Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria
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{"title"=>"Within-Genome evolution of REPINs: A new family of miniature mobile DNA in bacteria", "type"=>"journal", "authors"=>[{"first_name"=>"Frederic", "last_name"=>"Bertels", "scopus_author_id"=>"35180998100"}, {"first_name"=>"Paul B.", "last_name"=>"Rainey", "scopus_author_id"=>"7006507614"}], "year"=>2011, "source"=>"PLoS Genetics", "identifiers"=>{"isbn"=>"10.1371/journal.pgen.1002132", "pmid"=>"21698139", "doi"=>"10.1371/journal.pgen.1002132", "pui"=>"362058259", "issn"=>"15537390", "sgr"=>"79959843994", "scopus"=>"2-s2.0-79959843994"}, "id"=>"11b7d472-50da-3c03-a03d-4f1c4b440a27", "abstract"=>"<title>Author Summary</title> <p>DNA sequences that copy themselves throughout genomes, and make no specific contribution to reproductive success, are by definition “selfish.” Such DNA is a feature of the genomes of all organisms and evident by virtue of its repetitive nature. In bacteria the predominant repetitive sequences are short (∼20 bp), extragenic, and palindromic. These so-called REP sequences may occur many hundreds of times per genome, but their origins and means of dissemination have been a longstanding mystery. We show that REPs are components of higher-order replicative entities termed REPINs, which are themselves thought to be derived from REP sequences that flanked an ancestral autonomous selfish element. In this ancestral state the REP sequences were likely to have been critical for the movement of the selfish element, but were devoid of any capacity to replicate independently. REPINs, on the other hand, have evolved to have a life of their own, albeit one that exploits—even enslaves—a genetic element upon which their existence depends. REPINs are the ultimate non-autonomous, super-streamlined, selfish element and are widespread among bacteria.</p>", "link"=>"http://www.mendeley.com/research/withingenome-evolution-repins-new-family-miniature-mobile-dna-bacteria", "reader_count"=>52, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>8, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Other"=>1, "Student > Master"=>3, "Student > Bachelor"=>4, "Professor"=>6, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>8, "Researcher"=>14, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>14, "Other"=>1, "Student > Master"=>3, "Student > Bachelor"=>4, "Professor"=>6, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>37, "Medicine and Dentistry"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Brazil"=>2, "United Kingdom"=>1, "France"=>1, "Spain"=>1, "Russia"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/384615", "https://ndownloader.figshare.com/files/384642", "https://ndownloader.figshare.com/files/384667", "https://ndownloader.figshare.com/files/384709", "https://ndownloader.figshare.com/files/384781", "https://ndownloader.figshare.com/files/384818", "https://ndownloader.figshare.com/files/384870", "https://ndownloader.figshare.com/files/384902", "https://ndownloader.figshare.com/files/384926", "https://ndownloader.figshare.com/files/384959", "https://ndownloader.figshare.com/files/385027", "https://ndownloader.figshare.com/files/385047", "https://ndownloader.figshare.com/files/385069", "https://ndownloader.figshare.com/files/385107", "https://ndownloader.figshare.com/files/385118"], "description"=>"<div><p>Repetitive sequences are a conserved feature of many bacterial genomes. While first reported almost thirty years ago, and frequently exploited for genotyping purposes, little is known about their origin, maintenance, or processes affecting the dynamics of within-genome evolution. Here, beginning with analysis of the diversity and abundance of short oligonucleotide sequences in the genome of <em>Pseudomonas fluorescens</em> SBW25, we show that over-represented short sequences define three distinct groups (GI, GII, and GIII) of repetitive extragenic palindromic (REP) sequences. Patterns of REP distribution suggest that closely linked REP sequences form a functional replicative unit: REP doublets are over-represented, randomly distributed in extragenic space, and more highly conserved than singlets. In addition, doublets are organized as inverted repeats, which together with intervening spacer sequences are predicted to form hairpin structures in ssDNA or mRNA. We refer to these newly defined entities as REPINs (REP doublets forming hairpins) and identify short reads from population sequencing that reveal putative transposition intermediates. The proximal relationship between GI, GII, and GIII REPINs and specific REP-associated tyrosine transposases (RAYTs), combined with features of the putative transposition intermediate, suggests a mechanism for within-genome dissemination. Analysis of the distribution of REPs in a range of RAYT–containing bacterial genomes, including <em>Escherichia coli</em> K-12 and <em>Nostoc punctiforme</em>, show that REPINs are a widely distributed, but hitherto unrecognized, family of miniature non-autonomous mobile DNA.</p> </div>", "links"=>[], "tags"=>["within-genome", "miniature", "dna"], "article_id"=>135943, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.s001", "https://dx.doi.org/10.1371/journal.pgen.1002132.s002", "https://dx.doi.org/10.1371/journal.pgen.1002132.s003", "https://dx.doi.org/10.1371/journal.pgen.1002132.s004", "https://dx.doi.org/10.1371/journal.pgen.1002132.s005", "https://dx.doi.org/10.1371/journal.pgen.1002132.s006", "https://dx.doi.org/10.1371/journal.pgen.1002132.s007", "https://dx.doi.org/10.1371/journal.pgen.1002132.s008", "https://dx.doi.org/10.1371/journal.pgen.1002132.s009", "https://dx.doi.org/10.1371/journal.pgen.1002132.s010", "https://dx.doi.org/10.1371/journal.pgen.1002132.s011", "https://dx.doi.org/10.1371/journal.pgen.1002132.s012", "https://dx.doi.org/10.1371/journal.pgen.1002132.s013", "https://dx.doi.org/10.1371/journal.pgen.1002132.s014", "https://dx.doi.org/10.1371/journal.pgen.1002132.s015"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Within_Genome_Evolution_of_REPINs_a_New_Family_of_Miniature_Mobile_DNA_in_Bacteria/135943", "title"=>"Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-06-16 01:39:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/764400"], "description"=>"<p>Data shows comparisons to both a random model, and to the closely related <i>P. fluorescens</i> Pf0-1 genome. The random model is based on 100 genomes generated with the same dinucleotide content, replication bias and length as the SBW25 genome. <i>P. fluorescens</i> Pf0-1 shares the same GC-content as SBW25 and has a highly similar dinucleotide content (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002132#pgen.1002132.s012\" target=\"_blank\">Table S1</a>); coding density differs by 1.7% and the genome length differs by 4%.</p>", "links"=>[], "tags"=>["oligonucleotides", "genome"], "article_id"=>434782, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_common_oligonucleotides_in_the_genome_of_P_fluorescens_SBW25_/434782", "title"=>"Frequency of common oligonucleotides in the genome of <i>P. fluorescens</i> SBW25.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:19:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/764468"], "description"=>"<p>Data are next-neighbor distances for 1,053 GI, GII and GIII sequences in extragenic space, compared to a random model (inset). The peaks at 71 and 110 bp correspond to doublets of GI and GII sequences, respectively. The peak at 184 bp corresponds to GI–GIII tandem repeat clusters (see text). No significant deviation from the random model was noted for next-neighbor distances above 200 bp. The next-neighbor distances of 16-mers randomly assigned to extragenic space is the average of 10,000 simulations (inset).</p>", "links"=>[], "tags"=>["next-neighbor", "distances", "giii", "sequences", "genome"], "article_id"=>434837, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_next_neighbor_distances_for_GI_GII_and_GIII_sequences_in_the_genome_of_P_fluorescens_SBW25_/434837", "title"=>"Frequency of next-neighbor distances for GI, GII, and GIII sequences in the genome of <i>P. fluorescens</i> SBW25.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:20:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/764573"], "description"=>"<p>Data are average pairwise identity of REPs found as singlets, doublets and clusters (clusters contain more than three REPs). Error bars show standard deviation. Statistical testing (jackknife) shows the average pairwise identity of 16-mers from REP doublets (and clusters for GI and GIII, <i>P</i>-value<1e-10) to be significantly greater than the average pairwise identity of 16-mers obtained from REP singlets: this is true for comparisons within each of the REP groups (<i>P</i><1e-10 for GI; <i>P</i><1e-8 for GII and GIII).</p>", "links"=>[], "tags"=>["pairwise", "rep", "sequences"], "article_id"=>434950, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_pairwise_identity_of_REP_sequences_found_in_singlets_doublets_and_clusters_/434950", "title"=>"Average pairwise identity of REP sequences found in singlets, doublets, and clusters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:22:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/764667"], "description"=>"<p>(<i>A</i>) Alignment of 101 GI <u>REP</u> doublets forming hairp<u>in</u>s (REPINs) from SBW25 (37 are shown) shows a symmetrical (palindromic) organization comprised of two highly conserved regions separated by a spacer. Top line shows the consensus sequence followed by a graph displaying identity to the consensus (green denotes 100% identity). Two invariant regions of 16 bp are found in the left and right ends (LE, RE). These sequences are organized as inverted repeats and define the most abundant 16-mer in the SBW25 genome (black box). Each 16-mer overlaps a GI REP sequence (red box). (<i>B</i>) General REPIN features including LE and RE, each comprised of a highly conserved 16-mer (black) overlapping a REP sequence (red), with the two ends separated by a spacer. For a GI doublet the distance between the first residues of the two invariant 16-mers is 71 bp. Complementary bases permit formation of a hairpin structure (arrows). (<i>C</i>) Three excision events detected from Illumina sequencing reads reveal a putative transposition intermediate. Full-length sequences show three genomic regions located between 2,577,312–2,577,231, 3,857,520–3,857,439 and 5,683,545–5,683,624 bp on the SBW25 genome, each of which contains a REPIN. The partial sequences below each genomic region are Illumina reads from which the REPIN has been excised (see also <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002132#pgen.1002132.s006\" target=\"_blank\">Figure S6</a>). (<i>D</i>) Cartoon of the excised region indicating putative transposition intermediate. Note the 5′-tail, which generates an asymmetrical sequence. (<i>E</i>) Secondary structure prediction for the consensus GI REPIN shows that the conserved bases on each side can pair resulting in a long hairpin (<i>E</i>, left). Predictions for transposition intermediates in the same order as the alignments in (<i>C</i>): the second, third and fourth hairpin correspond to the first, second and third alignment. The single stranded 5′-tail is free to pair with a complementary sequence.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>435043, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_organization_and_predicted_secondary_structure_of_REPINs_/435043", "title"=>"General organization and predicted secondary structure of REPINs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:24:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/764749"], "description"=>"<p>The RAYT genes in SBW25 are <i>pflu3939</i>, <i>yafM</i> and <i>pflu2165</i>.</p>", "links"=>[], "tags"=>["giii", "repin", "clusters", "rayt", "genes", "sbw25"], "article_id"=>435121, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proximity_of_GI_GII_and_GIII_REPIN_clusters_to_RAYT_genes_in_the_P_fluorescens_SBW25_genome_/435121", "title"=>"Proximity of GI, GII, and GIII REPIN clusters to RAYT genes in the <i>P. fluorescens</i> SBW25 genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:25:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/764798"], "description"=>"<p>Data are the most abundant 16-mers found within the flanking non-coding DNA of RAYT genes from 18 genomes. In order to include related 16-mers, a set of degenerate sequences was produced by allowing up to two substitutions per 16-mer.</p>", "links"=>[], "tags"=>["singlet", "doublet", "ratios", "rep", "sequences", "bacterial"], "article_id"=>435171, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_REP_singlet_to_doublet_ratios_for_REP_sequences_from_bacterial_genomes_/435171", "title"=>"REP singlet to doublet ratios for REP sequences from bacterial genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:26:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/764911"], "description"=>"<p>Data are the frequency of REP clusters (from doublets to cluster of 18 REPs) found in extragenic space compared to a null model based on the random assignment of 560×71 bp and 560×110 bp segments (to extragenic space). REP clusters containing an uneven number of REP sequences are included in the next lower cluster size (REP singlets are omitted).</p>a<p>Observed occurrences from the SBW25 genome.</p>b<p>Expected values (means and standard deviation) based on 10,000 simulations.</p>c<p>The proportion of times the observed frequency was less than or equal to the expected value.</p>d<p>The proportion of times the observed frequency was greater than or equal to the expected value.</p>", "links"=>[], "tags"=>["rep", "doublets", "sbw25"], "article_id"=>435288, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_REP_doublets_within_the_SBW25_genome_/435288", "title"=>"Frequency of REP doublets within the SBW25 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:28:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/764932"], "description"=>"a<p>16-mers were sorted into three groups (GI, GII and GIII) using a grouping algorithm (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002132#pgen.1002132.s003\" target=\"_blank\">Figure S3</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002132#pgen.1002132.s004\" target=\"_blank\">Figure S4</a>).</p>b<p>Sequence of the most common 16-mer from each group.</p>c<p>Each GI, GII and GIII sequence either contains, or overlaps, an imperfect palindrome (the palindromic core).</p>", "links"=>[], "tags"=>["repetitive", "groups", "sbw25"], "article_id"=>435310, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Short_repetitive_sequence_groups_in_the_SBW25_genome_/435310", "title"=>"Short repetitive sequence groups in the SBW25 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:28:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/764961"], "description"=>"<p>Data are the number of REPs occurring as clusters (from singlets to clusters of 12) in extragenic space compared to expectations from a null model based on the random assignment of 1,422 16-mers (to extragenic space) (see text).</p>a<p>Observed occurrences from the SBW25 genome.</p>b<p>Expected values (means and standard deviation) based on 10,000 simulations.</p>c<p>The proportion of times the observed frequency was less than or equal to the expected value.</p>d<p>The proportion of times the observed frequency was greater than or equal to the expected value.</p>", "links"=>[], "tags"=>["rep", "clusters", "sbw25"], "article_id"=>435337, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_REP_clusters_within_the_SBW25_genome_/435337", "title"=>"Frequency of REP clusters within the SBW25 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:28:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/764982"], "description"=>"a<p>In order to identify closely related members of each GI, GII and GIII sequence family extragenic space was searched for all possible sequences that differed by up to four substitutions. The number in brackets is the number of variant sequences: e.g., with no substitutions there are just the three sequences (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002132#pgen-1002132-t001\" target=\"_blank\">Table 1</a>); allowing one substitution there are 147 different sequences, and so forth. The number found in extragenic space was compared to a null (random) model based on randomly assembled extragenic space (see text).</p>b<p>Data are means and standard deviation from 100 independent extragenic space randomizations.</p>", "links"=>[], "tags"=>["giii", "16-mers", "extragenic", "sbw25"], "article_id"=>435365, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Frederic Bertels", "Paul B. Rainey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002132.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_GI_GII_and_GIII_16_mers_in_the_extragenic_space_of_the_SBW25_genome_/435365", "title"=>"Frequency of GI, GII, and GIII 16-mers in the extragenic space of the SBW25 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:29:25"}

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