Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus
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{"title"=>"Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus", "type"=>"journal", "authors"=>[{"first_name"=>"Kui", "last_name"=>"Lin", "scopus_author_id"=>"35213345200"}, {"first_name"=>"Erik", "last_name"=>"Limpens", "scopus_author_id"=>"6507786393"}, {"first_name"=>"Zhonghua", "last_name"=>"Zhang", "scopus_author_id"=>"8087401200"}, {"first_name"=>"Sergey", "last_name"=>"Ivanov", "scopus_author_id"=>"7403092382"}, {"first_name"=>"Diane G O", "last_name"=>"Saunders", "scopus_author_id"=>"36341095400"}, {"first_name"=>"Desheng", "last_name"=>"Mu", "scopus_author_id"=>"56031704800"}, {"first_name"=>"Erli", "last_name"=>"Pang", "scopus_author_id"=>"37038295900"}, {"first_name"=>"Huifen", "last_name"=>"Cao", "scopus_author_id"=>"56031448100"}, {"first_name"=>"Hwangho", "last_name"=>"Cha", "scopus_author_id"=>"56031559100"}, {"first_name"=>"Tao", "last_name"=>"Lin", "scopus_author_id"=>"55357738600"}, {"first_name"=>"Qian", "last_name"=>"Zhou", "scopus_author_id"=>"56410038100"}, {"first_name"=>"Yi", "last_name"=>"Shang", "scopus_author_id"=>"55388478400"}, {"first_name"=>"Ying", "last_name"=>"Li", "scopus_author_id"=>"56008379600"}, {"first_name"=>"Trupti", "last_name"=>"Sharma", "scopus_author_id"=>"56031757600"}, {"first_name"=>"Robin", "last_name"=>"van Velzen", "scopus_author_id"=>"33368372000"}, {"first_name"=>"Norbert", "last_name"=>"de Ruijter", "scopus_author_id"=>"6602615186"}, {"first_name"=>"Duur K.", "last_name"=>"Aanen", "scopus_author_id"=>"6603457622"}, {"first_name"=>"Joe", "last_name"=>"Win", "scopus_author_id"=>"7801494299"}, {"first_name"=>"Sophien", "last_name"=>"Kamoun", "scopus_author_id"=>"16157156400"}, {"first_name"=>"Ton", "last_name"=>"Bisseling", "scopus_author_id"=>"7005318657"}, {"first_name"=>"René", "last_name"=>"Geurts", "scopus_author_id"=>"6603603212"}, {"first_name"=>"Sanwen", "last_name"=>"Huang", "scopus_author_id"=>"9533252400"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-84893748588", "pmid"=>"24415955", "doi"=>"10.1371/journal.pgen.1004078", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "issn"=>"15537390", "pui"=>"372348862", "sgr"=>"84893748588"}, "id"=>"ff65bec1-d87f-3edd-925d-85fc2ea638ba", "abstract"=>"Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.", "link"=>"http://www.mendeley.com/research/single-nucleus-genome-sequencing-reveals-high-similarity-among-nuclei-endomycorrhizal-fungus", "reader_count"=>152, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>8, "Researcher"=>45, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>56, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>18, "Student > Bachelor"=>8, "Professor"=>8}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>8, "Researcher"=>45, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>56, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>18, "Student > Bachelor"=>8, "Professor"=>8}, "reader_count_by_subject_area"=>{"Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>128, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>128}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>5, "United Kingdom"=>3, "Switzerland"=>1, "India"=>1, "Canada"=>1, "Netherlands"=>4, "Norway"=>2, "Taiwan"=>1, "Brazil"=>1, "Mexico"=>1, "Italy"=>1, "Australia"=>2, "France"=>2, "Indonesia"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1343668"], "description"=>"<p>(<b>A</b>) Sytox Green stained spore containing numerous nuclei. (<b>B</b>) Single Sytox-stained nucleus trapped with a micropipette. (<b>C</b>) Level of homology between four individual nuclei (N6, N31, N33 and N36) and 2 mycelium DNA samples (DNA1 and DNA2). Presented are the 10 largest contigs of the reference genome (representing ∼1,278 kb). The occurrence of SNPs (marked in blue) and INDELs (marked in red), and gene distributions, in the different assemblies are indicated.</p>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "daom197198w"], "article_id"=>898245, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_sequence_of_single_R_irregularis_DAOM197198w_nuclei_/898245", "title"=>"Genome sequence of single <i>R. irregularis</i> DAOM197198w nuclei.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343677"], "description"=>"<p>The top part indicates the various regions within the <i>R. irregularis</i> DAOM197198 45S rDNA reference sequence (Genbank JF439109). Position means the position of each polymorphic site on the reference. G1: genotype identical to reference; G2: polymorphic nucleotide. The six histograms show the numbers of sequenced reads supporting the two genotypes for N6, N31, N33, N36 and mycelium DNA samples DNA1 and DNA2. The dashed lines indicate the average sequencing depth for each sample.</p>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "polymorphisms", "45s", "rdna"], "article_id"=>898247, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_polymorphisms_in_the_R_irregularis_45S_rDNA_repeat_unit_in_four_individual_nuclei_/898247", "title"=>"Overview of polymorphisms in the <i>R. irregularis</i> 45S rDNA repeat unit in four individual nuclei.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343680"], "description"=>"<p>The amino acid alignment was trimmed as explained in the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004078#s3\" target=\"_blank\">Materials and methods</a> section to remove non-informative positions, resulting in 26,604 positions. The tree was estimated using the rtREV evolutionary model implemented in RAxML. Bootstrap analysis was performed based on 100 replicates, and the three nodes with support below 100 are indicated. Scale bar indicates average number of amino acid substitutions per site.</p>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "derived", "concatenation", "35", "single-copy"], "article_id"=>898250, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ML_tree_derived_from_the_concatenation_of_35_widespread_single_copy_genes_/898250", "title"=>"ML tree derived from the concatenation of 35 widespread, single-copy genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343687"], "description"=>"<p>Percentage of predicted proteome representing putative effectors, using stringent (lacking transmembrane domains; yellow bars) or relaxed criteria (including proteins with predicted single transmembrane domain that overlapped with the signal peptide; blue bars).</p>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "secretomes", "43"], "article_id"=>898257, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_secretomes_of_R_irregularis_and_other_43_fungi_/898257", "title"=>"Comparison of secretomes of <i>R. irregularis</i> and other 43 fungi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343697"], "description"=>"<p>Clusters were determined using hierarchical clustering of the top 100 ranked tribes containing putative effector candidates. A. Rank associated with each tribe based on their content of effector features. B. Score for number of members containing a nuclear localization signals (NLS). C. Score for number of members classified as repeat containing (RCPs). D. Score reflecting number of members classified as small and cysteine rich (SCRs). E. Score for number of members not annotated by searches against swissprot. F. Average protein sequence length for tribe members (ranging from 55 to 856 amino acids). Stars indicate tribes that contain members with similarity to the characterised effector SP7.</p>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "100", "ranked", "tribes", "containing", "putative", "effector"], "article_id"=>898267, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_100_ranked_protein_tribes_containing_putative_effector_candidates_/898267", "title"=>"Top 100 ranked protein tribes containing putative effector candidates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343698"], "description"=>"<p>N50: the length for which the contigs (scaffolds) of that length or longer contains at least half of the total lengths of the contigs (scaffolds).</p>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "genome", "assemblies"], "article_id"=>898268, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_seven_genome_assemblies_from_R_irregularis_DAOM197198w_/898268", "title"=>"Characteristics of the seven genome assemblies from <i>R. irregularis</i> DAOM197198w.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 03:08:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1343716", "https://ndownloader.figshare.com/files/1343717", "https://ndownloader.figshare.com/files/1343718", "https://ndownloader.figshare.com/files/1343719", "https://ndownloader.figshare.com/files/1343720", "https://ndownloader.figshare.com/files/1343721", "https://ndownloader.figshare.com/files/1343722", "https://ndownloader.figshare.com/files/1343723", "https://ndownloader.figshare.com/files/1343724", "https://ndownloader.figshare.com/files/1343725", "https://ndownloader.figshare.com/files/1343726", "https://ndownloader.figshare.com/files/1343727", "https://ndownloader.figshare.com/files/1343728", "https://ndownloader.figshare.com/files/1343729", "https://ndownloader.figshare.com/files/1343730", "https://ndownloader.figshare.com/files/1343731", "https://ndownloader.figshare.com/files/1343732", "https://ndownloader.figshare.com/files/1343733", "https://ndownloader.figshare.com/files/1343734", "https://ndownloader.figshare.com/files/1343735", "https://ndownloader.figshare.com/files/1343736", "https://ndownloader.figshare.com/files/1343737"], "description"=>"<div><p>Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied <i>de novo</i> genome sequencing of individual nuclei of <i>Rhizophagus irregularis</i>. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of <i>Rhizophagus irregularis</i> with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.</p></div>", "links"=>[], "tags"=>["Agroecology", "Soil science", "genetics", "genomics", "Plant science", "nucleus", "genome", "sequencing", "reveals", "nuclei", "endomycorrhizal"], "article_id"=>898286, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Kui Lin", "Erik Limpens", "Zhonghua Zhang", "Sergey Ivanov", "Diane G. O. Saunders", "Desheng Mu", "Erli Pang", "Huifen Cao", "Hwangho Cha", "Tao Lin", "Qian Zhou", "Yi Shang", "Ying Li", "Trupti Sharma", "Robin van Velzen", "Norbert de Ruijter", "Duur K. Aanen", "Joe Win", "Sophien Kamoun", "Ton Bisseling", "René Geurts", "Sanwen Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004078.s001", "https://dx.doi.org/10.1371/journal.pgen.1004078.s002", "https://dx.doi.org/10.1371/journal.pgen.1004078.s003", "https://dx.doi.org/10.1371/journal.pgen.1004078.s004", "https://dx.doi.org/10.1371/journal.pgen.1004078.s005", "https://dx.doi.org/10.1371/journal.pgen.1004078.s006", "https://dx.doi.org/10.1371/journal.pgen.1004078.s007", "https://dx.doi.org/10.1371/journal.pgen.1004078.s008", "https://dx.doi.org/10.1371/journal.pgen.1004078.s009", "https://dx.doi.org/10.1371/journal.pgen.1004078.s010", "https://dx.doi.org/10.1371/journal.pgen.1004078.s011", "https://dx.doi.org/10.1371/journal.pgen.1004078.s012", "https://dx.doi.org/10.1371/journal.pgen.1004078.s013", "https://dx.doi.org/10.1371/journal.pgen.1004078.s014", "https://dx.doi.org/10.1371/journal.pgen.1004078.s015", "https://dx.doi.org/10.1371/journal.pgen.1004078.s016", "https://dx.doi.org/10.1371/journal.pgen.1004078.s017", "https://dx.doi.org/10.1371/journal.pgen.1004078.s018", "https://dx.doi.org/10.1371/journal.pgen.1004078.s019", "https://dx.doi.org/10.1371/journal.pgen.1004078.s020", "https://dx.doi.org/10.1371/journal.pgen.1004078.s021", "https://dx.doi.org/10.1371/journal.pgen.1004078.s022"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Single_Nucleus_Genome_Sequencing_Reveals_High_Similarity_among_Nuclei_of_an_Endomycorrhizal_Fungus_/898286", "title"=>"Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-09 03:08:07"}

PMC Usage Stats | Further Information

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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/Computational biology", "average_usage"=>[341, 529]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[333]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[292, 461]}, {"subject_area"=>"/Biology and life sciences/Mycology", "average_usage"=>[348, 543]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[310]}, {"subject_area"=>"/Biology and life sciences/Plant science", "average_usage"=>[278, 438]}]}

F1000Prime | Further Information

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