Instability of Plastid DNA in the Nuclear Genome
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{"title"=>"Instability of plastid DNA in the nuclear genome", "type"=>"journal", "authors"=>[{"first_name"=>"Anna E.", "last_name"=>"Sheppard", "scopus_author_id"=>"56428668100"}, {"first_name"=>"Jeremy N.", "last_name"=>"Timmis", "scopus_author_id"=>"7004708107"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"pmid"=>"19119415", "doi"=>"10.1371/journal.pgen.1000323", "sgr"=>"58949104692", "isbn"=>"1553-7404 (Electronic)", "scopus"=>"2-s2.0-58949104692", "issn"=>"15537390", "pui"=>"354135296"}, "id"=>"ba89289b-6360-378e-9266-d3e3e83dda41", "abstract"=>"Functional gene transfer from the plastid (chloroplast) and mitochondrial genomes to the nucleus has been an important driving force in eukaryotic evolution. Non-functional DNA transfer is far more frequent, and the frequency of such transfers from the plastid to the nucleus has been determined experimentally in tobacco using transplastomic lines containing, in their plastid genome, a kanamycin resistance gene (neo) readymade for nuclear expression. Contrary to expectations, non-Mendelian segregation of the kanamycin resistance phenotype is seen in progeny of some lines in which neo has been transferred to the nuclear genome. Here, we provide a detailed analysis of the instability of kanamycin resistance in nine of these lines, and we show that it is due to deletion of neo. Four lines showed instability with variation between progeny derived from different areas of the same plant, suggesting a loss of neo during somatic cell division. One line showed a consistent reduction in the proportion of kanamycin-resistant progeny, suggesting a loss of neo during meiosis, and the remaining four lines were relatively stable. To avoid genomic enlargement, the high frequency of plastid DNA integration into the nuclear genome necessitates a counterbalancing removal process. This is the first demonstration of such loss involving a high proportion of recent nuclear integrants. We propose that insertion, deletion, and rearrangement of plastid sequences in the nuclear genome are important evolutionary processes in the generation of novel nuclear genes. This work is also relevant in the context of transgenic plant research and crop production, because similar processes to those described here may be involved in the loss of plant transgenes.", "link"=>"http://www.mendeley.com/research/instability-plastid-dna-nuclear-genome-2", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Ph. D. Student"=>3, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Ph. D. Student"=>3, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>14}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "Switzerland"=>1}, "group_count"=>0}

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  • {"month"=>"4", "year"=>"2021", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"3"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/912336"], "description"=>"<p>The percentage of kanamycin resistant progeny from the seed capsules which gave the highest and lowest kr∶ks ratios for each of kr2.1-2.10 are shown. Approximately 200–250 seeds from each capsule were tested for kanamycin resistance. <i>P</i> values correspond to deviation from 3∶1 kr∶ks.</p><p>NS <i>P</i>>0.01, ** <i>P</i><0.01, *** <i>P</i><0.001.</p>a<p>This is the only seed capsule of kr2.2 which deviated significantly from 75% kanamycin resistance, so given the level of significance it is likely to represent random variation rather than a biological effect.</p>", "links"=>[], "tags"=>["kanamycin", "self-fertilised", "capsules"], "article_id"=>582800, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.t001", "stats"=>{"downloads"=>6, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Segregation_of_kanamycin_resistance_in_individual_self_fertilised_seed_capsules_of_kr2_1_2_10_/582800", "title"=>"Segregation of kanamycin resistance in individual self-fertilised seed capsules of kr2.1-2.10.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:15:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/911978"], "description"=>"<p>DNA slot blotting was performed using pooled DNA from at least 20 plants grown from seeds of a normally segregating self-fertilised seed capsule (75% kan<sup>R</sup>) and pooled DNA from at least 20 plants grown from a capsule which showed no kanamycin resistant progeny (0% kan<sup>R</sup>) for each of kr2.3, kr2.5 and kr2.10 (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000323#pgen-1000323-g001\" target=\"_blank\">Figure 1</a>), as well as a wildtype control. Triplicates of each sample were probed with <i>neo</i> or <i>aadA</i> probes, followed by probing with ribosomal DNA as a loading control. The graphs show average hybridisation to <i>neo</i> (A) or <i>aadA</i> (B) after normalisation to ribosomal DNA hybridisation. Error bars show standard deviation. * <i>P</i><0.05 ** <i>P</i><0.01, *** <i>P</i><0.001; Student's <i>t</i>-test.</p>", "links"=>[], "tags"=>["dna", "blot"], "article_id"=>582436, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantification_of_DNA_blot_analysis_/582436", "title"=>"Quantification of DNA blot analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:13:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/911600"], "description"=>"<p>The percentages of kanamycin resistant progeny from a number of self-fertilised seed capsules are shown for kr2.3 (A), kr2.5 (B), kr2.7 (C) and kr2.10 (D). Each box represents a seed capsule, with the percentage of kanamycin resistant progeny from that capsule shown. Approximately 200–250 seeds from each capsule were tested for kanamycin resistance. Lines represent branches (not to scale) and are included to show the branching pattern of the plants from which individual seed capsules were progeny tested. Seed capsules that deviate significantly (<i>P</i><0.01) from the expected 75% kanamycin resistant progeny are highlighted with grey shading. Arrows indicate seed capsules which were used for PCR and DNA blot analysis (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000323#pgen-1000323-g003\" target=\"_blank\">Figures 3</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000323#pgen-1000323-g004\" target=\"_blank\">4</a>). ** <i>P</i><0.01, *** <i>P</i><0.001.</p>", "links"=>[], "tags"=>["kanamycin"], "article_id"=>582057, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.g001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Instability_of_kanamycin_resistance_/582057", "title"=>"Instability of kanamycin resistance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:11:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/912273"], "description"=>"<p>Primers used in this study.</p>", "links"=>[], "tags"=>["Evolutionary biology", "evolutionary biology/plant genomes and evolution", "genetics and genomics", "plant biology"], "article_id"=>582731, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.t003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_in_this_study_/582731", "title"=>"Primers used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:15:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/912143"], "description"=>"<p>A. Partial sequence of the kr2.5 nuclear integrant. Blue text indicates <i>aadA</i> sequence, beginning from the start codon, and green text indicates plastid sequence, with the two bold regions being identical. The box highlights a 3 bp region of overlap between <i>aadA</i> and plastid sequences. Black text indicates non-plastid sequence of unknown origin. B. Structure of the transplastome showing the origin of kr2.5 nuclear integrant sequences (not to scale). <i>Neo</i> and <i>aadA</i> are represented by red and blue arrows respectively. They are present in two copies as they are located within the inverted repeats (shown in grey). The green arrow indicates plastid sequence adjacent to <i>aadA</i> in the kr2.5 nuclear integrant. In each case, the direction of the arrow corresponds to the direction of the sequence as written in part A.</p>", "links"=>[], "tags"=>["Evolutionary biology", "evolutionary biology/plant genomes and evolution", "genetics and genomics", "plant biology"], "article_id"=>582606, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.g005", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Origin_and_partial_sequence_of_the_kr2_5_nuclear_integrant_/582606", "title"=>"Origin and partial sequence of the kr2.5 nuclear integrant.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:14:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/912307"], "description"=>"<p>The total number of kanamycin resistant and sensitive seedlings from all seed capsules of kr2.1-2.10, excluding those which deviated significantly (<i>P</i><0.01) from 3∶1 kr∶ks, are shown. <i>P</i> values correspond to deviation from 3∶1 kr∶ks.</p><p>NS <i>P</i>>0.01, ** <i>P</i><0.01, *** <i>P</i><0.001.</p>a<p>In this case the one seed capsule which deviated significantly from 3∶1 kr∶ks was included in the analysis (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000323#pgen-1000323-t001\" target=\"_blank\">Table 1</a>).</p>", "links"=>[], "tags"=>["segregation", "kanamycin", "self-fertilised", "progeny"], "article_id"=>582768, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.t002", "stats"=>{"downloads"=>4, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overall_segregation_of_kanamycin_resistance_in_self_fertilised_progeny_of_kr2_1_2_10_/582768", "title"=>"Overall segregation of kanamycin resistance in self-fertilised progeny of kr2.1-2.10.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 07:15:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/911731"], "description"=>"<p>Each box represents a seed capsule. Where one number is shown, it indicates the percentage of kanamycin resistant progeny from a backcross to male wildtype. Where two numbers are shown, that flower was used for both self-fertilisation and backcrossing to female wildtype. The numbers indicate the percentage of kanamycin resistant progeny from self-fertilisation and backcrossing respectively. Each number represents approximately 100–150 seeds which were tested for kanamycin resistance. Lines represent branches (not to scale) and are included to show the branching pattern of the plants from which individual seed capsules were progeny tested. ND not determined.</p>", "links"=>[], "tags"=>["instability", "homozygous", "descendents"], "article_id"=>582198, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_instability_in_homozygous_descendents_of_kr2_3_A_kr2_7_B_and_kr2_10_C_/582198", "title"=>"Analysis of instability in homozygous descendents of kr2.3 (A), kr2.7 (B) and kr2.10 (C).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:12:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/911843"], "description"=>"<p>A–C. PCR of <i>neo</i> from 6 plants grown from seeds of a normally segregating self-fertilised seed capsule (75% kan<sup>R</sup>) and 6 plants grown from seeds of a capsule which showed no kanamycin resistant progeny (0% kan<sup>R</sup>) for each of kr2.3 (A), kr2.5 (B) and kr2.10 (C) (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000323#pgen-1000323-g001\" target=\"_blank\">Figure 1</a>). D. PCR of <i>neo</i> from progeny of a self-fertilised seed capsule of kr2.9 which gave 50% kanamycin resistant progeny. Results for 12 plants are shown; this is representative of a larger experiment in which 36 plants were tested (see text). In all cases control PCRs with <i>rbcS</i> primers are also shown. The <i>neo</i> primers amplify a single product of approximately 800 bp. The <i>rbcS</i> primers amplify two products of approximately 850 bp and 1 kb. -ve no template.</p>", "links"=>[], "tags"=>["kr", "lines", "reduced", "levels", "kanamycin"], "article_id"=>582302, "categories"=>["Evolutionary Biology", "Genetics", "Plant Biology"], "users"=>["Anna E. Sheppard", "Jeremy N. Timmis"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000323.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCR_analysis_of_kr_lines_with_reduced_levels_of_kanamycin_resistance_/582302", "title"=>"PCR analysis of kr lines with reduced levels of kanamycin resistance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:12:50"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"7", "full-text"=>"2", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}

Relative Metric

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