High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid Miscanthus sinensis
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{"title"=>"High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid miscanthus sinensis", "type"=>"journal", "authors"=>[{"first_name"=>"Xue Feng", "last_name"=>"Ma", "scopus_author_id"=>"7404550166"}, {"first_name"=>"Elaine", "last_name"=>"Jensen", "scopus_author_id"=>"36782251800"}, {"first_name"=>"Nickolai", "last_name"=>"Alexandrov", "scopus_author_id"=>"7004299612"}, {"first_name"=>"Maxim", "last_name"=>"Troukhan", "scopus_author_id"=>"6506719589"}, {"first_name"=>"Liping", "last_name"=>"Zhang", "scopus_author_id"=>"55286133500"}, {"first_name"=>"Sian", "last_name"=>"Thomas-Jones", "scopus_author_id"=>"55285703700"}, {"first_name"=>"Kerrie", "last_name"=>"Farrar", "scopus_author_id"=>"7004033160"}, {"first_name"=>"John", "last_name"=>"Clifton-Brown", "scopus_author_id"=>"6603044413"}, {"first_name"=>"Iain", "last_name"=>"Donnison", "scopus_author_id"=>"6603445147"}, {"first_name"=>"Timothy", "last_name"=>"Swaller", "scopus_author_id"=>"6504014433"}, {"first_name"=>"Richard", "last_name"=>"Flavell", "scopus_author_id"=>"7202212363"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84863341874", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0033821", "pui"=>"364461221", "sgr"=>"84863341874", "issn"=>"19326203", "pmid"=>"22439001"}, "id"=>"a831ef8f-7caf-3625-b52d-3ad11c032f55", "abstract"=>"We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.", "link"=>"http://www.mendeley.com/research/high-resolution-genetic-mapping-genome-sequencing-reveals-genome-duplication-tetraploid-genetic-stru-3", "reader_count"=>161, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>8, "Researcher"=>47, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>55, "Student > Postgraduate"=>3, "Student > Master"=>21, "Other"=>6, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>8, "Researcher"=>47, "Student > Doctoral Student"=>6, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/341716"], "description"=>"<div><p>We have created a high-resolution linkage map of <em>Miscanthus sinensis</em>, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since <em>Miscanthus</em> has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the <em>M. sinensis</em> composite linkage map to the genomes of sorghum, maize, rice, and <em>Brachypodium distachyon</em> indicate that sorghum has the closest syntenic relationship to <em>Miscanthus</em> compared to other species. The comparative results revealed that each pair of the 19 <em>M. sinensis</em> linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of <em>M. sinensis</em> and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of <em>M. sinensis</em>. The results clearly demonstrate, for the first time, that the diploid <em>M. sinensis</em> is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of <em>Miscanthus</em> as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the <em>Miscanthus</em> genus.</p> </div>", "links"=>[], "tags"=>["genome", "sequencing", "reveals", "duplication", "tetraploid", "diploid"], "article_id"=>127553, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Cell Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/High_Resolution_Genetic_Mapping_by_Genome_Sequencing_Reveals_Genome_Duplication_and_Tetraploid_Genetic_Structure_of_the_Diploid_Miscanthus_sinensis_/127553", "title"=>"High Resolution Genetic Mapping by Genome Sequencing Reveals Genome Duplication and Tetraploid Genetic Structure of the Diploid <em>Miscanthus sinensis</em>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-16 02:05:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/667114"], "description"=>"<p>(A) Processing workflow of the NGS data analysis. (B) Distribution of the alignment lengths for <i>Miscanthus</i> reads matching the sorghum genome. (C) Correlation between the numbers of reads per restriction site for two plants: Mb111 and P62, having the largest number of reads. Only reads mapped in chromosome 1 of sorghum were used as an example. Similar correlations were observed for almost all other pairs of plants and other chromosomes. (D) Coverage of SNPs by plants.</p>", "links"=>[], "tags"=>["nucleotide", "polymorphism"], "article_id"=>337589, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_analysis_and_single_nucleotide_polymorphism_SNP_marker_calling_/337589", "title"=>"Sequence analysis and single nucleotide polymorphism (SNP) marker calling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-16 02:06:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/667272"], "description"=>"<p>The linkage groups (LGs) are named from LG1 to LG19 in agreement with their syntenic relationship to the already defined 10 sorghum chromosomes. On each linkage, the gray or black lines represent mapped markers; the right-shifted red lines signify framework markers. The triangle next to each linkage group represents tentative centromere position of the linkage. The details of the composite map were given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033821#pone.0033821.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["composite"], "article_id"=>337751, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linkage_length_and_marker_distribution_of_the_composite_genetic_map_/337751", "title"=>"Linkage length and marker distribution of the composite genetic map.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-16 02:09:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/667405"], "description"=>"<p>The image is produced with CheckMatrix (<a href=\"http://www.atgc.org/XLinkage/\" target=\"_blank\">http://www.atgc.org/XLinkage/</a>) to validate and verify the quality of the composite map using BIT score (low-left diagonal) and REC score (top-right diagonal). Red color represents tight linkage; yellow represents weak linkage; green to blue represents no linkage. The red along the diagonal, but lack of red off the diagonal, indicate that marker assignments and orders in the 19 linkage groups are supported by both JoinMap and CheckMatrix.</p>", "links"=>[], "tags"=>["linkage"], "article_id"=>337881, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphical_representation_of_the_high_quality_linkage_map_of_M_sinensis_/337881", "title"=>"Graphical representation of the high quality linkage map of <i>M. sinensis</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-16 02:11:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/667541"], "description"=>"<p>The big gap in each chromosome plot corresponds to centromere heterochromatic region that inhibits recombination. The image shows genome-wide sequence duplications and chromosome rearrangements in <i>M. sinensis</i> compared to sorghum.</p>", "links"=>[], "tags"=>["alignment", "19", "linkage", "groups", "10", "chromosomes"], "article_id"=>338009, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Syntenic_alignment_between_the_19_linkage_groups_of_M_sinensis_and_10_chromosomes_of_sorghum_/338009", "title"=>"Syntenic alignment between the 19 linkage groups of <i>M. sinensis</i> and 10 chromosomes of sorghum.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-16 02:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/667702"], "description"=>"<p>(A) Chromosome fusion in LG8 of <i>M. sinensis</i> was observed between two sorghum syntenic chromosomes 4 and 7; chromosome 7 is inserted in the middle of chromosome 4 in telemore-centromere inverted order. However, the other duplicated copies of chromosomes 4 and 7 are not fused, corresponding to LG7 and LG13 in <i>M. sinensis</i>, respectively. Also, a common paracentric inversion in the long arm of the syntenic chromosome 4 was seen in both the fused copy (LG8) and the non-fused copy (LG7) of <i>M. sinensis</i>. (B) The fusion of sorghum syntenic chromosomes 4 and 7 in <i>M. sinensis</i> LG8 was also similarly observed in chromosome 3 of <i>B. distachyon</i>. (C) The same paracentric inversion between the long arm of the sorghum syntenic chromosome 4 and <i>M. sinensis</i> LG7 and LG8 was also seen when sorghum was compared to switchgrass, rice, and maize, but only partially seen when compared to <i>B. distachyon</i>.</p>", "links"=>[], "tags"=>["rearrangements", "compared", "sorghum"], "article_id"=>338178, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosome_structural_rearrangements_of_M_sinensis_when_compared_to_sorghum_and_several_other_species_/338178", "title"=>"Chromosome structural rearrangements of <i>M. sinensis</i> when compared to sorghum and several other species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-16 02:16:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/667825"], "description"=>"<p>Mapping data summary of the parental and the composite maps.</p>", "links"=>[], "tags"=>["composite"], "article_id"=>338301, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Xue-Feng Ma", "Elaine Jensen", "Nickolai Alexandrov", "Maxim Troukhan", "Liping Zhang", "Sian Thomas-Jones", "Kerrie Farrar", "John Clifton-Brown", "Iain Donnison", "Timothy Swaller", "Richard Flavell"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033821.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mapping_data_summary_of_the_parental_and_the_composite_maps_/338301", "title"=>"Mapping data summary of the parental and the composite maps.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-16 02:18:21"}

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Relative Metric

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