Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes - Silene latifolia and S. vulgaris
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{"title"=>"Genomic diversity in two related plant species with and without sex chromosomes - silene latifolia and S. vulgaris", "type"=>"journal", "authors"=>[{"first_name"=>"Radim", "last_name"=>"Cegan", "scopus_author_id"=>"36343235500"}, {"first_name"=>"Boris", "last_name"=>"Vyskot", "scopus_author_id"=>"7004551749"}, {"first_name"=>"Eduard", "last_name"=>"Kejnovsky", "scopus_author_id"=>"6603338680"}, {"first_name"=>"Zdenek", "last_name"=>"Kubat", "scopus_author_id"=>"14119953300"}, {"first_name"=>"Hana", "last_name"=>"Blavet", "scopus_author_id"=>"55043174200"}, {"first_name"=>"Jan", "last_name"=>"Šafář", "scopus_author_id"=>"7004502175"}, {"first_name"=>"Jaroslav", "last_name"=>"Doležel", "scopus_author_id"=>"7006010156"}, {"first_name"=>"Nicolas", "last_name"=>"Blavet", "scopus_author_id"=>"36343308200"}, {"first_name"=>"Roman", "last_name"=>"Hobza", "scopus_author_id"=>"6506422864"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203", "pmid"=>"22393373", "scopus"=>"2-s2.0-84857671845", "doi"=>"10.1371/journal.pone.0031898", "sgr"=>"84857671845", "pui"=>"364355262"}, "id"=>"0b30671f-28de-33af-850a-6dfc9fc385ee", "abstract"=>"BACKGROUND: Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.", "link"=>"http://www.mendeley.com/research/genomic-diversity-two-related-plant-species-without-sex-chromosomes-silene-latifolia-s-vulgaris", "reader_count"=>34, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>27, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Poland"=>1, "Brazil"=>1, "France"=>1, "Portugal"=>1, "Costa Rica"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/673278"], "description"=>"<p>Mitotic metaphase chromosomes of <i>S. latifolia</i> (A, F, K), <i>S. dioica</i> (B, G, L), <i>S. chalcedonica</i> (C, H, M), <i>S. vulgaris</i> (D, I, N) and <i>Dianthus caryophyllus</i> (E, J, O) were counterstained with DAPI (blue). The probes for each element (<i>Ogre</i> – reverse transcriptase (A–E), <i>Retand</i> – reverse transcriptase (F–J) and <i>Copia</i> – reverse transcriptase (K–O)) were labeled with Cy3-conjugated nucleotides (red). The probe for X.43.1. subtelomeric repeat (A, B, F, G, K, L) was labeled with Spectrum Green (green). The X and Y chromosomes are indicated, bar indicates 10 µm.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Chromosome biology", "Molecular cell biology", "Plant science", "Plant biotechnology", "transcriptases", "retroelements", "revealed"], "article_id"=>343752, "categories"=>["Biological Sciences"], "users"=>["Radim Cegan", "Boris Vyskot", "Eduard Kejnovský", "Zdenek Kubat", "Hana Blavet", "Jan Šafář", "Jaroslav Doležel", "Nicolas Blavet", "Roman Hobza"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0031898.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosomal_distribution_of_the_reverse_transcriptases_of_Ogre_Retand_and_Copia_retroelements_in_five_species_from_the_Caryophyllaceae_family_as_revealed_by_FISH_/343752", "title"=>"Chromosomal distribution of the reverse transcriptases of <i>Ogre</i>, <i>Retand</i> and <i>Copia</i> retroelements in five species from the <i>Caryophyllaceae</i> family as revealed by FISH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-29 01:02:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/673519"], "description"=>"<p>Ratios % SV/% SL below 1.0 indicate elements that are more expanded in <i>S. latifolia</i> genome, and ratios % SV/% SL higher than 1.0 show elements that are more expanded in <i>S. vulgaris</i>.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Chromosome biology", "Molecular cell biology", "Plant science", "Plant biotechnology", "clones", "containing", "respective", "elements", "screened"], "article_id"=>343984, "categories"=>["Biological Sciences"], "users"=>["Radim Cegan", "Boris Vyskot", "Eduard Kejnovský", "Zdenek Kubat", "Hana Blavet", "Jan Šafář", "Jaroslav Doležel", "Nicolas Blavet", "Roman Hobza"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0031898.t001", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_total_number_of_clones_from_the_S_vulgaris_short_insert_library_containing_respective_elements_and_the_proportion_of_total_screened_clones_in_comparison_with_the_S_latifolia_28_/343984", "title"=>"The total number of clones from the <i>S. vulgaris</i> short insert library containing respective elements and the proportion of total screened clones in comparison with the <i>S. latifolia</i>[28].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-29 01:06:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/673410"], "description"=>"<p><i>Retand</i> elements are represented on the X axis with indicated length in bp. The plots represent genomic copy numbers of individual insert regions calculated from numbers of similarity hits to the 454 read databases <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031898#pone.0031898-Macas1\" target=\"_blank\">[35]</a> of both male (SLM-all, blue) and female (SLF-all, red) <i>S. latifolia</i> individuals. The central panel displays a comparison of similarity of individual retroelements. Specific domains of retroelements are indicated.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Chromosome biology", "Molecular cell biology", "Plant science", "Plant biotechnology"], "article_id"=>343887, "categories"=>["Biological Sciences"], "users"=>["Radim Cegan", "Boris Vyskot", "Eduard Kejnovský", "Zdenek Kubat", "Hana Blavet", "Jan Šafář", "Jaroslav Doležel", "Nicolas Blavet", "Roman Hobza"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0031898.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_S_latifolia_Retand_2_and_S_vulgaris_BAC62M2_Retand_retrotransposons_/343887", "title"=>"Comparison of <i>S. latifolia</i> (Retand-2) and <i>S. vulgaris</i> (BAC62M2) <i>Retand</i> retrotransposons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-29 01:04:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/345250", "https://ndownloader.figshare.com/files/345282", "https://ndownloader.figshare.com/files/345330", "https://ndownloader.figshare.com/files/345365", "https://ndownloader.figshare.com/files/345392", "https://ndownloader.figshare.com/files/345421", "https://ndownloader.figshare.com/files/345460", "https://ndownloader.figshare.com/files/345496"], "description"=>"<div><h3>Background</h3><p>Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.</p><h3>Methodology/Principal Findings</h3><p>We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, <em>Silene latifolia</em> and <em>S. vulgaris</em>. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious <em>S. latifolia</em> (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious <em>S. vulgaris</em> (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of <em>S. latifolia</em> is larger mainly due to the expansion of <em>Ogre</em> retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in <em>S. vulgaris</em>, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the <em>Caryophyllaceae</em> family. The results of FISH (fluorescence <em>in situ</em> hybridization) on mitotic chromosomes with the <em>Retand</em> element indicate that large rearrangements occurred during the evolution of the <em>Caryophyllaceae</em> family.</p><h3>Conclusions/Significance</h3><p>Our data demonstrate that the evolution of genome size in the genus <em>Silene</em> is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.</p></div>", "links"=>[], "tags"=>["genetics", "genomics", "Chromosome biology", "Molecular cell biology", "Plant science", "Plant biotechnology", "genomic", "chromosomes"], "article_id"=>128255, "categories"=>["Biological Sciences"], "users"=>["Radim Cegan", "Boris Vyskot", "Eduard Kejnovský", "Zdenek Kubat", "Hana Blavet", "Jan Šafář", "Jaroslav Doležel", "Nicolas Blavet", "Roman Hobza"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0031898.s001", "https://dx.doi.org/10.1371/journal.pone.0031898.s002", "https://dx.doi.org/10.1371/journal.pone.0031898.s003", "https://dx.doi.org/10.1371/journal.pone.0031898.s004", "https://dx.doi.org/10.1371/journal.pone.0031898.s005", "https://dx.doi.org/10.1371/journal.pone.0031898.s006", "https://dx.doi.org/10.1371/journal.pone.0031898.s007", "https://dx.doi.org/10.1371/journal.pone.0031898.s008"], "stats"=>{"downloads"=>19, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Diversity_in_Two_Related_Plant_Species_with_and_without_Sex_Chromosomes_Silene_latifolia_and_S_vulgaris_/128255", "title"=>"Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes - <em>Silene latifolia</em> and <em>S. vulgaris</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-29 02:17:35"}

PMC Usage Stats | Further Information

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Relative Metric

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