Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements
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{"title"=>"Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements", "type"=>"journal", "authors"=>[{"first_name"=>"Jianbo", "last_name"=>"Zhang", "scopus_author_id"=>"36097325500"}, {"first_name"=>"Tao", "last_name"=>"Zuo", "scopus_author_id"=>"55864996700"}, {"first_name"=>"Thomas", "last_name"=>"Peterson", "scopus_author_id"=>"7202318095"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84884660374", "doi"=>"10.1371/journal.pgen.1003691", "pui"=>"369887330", "pmid"=>"23966872", "scopus"=>"2-s2.0-84884660374", "issn"=>"15537390"}, "id"=>"da16fed4-2ce6-3a7f-8f70-f38c7b2bf3b1", "abstract"=>"Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of Ac/Ds transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (~0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking Ac/Ds and other hAT family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome.", "link"=>"http://www.mendeley.com/research/generation-tandem-direct-duplications-reversedends-transposition-maize-ac-elements", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Master"=>2, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>9, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Master"=>2, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>24, "Medicine and Dentistry"=>2, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Argentina"=>1, "Brazil"=>1, "Germany"=>2}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1171978"], "description"=>"<p>The two lines indicate sister chromatids of maize chromosome 1, joined at the centromere (black). The blue boxes are exons 3, 2, and 1 (left to right) of the <i>p1</i> gene. Red lines with arrowhead(s) indicate <i>Ac/fAc</i> insertions, and the open and solid arrowheads indicate the 3′ and 5′ ends, respectively, of <i>Ac</i>/<i>fAc</i>. The short horizontal arrows show the orientations and approximate positions of PCR primers, and the numbers below are the primer names. The green/black triangles indicate the transposon target site sequences and target site duplications. (<i>A</i>) <i>Ac</i> transposase cleaves the lower chromatid at the 3′ end of <i>fAc</i> and the 5′ end of <i>Ac</i> (arrows). (<i>B</i>) Following transposase cleavage, the internal <i>p1</i> genomic sequences are joined to form a circle. Dotted lines indicate the insertion of the <i>fAc</i> and <i>Ac</i> termini into the a/b site on the sister chromatid. (<i>C</i>) Transposon ends insert into the upper sister chromatid at a proximal site. (<i>D</i>) The <i>Ac</i> 5′ end joins to the distal side (green) of the target site and the <i>fAc</i> 3′ end joins to the proximal side (black) of the target site to generate a proximal deletion (upper chromatid) and a direct duplication (lower chromatid). The shaded arrows encompass the duplicated segments. For animation, please see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003691#pgen.1003691.s006\" target=\"_blank\">Movie S1</a>.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "ends", "transposition", "generates"], "article_id"=>774228, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reversed_Ac_ends_transposition_generates_direct_duplication_/774228", "title"=>"Reversed <i>Ac</i> ends transposition generates direct duplication.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171980"], "description"=>"<p>The white and red phenotypic twinned sectors are outlined. The remainder of the ear has the orange-variegated phenotype specified by the progenitor <i>P1-ovov454</i> allele.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "twinned", "sectors", "t1", "t481"], "article_id"=>774230, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ears_with_twinned_sectors_T1_left_and_T481_right_/774230", "title"=>"Ears with twinned sectors T1 (left) and T481 (right).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171983"], "description"=>"<p>Lane 1: DNA ladder; lanes 2 and 5: water (negative control); lanes 3 and 4: <i>P1-ovov454</i>, <i>P1-rr-T1</i>; lanes 6 and 7: <i>P1-ovov454</i>, <i>P1-rr-T481</i>. Note that primers 1 and 2 are specific for each allele.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "twinned", "alleles", "primers"], "article_id"=>774233, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCR_analysis_of_the_twinned_alleles_with_primers_1_2_Ac5_/774233", "title"=>"PCR analysis of the twinned alleles with primers 1+2+Ac5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171987"], "description"=>"<p>(<i>A</i>) Diagram shows the structure of the progenitor <i>P1-ovov454</i> allele prior to RET. Two sister chromatids are shown, with symbols as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003691#pgen-1003691-g001\" target=\"_blank\">Figure 1</a>. The dotted box shows the a/b target site region, whose sequence is indicated above. The color of the letters in the sequences matches the chromatid line color. (<i>B</i>) PCR amplification of the deletion/duplication breakpoints in <i>p1-ww-T1</i> and <i>P1-rr-T1</i> with primers 2+Ac3 (upper panel) or 1+Ac5 (lower panel). Lane 1: DNA ladder, lane 2: <i>p1-ww[4Co63]</i>, lane 3: <i>P1-ovov454/p1-ww[4Co63]</i>, lane 4: <i>p1-ww-T1/p1-ww[4Co63]</i>, lane 5: <i>P1-rr-T1/p1-ww[4Co63]</i>. (<i>C</i>) Sister chromatid structures of <i>p1-ww-T1</i> (upper) and <i>P1-rr-T1</i> (lower). Sequences of the deletion and duplication breakpoints (dotted boxes) are shown in color matching the chromatid line color. Note that each breakpoint has a copy of the 8 bp TSD GCGCTTTA which is present in a single copy at the a/b target site in the progenitor allele.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "sequences", "reciprocal", "alleles", "generated", "reversed", "ends"], "article_id"=>774237, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Breakpoint_sequences_of_reciprocal_duplication_deletion_alleles_P1_rr_T1_and_p1_ww_T1_generated_by_Reversed_Ends_Transposition_/774237", "title"=>"Breakpoint sequences of reciprocal duplication/deletion alleles <i>P1-rr-T1</i> and <i>p1-ww-T1</i> generated by Reversed Ends Transposition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171988"], "description"=>"<p>(<i>A</i>) Structure of progenitor <i>P1-ovov454</i> allele (upper), and predicted structures of the <i>P1-rr-Twin</i> (duplication) and <i>p1-ww-Twin</i> (deletion) alleles (lower) generated via reversed <i>Ac</i> ends transposition. Blue lines and boxes indicate <i>p1</i> sequences, green lines indicate sequences proximal to <i>p1</i>, and gray boxes indicate sequences homologous to probe 15. The short vertical black lines indicate <i>Sal</i>I sites, and red asterisks (*) mark methylated <i>Sal</i>I sites. The other symbols have the same meaning as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003691#pgen-1003691-g001\" target=\"_blank\">Figure 1</a>. (<i>B</i>) DNA gel blot. Genomic DNA was digested with <i>Sal</i>I and hybridized with <i>p1</i> genomic probe 15 (gray boxes in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003691#pgen-1003691-g005\" target=\"_blank\">Figure 5<i>A</i></a>). Lane 1: <i>p1-ww[4Co63]</i>, Lane 2: <i>P1-ovov454</i>/<i>p1-ww[4Co63]</i>, Lane 3: <i>P1-rr-T1</i>, Lane 4: <i>p1-ww-T1/p1-ww[4Co63]</i>, Lane 5: <i>P1-rr-T481</i>.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "gel", "blot", "twinned"], "article_id"=>774238, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_gel_blot_analysis_of_the_twinned_alleles_/774238", "title"=>"DNA gel blot analysis of the twinned alleles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171989"], "description"=>"<p>Red lines with arrowhead(s) indicate the <i>dhAT</i> family elements associated with each duplication; solid and open arrowheads indicate the transposon 5′ and 3′ ends, respectively. The truncated solid arrowhead in <i>dhAT-Zm13</i> indicates a deletion of 12 bp from the 5′ TIR. The blue lines represent duplicated segments. The blue triangles indicate the transposon target site duplications. Numbers above each line indicate the length of that segment. Sequences and genomic positions are shown in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003691#pgen.1003691.s009\" target=\"_blank\">Text S2</a>.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "duplications", "maize", "generated", "reversed-ends"], "article_id"=>774239, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tandem_direct_duplications_in_maize_generated_by_Reversed_Ends_Transposition_/774239", "title"=>"Tandem direct duplications in maize generated by Reversed-Ends Transposition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171990"], "description"=>"<p>PCR primers.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science"], "article_id"=>774240, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCR_primers_/774240", "title"=>"PCR primers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171991"], "description"=>"<p>The lengths of the duplications.</p>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "lengths"], "article_id"=>774241, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_lengths_of_the_duplications_/774241", "title"=>"The lengths of the duplications.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-15 04:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1171993", "https://ndownloader.figshare.com/files/1171994", "https://ndownloader.figshare.com/files/1171995", "https://ndownloader.figshare.com/files/1171996", "https://ndownloader.figshare.com/files/1171998", "https://ndownloader.figshare.com/files/1171999", "https://ndownloader.figshare.com/files/1172000", "https://ndownloader.figshare.com/files/1172001", "https://ndownloader.figshare.com/files/1172003"], "description"=>"<div><p>Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated <i>de novo</i> from a maize allele containing two Class II <i>Ac/Ds</i> transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of <i>Ac/Ds</i> transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (∼0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking <i>Ac/Ds</i> and other <i>hAT</i> family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome.</p></div>", "links"=>[], "tags"=>["genetics", "genomics", "Plant science", "tandem", "duplications", "reversed-ends", "transposition", "maize", "elements"], "article_id"=>774243, "categories"=>["Biological Sciences"], "users"=>["Jianbo Zhang", "Tao Zuo", "Thomas Peterson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003691.s001", "https://dx.doi.org/10.1371/journal.pgen.1003691.s002", "https://dx.doi.org/10.1371/journal.pgen.1003691.s003", "https://dx.doi.org/10.1371/journal.pgen.1003691.s004", "https://dx.doi.org/10.1371/journal.pgen.1003691.s005", "https://dx.doi.org/10.1371/journal.pgen.1003691.s006", "https://dx.doi.org/10.1371/journal.pgen.1003691.s007", "https://dx.doi.org/10.1371/journal.pgen.1003691.s008", "https://dx.doi.org/10.1371/journal.pgen.1003691.s009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Generation_of_Tandem_Direct_Duplications_by_Reversed_Ends_Transposition_of_Maize_Ac_Elements/774243", "title"=>"Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize <i>Ac</i> Elements", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-15 04:33:56"}

PMC Usage Stats | Further Information

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Relative Metric

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