Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus
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{"title"=>"Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus", "type"=>"journal", "authors"=>[{"first_name"=>"Todd A.", "last_name"=>"Gray", "scopus_author_id"=>"7202788161"}, {"first_name"=>"Janet A.", "last_name"=>"Krywy", "scopus_author_id"=>"26638860500"}, {"first_name"=>"Jessica", "last_name"=>"Harold", "scopus_author_id"=>"55808426900"}, {"first_name"=>"Michael J.", "last_name"=>"Palumbo", "scopus_author_id"=>"7102569576"}, {"first_name"=>"Keith M.", "last_name"=>"Derbyshire", "scopus_author_id"=>"7004620088"}], "year"=>2013, "source"=>"PLoS Biology", "identifiers"=>{"pmid"=>"23874149", "doi"=>"10.1371/journal.pbio.1001602", "sgr"=>"84880938874", "isbn"=>"1545-7885 (Electronic)\\r1544-9173 (Linking)", "scopus"=>"2-s2.0-84880938874", "issn"=>"15449173", "pui"=>"369462988"}, "id"=>"9435cb12-6d74-3c30-b4a2-2d7f409bc45b", "abstract"=>"Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism.", "link"=>"http://www.mendeley.com/research/distributive-conjugal-transfer-mycobacteria-generates-progeny-meioticlike-genomewide-mosaicism-allow-1", "reader_count"=>83, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>7, "Student > Master"=>13, "Other"=>2, "Student > Bachelor"=>10, "Lecturer > Senior Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>7, "Student > Master"=>13, "Other"=>2, "Student > Bachelor"=>10, "Lecturer > Senior Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>18, "Agricultural and Biological Sciences"=>39, "Medicine and Dentistry"=>6, "Chemistry"=>2, "Social Sciences"=>2, "Computer Science"=>1, "Immunology and Microbiology"=>7, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>7}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>39}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>18}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Venezuela"=>2, "Argentina"=>1, "United States"=>5, "Norway"=>1, "Japan"=>2, "United Kingdom"=>1, "Switzerland"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1114487"], "description"=>"<p>The total number of base pairs in donor-derived segments was calculated for three transconjugant cohorts (itemized lists appear in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio.1001602.s008\" target=\"_blank\">Tables S2</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio.1001602.s010\" target=\"_blank\">S4</a>). The total DNA can be subdivided into DNA associated with the selected <i>Km<sup>r</sup></i> gene, <i>esx1</i>, and unselected DNA. Transconjugant cohorts are recipient-proficient F1 transconjugants (<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g001\" target=\"_blank\">Figure 1</a>); donor-proficient F1 transconjugants (<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g002\" target=\"_blank\">Figure 2</a>), for which <i>esx1</i> was enriched by screening for donor function; and backcross transconjugants that are either donor or recipient-proficient (<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g004\" target=\"_blank\">Figures 4</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g005\" target=\"_blank\">5</a>). Donor percentages assume 7 Mb of DNA per transconjugant genome, whereas percentages for segments that spanned <i>Km<sup>r</sup></i>, <i>esx1</i>, or were transferred but not selected were calculated per the total amount of donor DNA transferred in that cohort.</p>a<p>The percentage for <i>esx1</i> segments in the backcrosses was calculated for the three donor-proficient derivatives.</p>b<p>Unselected segments are not contiguous with the donor-derived <i>Km<sup>r</sup></i> gene or <i>esx1</i> locus.</p>c<p>Only three of the transferred segments were unchanged from their ancestral F1 parental boundaries, with the remainder representing subdivided fragments of previously uninterrupted donor tracts.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "contributions", "donor-derived", "dna"], "article_id"=>742043, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.t001", "stats"=>{"downloads"=>6, "page_views"=>161, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Total_contributions_of_donor_derived_DNA_in_transconjugants_/742043", "title"=>"Total contributions of donor-derived DNA in transconjugants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114486"], "description"=>"<p>The parental donor and recipient strains are schematically shown at the top, with their native chromosomes (blue and yellow circles, respectively) that confer different phenotypes (pink and blue backgrounds, respectively). Co-incubation of the donor and recipient strains on solid media (agar plates) or in a biofilm, permits conjugation. For <i>oriT</i>-mediated transfer (left), all transferred segments of DNA are linked to <i>oriT</i>, which limits the extent of genetic diversity among the transconjugants. This contrasts with distributive conjugal transfer (DCT), wherein random segments of the donor chromosome are transferred to the recipient, generating unique transconjugants. Each transconjugant has a novel genotype that confers a unique phenotypic profile (different colored background). Importantly, multiple rounds of <i>oriT</i>-mediated transfer events with different donors would be required to approach the variation observed from a single DCT event. Under certain conditions, any transconjugant phenotype may have a growth advantage over other transconjugants and the parental strains. Such evolutionary selection can give rise to emergent strains or species. Transconjugants that share a specific phenotypic trait can be sequenced to identify SNPs that mark a shared genomic region associated with that trait. An F1 transconjugant with a specific donor-derived trait can be repetitively backcrossed with the recipient strain to introgress the functional donor gene into the recipient background.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "evolutionary", "distributive", "conjugal"], "article_id"=>742042, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g007", "stats"=>{"downloads"=>3, "page_views"=>64, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphic_summary_of_the_evolutionary_and_gene_mapping_potential_of_distributive_conjugal_transfer_in_comparison_to_oriT_mediated_transfer_/742042", "title"=>"Graphic summary of the evolutionary and gene mapping potential of distributive conjugal transfer in comparison to <i>oriT</i>-mediated transfer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114481"], "description"=>"<p>To generate the initial F1 progeny, a kanamycin-resistant (Kan) mc<sup>2</sup>155 donor strain (blue square) was crossed with an apramycin-resistant (Apy) mc<sup>2</sup>874 recipient (yellow circle). The doubly resistant F1 transconjugants (K/A) were screened to identify donor-proficient progeny (green squares; see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g002\" target=\"_blank\">Figure 2</a>). Donor-proficient F1 derivatives were then backcrossed with a derivative of the original mc<sup>2</sup>874 recipient strain that was marked with a plasmid encoding hygromycin resistance (Hyg). Doubly resistant transconjugants (K/H) were selected to create the N1 generation of transconjugants. As for the F1 stage, the N1 transconjugants were screened to identify donor-proficient progeny (squares) before backcrossing to the apramycin-resistant mc<sup>2</sup>874 recipient to generate the N2 generation. This process was reiterated to genetically purify the donor-determining genes in the mc<sup>2</sup>874 recipient background. Donor-proficient (square) or recipient-proficient (circle) progeny were isolated at either the N3 or the N6 stage, and their genomic DNA was isolated and the sequence determined (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g004\" target=\"_blank\">Figures 4</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g005\" target=\"_blank\">5</a>, respectively). The progressive purifying selection of the <i>Km<sup>r</sup></i> and mating identity genes is depicted by the reduced portion of the mc<sup>2</sup>155 DNA (blue sector) through each generation in the mc<sup>2</sup>874 genome (yellow circle) at right, and by the gradual conversion of the progeny background from green to yellow.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "pedigree", "backcross", "introgression"], "article_id"=>742037, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g003", "stats"=>{"downloads"=>2, "page_views"=>145, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_pedigree_showing_the_backcross_introgression_strategy_/742037", "title"=>"A pedigree showing the backcross introgression strategy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114480"], "description"=>"<p>(A) A Circos plot depicts the fragmented genotype of 10 donor-proficient transconjugant genomes. Color key is the same as <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g001\" target=\"_blank\">Figure 1</a>. Strains are from outer to inner circle, respectively: Km4.5a, 2.2b, 0,8, 0.1a, 5.7, 6.9b, 6.9a, 6.4b, 1.5, and 0.1b. (B) An expanded map of the region inherited by all donor-proficient progeny, which includes a single contiguous segment of mc<sup>2</sup>155 DNA encompassing the <i>esx1</i> locus (black). Clones are in the same order, outside-to-inside as in (A), and are labeled to indicate the location of the <i>Km<sup>r</sup></i> gene used in selection. Colored bars indicate the extent of DNA inherited from mc<sup>2</sup>155 in the recipient genome (yellow). The <i>esx1</i> locus extends from 74,600 to 107,334 bp in mc<sup>2</sup>155.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "dct", "determinant", "donor-recipient"], "article_id"=>742036, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g002", "stats"=>{"downloads"=>0, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Exploiting_DCT_to_identify_esx1_as_a_determinant_of_donor_recipient_function_/742036", "title"=>"Exploiting DCT to identify <i>esx1</i> as a determinant of donor-recipient function.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114488", "https://ndownloader.figshare.com/files/1114489", "https://ndownloader.figshare.com/files/1114490", "https://ndownloader.figshare.com/files/1114492", "https://ndownloader.figshare.com/files/1114493", "https://ndownloader.figshare.com/files/1114494", "https://ndownloader.figshare.com/files/1114495", "https://ndownloader.figshare.com/files/1114496", "https://ndownloader.figshare.com/files/1114497", "https://ndownloader.figshare.com/files/1114498"], "description"=>"<div><p>Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic <i>oriT</i>-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in <i>M. smegmatis</i>. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant <i>Mycobacterium tuberculosis</i> and <i>Mycobacterium canettii</i> species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism.</p></div>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "conjugal", "mycobacteria", "generates", "progeny", "meiotic-like", "genome-wide", "allowing", "mating"], "article_id"=>742044, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1001602.s001", "https://dx.doi.org/10.1371/journal.pbio.1001602.s002", "https://dx.doi.org/10.1371/journal.pbio.1001602.s003", "https://dx.doi.org/10.1371/journal.pbio.1001602.s004", "https://dx.doi.org/10.1371/journal.pbio.1001602.s005", "https://dx.doi.org/10.1371/journal.pbio.1001602.s006", "https://dx.doi.org/10.1371/journal.pbio.1001602.s007", "https://dx.doi.org/10.1371/journal.pbio.1001602.s008", "https://dx.doi.org/10.1371/journal.pbio.1001602.s009", "https://dx.doi.org/10.1371/journal.pbio.1001602.s010"], "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distributive_Conjugal_Transfer_in_Mycobacteria_Generates_Progeny_with_Meiotic_Like_Genome_Wide_Mosaicism_Allowing_Mapping_of_a_Mating_Identity_Locus_/742044", "title"=>"Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114483"], "description"=>"<p>Circos plots of recipient-proficient backcross transconjugants showing F1 parental (outer ring) and backcross progeny (inner ring) for each strain pair. In the third backcross step, none (Km0.8BC) or part (Km6.9BC) of <i>esx1</i> was transferred to the isolates shown, coincident with reversion to a recipient phenotype. The part of mc<sup>2</sup>155 <i>esx1</i> present in Km 6.9BC indicates that these mc<sup>2</sup>155 genes are insufficient to confer donor identity. Nomenclature and color codes are the same as in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g004\" target=\"_blank\">Figure 4</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "introgression", "excludes", "regions", "insufficient", "mating", "recipient-proficient"], "article_id"=>742039, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g005", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Backcross_introgression_excludes_regions_of_esx1_as_insufficient_for_mating_identity_in_recipient_proficient_transconjugants_/742039", "title"=>"Backcross introgression excludes regions of <i>esx1</i> as insufficient for mating identity in recipient-proficient transconjugants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114484"], "description"=>"<p>A schematic guide encompassing 73 kb to 122 kb of the mc<sup>2</sup>155 reference genome, including the <i>esx1</i><sub>D</sub> locus genes (black filled, <i>ms0055</i> at 74.6 kb through <i>ms0083</i> at 107.3 kb). A repetitive IS element cluster absent in the recipient (<i>ms0072–0074</i>) is gray-filled. Below are key clones from crosses that progressively defined the <i>mid</i> gene candidates. Donor-proficient transconjugant clones had inherited mc<sup>2</sup>155 sequences sufficient to convey the donor phenotype. Recipient-proficient transconjugants inherited mc<sup>2</sup>155 sequences that were insufficient to impart the donor phenotype. Considered together, the key <i>mid</i> candidate regions span 6,923 bp of mc<sup>2</sup>155 DNA, from 90,697 to 94,949 and from 100,295 to 102,966. These regions span <i>esx1<sub>ms</sub></i> genes <i>ms0069–0071</i> and <i>ms0076–0078</i> as shown in the expansion at the bottom. The amino acid identities between the encoded proteins of mc<sup>2</sup>155 and mc<sup>2</sup>874 are notably low for the left region, consistent with functional disparity.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "locus", "defined", "f1", "backcross", "introgression"], "article_id"=>742040, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g006", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_mid_locus_within_esx1_as_defined_by_the_F1_association_mapping_and_backcross_introgression_analyses_/742040", "title"=>"The <i>mid</i> locus within <i>esx1</i>, as defined by the F1 association mapping and backcross introgression analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114482"], "description"=>"<p>Circos plots of donor-proficient backcross transconjugants showing F1 parental (outer ring) and backcross progeny (inner ring) for each strain pair. Km1.4BC was isolated from N3 progeny and Km0.1BCb from N6 progeny. Backcross (BC) strain names are based on their parent; thus, Km0.1BCb is the second (b), independent transconjugant derived from parent Km0.1. The expanded arc focuses on the <i>esx1</i> locus (black). Color key is the same as <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio-1001602-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "introgression", "refines", "mating-identity", "locus", "donor-proficient"], "article_id"=>742038, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g004", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Backcross_introgression_refines_esx1_as_a_mating_identity_locus_in_donor_proficient_transconjugants_/742038", "title"=>"Backcross introgression refines <i>esx1</i> as a mating-identity locus in donor-proficient transconjugants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1114479"], "description"=>"<p>(A) Conjugation and genome comparison protocol. Sequence reads for each transconjugant were aligned with the reference donor genome and viewed with IGV. Columns of colored nucleotides mark informative SNPs between the recipient and donor strains, while random colored nucleotides indicate sequence errors. (B) A Circos plot depicts the mosaic nature of 12 <i>M. smegmatis</i> transconjugant genomes. mc<sup>2</sup>155 donor DNA segments (alternating blue and magenta, or green) replaced homologous recipient sequences (yellow). Positions of integrated kanamycin genes (<i>Km</i>) are shown around the periphery (green arrows), and transferred donor DNA segments containing the <i>Km</i> gene are shown in green. Strain nomenclature is based on the genomic location of the <i>Km</i> gene in Mb, thus Km0.1 is inserted at coordinate 0.1 Mb in mc<sup>2</sup>155. Strains are from outer to inner circle, respectively: Km6.9e, Km0.1f, Km6.9d, Km3.2, Km6.9c, Km0.1e, Km3.8, Km4.5b, Km2.2a, Km0.1d, Km0.1c, and Km6.4a. The innermost circle is a compilation of all segments of mc<sup>2</sup>155 DNA, showing that almost all regions of the donor chromosome were transferred despite the small sample size. (C) Microcomplexity of parental SNP profiles at some transconjugant recombination sites. Compiled sequence read landscapes are shown for mc<sup>2</sup>874 and one transconjugant (Km6.9e) aligned to the mc<sup>2</sup>155 sequence (top) for a 1 kb segment of the genome (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001602#pbio.1001602.s008\" target=\"_blank\">Table S2</a>, coordinates 470,385–471,385). The presence of informative SNPs (each color represents a different base) indicates recipient sequences, while segments lacking SNPs define donor sequence. Accordingly, parental genotype segments are shown in the schematic below with recipient (yellow) and donor (blue and magenta) genotypes interspersed throughout this 1 kb region. Note that rare cases of isolated recipient SNPs in our designated donor segments are excluded by our stringent criterion requiring two consecutive SNPs to conclusively establish parental origin. The lower panel shows the same sequences aligned to the mc<sup>2</sup>874 sequence, in which the SNPs now indicate donor sequence. This reciprocal alignment confirms the assignment of donor and recipient sequences in the schematic map.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary genetics", "Genomic evolution", "genetics", "Molecular genetics", "Gene identification and analysis", "Genetic screens", "Genome-wide association studies", "genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Microbial evolution", "Microbial pathogens", "pathogenesis", "Model organisms", "Prokaryotic models", "Molecular cell biology", "transconjugant", "genomes", "mosaics"], "article_id"=>742035, "categories"=>["Biological Sciences"], "users"=>["Todd A. Gray", "Janet A. Krywy", "Jessica Harold", "Michael J. Palumbo", "Keith M. Derbyshire"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1001602.g001", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mycobacterial_transconjugant_genomes_are_complex_mosaics_of_their_parental_strains_/742035", "title"=>"Mycobacterial transconjugant genomes are complex mosaics of their parental strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-09 02:04:11"}

PMC Usage Stats | Further Information

  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"7"}
  • {"unique-ip"=>"15", "full-text"=>"13", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"10", "cited-by"=>"0", "year"=>"2013", "month"=>"8"}
  • {"unique-ip"=>"27", "full-text"=>"25", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"37", "cited-by"=>"0", "year"=>"2013", "month"=>"9"}
  • {"unique-ip"=>"26", "full-text"=>"29", "pdf"=>"10", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2013", "month"=>"10"}
  • {"unique-ip"=>"17", "full-text"=>"13", "pdf"=>"4", "abstract"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"11"}
  • {"unique-ip"=>"14", "full-text"=>"12", "pdf"=>"4", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"12"}
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Relative Metric

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