation and Profrep analysis. (C) Annotation of repeats in the DH-Pahang genome obtained from the Banana Genome Hub.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "genome analysis", "Genome annotation", "Comparative genomics", "genetics", "Genetic elements", "Mobile genetic elements", "transposable elements", "genomics", "100-pahang"], "article_id"=>1058431, "categories"=>["Biological Sciences"], "users"=>["Petr Novak", "Eva Hřibová", "Pavel Neumann", "Andrea Koblížková", "Jaroslav Doležel", "Jiří Macas"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0098918.g006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_100_Pahang_assembly_using_Profrep_/1058431", "title"=>"Analysis of 100-Pahang assembly using Profrep.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:06:33"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"11", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"9", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"10", "full-text"=>"7", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
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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/Biotechnology", "average_usage"=>[310, 499]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[333]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[278, 438]}]}
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