Numerous Transitions of Sex Chromosomes in Diptera
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{"title"=>"Numerous Transitions of Sex Chromosomes in Diptera", "type"=>"journal", "authors"=>[{"first_name"=>"Beatriz", "last_name"=>"Vicoso", "scopus_author_id"=>"14046213900"}, {"first_name"=>"Doris", "last_name"=>"Bachtrog", "scopus_author_id"=>"6602536584"}], "year"=>2015, "source"=>"PLoS Biology", "identifiers"=>{"sgr"=>"84929484746", "doi"=>"10.1371/journal.pbio.1002078", "pui"=>"604135625", "issn"=>"15457885", "pmid"=>"25879221", "isbn"=>"1545-7885", "scopus"=>"2-s2.0-84929484746"}, "id"=>"8727344c-4385-3b4b-a58a-f10dabea747b", "abstract"=>"Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.", "link"=>"http://www.mendeley.com/research/numerous-transitions-sex-chromosomes-diptera", "reader_count"=>138, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>7, "Librarian"=>1, "Student > Doctoral Student"=>8, "Researcher"=>27, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>8, "Student > Master"=>24, "Other"=>1, "Student > Bachelor"=>17, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>7, "Librarian"=>1, "Student > Doctoral Student"=>8, "Researcher"=>27, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>8, "Student > Master"=>24, "Other"=>1, "Student > Bachelor"=>17, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>28, "Agricultural and Biological Sciences"=>97, "Medicine and Dentistry"=>2, "Design"=>1, "Neuroscience"=>1, "Psychology"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Psychology"=>{"Psychology"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>97}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>28}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Canada"=>1, "Sweden"=>1, "Austria"=>1, "Netherlands"=>1, "Czech Republic"=>1, "United States"=>3, "Poland"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2024588"], "description"=>"<p><b>A,B,C</b>: Male/female coverage versus percentage of SNPs found in males (SNPs in the male sample/total number of SNPs) for scaffolds from the autosomes (black), fully differentiated (red), and newly evolved (blue) X chromosomes of <i>Drosophila miranda</i> (A), <i>Drosophila albomicans</i> (B), and <i>Drosophila busckii</i> (C). <b>D</b>: The neo-X (in blue) of <i>Scaptodrosophila lebanonensis</i> (D) is fully degenerated; it shows a 2-fold reduction in male versus female expression but no excess of male SNPs, similar to the ancestral X. <b>E,F</b>: The Muller elements of <i>Holcocephala fusca</i> (E) and <i>Mayetiola destructor</i> (F) that have intermediate levels of male to female coverage, in blue, have SNP patterns that are inconsistent with newly derived sex-chromosomes (no excess of male SNPs). <b>G,H</b>: No evidence of differentiated sex chromosomes using coverage or SNPs in <i>Calliphora erythrocephala</i> (G) and <i>Megaselia abdita</i> (H). The lines intersect at the median, and extend to the 10% and 90% percentiles. Data to generate this graph are to be found in file “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s001\" target=\"_blank\">S1 Data</a>” and “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s002\" target=\"_blank\">S2 Data</a>.”</p>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382637, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1002078.g002", "stats"=>{"downloads"=>4, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detecting_neo_sex_chromosomes_/1382637", "title"=>"Detecting neo-sex chromosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-16 03:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/2024587"], "description"=>"<p>Different chromosomal elements (designated elements A–F) have become sex-linked in different families of Diptera (indicated by different colors along the phylogeny). Elements were classified as X-linked when they were over-represented among our candidate X scaffolds, based on their male/female coverage (see <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#sec010\" target=\"_blank\">Materials and Methods</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s006\" target=\"_blank\">S1</a>–<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s008\" target=\"_blank\">S3</a> Figs.) or if they showed an excess of SNPs in the heterogametic sex (Figs. <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.g002\" target=\"_blank\">2</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s010\" target=\"_blank\">S5</a>). Bold lines indicate a transition of a sex chromosome at a particular branch of the tree and was inferred using parsimony. Dashed lines indicate instances where partial Muller elements segregate as a sex chromosome (see Figs. <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.g002\" target=\"_blank\">2</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s010\" target=\"_blank\">S5</a>, <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s011\" target=\"_blank\">S6</a> and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s013\" target=\"_blank\">S1 Table</a> for more details). Data to generate the phylogeny are to be found in file “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s016\" target=\"_blank\">S2 Text</a>” and “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s017\" target=\"_blank\">S3 Text</a>.” Images drawn by Doris Bachtrog.</p>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382636, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1002078.g001", "stats"=>{"downloads"=>4, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sex_chromosomes_in_Diptera_mapped_along_a_fly_phylogeny_13_/1382636", "title"=>"Sex chromosomes in Diptera, mapped along a fly phylogeny [13].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-16 03:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/2024592"], "description"=>"<p>Overview of groups sequenced.</p>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382641, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1002078.t001", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_groups_sequenced_/1382641", "title"=>"Overview of groups sequenced.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-16 03:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/2024590"], "description"=>"<p>(approximated by the corresponding autosomal value in <i>D. melanogaster</i>; for <i>D. melanogaster</i>, <i>E. hians</i> was used to approximate autosomal expression). Female tissues are in red, male tissues in blue. Dots represent the median and bars their approximate confidence interval (median +/- 1.57 x IQR/√<i>n</i>, where IQR is the interquantile range and <i>n</i> the sample size; this is equivalent to the notch size of a boxplot). Asterisks denote significant increases or decreases in X-linked expression relative to the ancestral level: * <i>p</i> < 0.05, ** <i>p</i> < 0.01, *** <i>p</i> < 0.001, estimated by comparing X-linked and autosomal values using a Wilcoxon test. Data to generate this graph are to be found in file “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s003\" target=\"_blank\">S3 Data.”</a></p>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382639, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1002078.g004", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_on_the_X_relative_to_the_expression_of_the_proto_X_/1382639", "title"=>"Expression on the X relative to the expression of the proto-X", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-16 03:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/2024591"], "description"=>"<p>, for different tissues of <i>D. melanogaster</i> (A), <i>T. minor</i> (B), <i>E. hians</i> (C), <i>M. destructor</i> (D), and <i>G. morsitans</i> (E). In <i>D. melanogaster</i>, <i>T. minor</i>, <i>E. hians</i>, and <i>G. morsitans</i>, the somatic tissue corresponds to the head; in <i>M. destructor</i>, publicly available antenna reads were used. Asterisks denote significant differences between the male to female ratio of expression on the X and the autosomes: * <i>p</i> < 0.05, *** <i>p</i> < 0.001, estimated using a Wilcoxon test. Data to generate this graph are to be found in file “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s003\" target=\"_blank\">S3 Data.”</a></p>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382640, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1002078.g005", "stats"=>{"downloads"=>6, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportion_of_male_and_female_biased_genes_on_the_X_and_the_autosomes_/1382640", "title"=>"Proportion of male- and female-biased genes on the X and the autosomes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-16 03:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/2024589"], "description"=>"<p>Log2 of the male to female ratio of expression for the X (brown) and autosomes (grey) of several fly species. All boxplots represent whole-body male-to-female comparisons. Two approaches were used to identify X-linked and autosomal genes: (1) Genes were considered X-linked if their reciprocal-best-hit in <i>D. melanogaster</i> was located on the Muller element(s) that correspond to the X in the species, as shown in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.g001\" target=\"_blank\">Fig. 1B and C</a>, and (2) genes were classified as X-linked if they were located on a scaffold that had reduced male/female coverage, as shown on panel B. Scaffolds in the brown rectangles were classified as X-linked; scaffolds in the grey rectangles were classified as autosomal. The first classification was used to compare the male to female ratio of expression of genes on the X and autosomes in panel A and the second classification was used in panel C. Asterisks denote significant differences between the male to female ratio of expression on the X and the autosomes: * <i>p</i> < 0.05, *** <i>p</i> < 0.001, estimated using a Wilcoxon test. Data to generate this graph are to be found in file “<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002078#pbio.1002078.s003\" target=\"_blank\">S3 Data.”</a></p>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382638, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1002078.g003", "stats"=>{"downloads"=>4, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assessing_dosage_compensation_in_Diptera_using_RNA_seq_/1382638", "title"=>"Assessing dosage compensation in Diptera using RNA-seq:", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-16 03:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/2024593", "https://ndownloader.figshare.com/files/2024594", "https://ndownloader.figshare.com/files/2024595", "https://ndownloader.figshare.com/files/2024596", "https://ndownloader.figshare.com/files/2024597", "https://ndownloader.figshare.com/files/2024598", "https://ndownloader.figshare.com/files/2024599", "https://ndownloader.figshare.com/files/2024600", "https://ndownloader.figshare.com/files/2024601", "https://ndownloader.figshare.com/files/2024602", "https://ndownloader.figshare.com/files/2024603", "https://ndownloader.figshare.com/files/2024604", "https://ndownloader.figshare.com/files/2024605", "https://ndownloader.figshare.com/files/2024606", "https://ndownloader.figshare.com/files/2024607", "https://ndownloader.figshare.com/files/2024608", "https://ndownloader.figshare.com/files/2024609", "https://ndownloader.figshare.com/files/2024610"], "description"=>"<div><p>Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model <i>Drosophila melanogaster</i>, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.</p></div>", "links"=>[], "tags"=>["Sex chromosomes", "sex chromosome configurations", "sex chromosome variation", "heteromorphic sex chromosomes", "ZW sex chromosomes", "study sex chromosome biology", "XY sex chromosomes", "sex chromosome karyotypes", "sex chromosome", "model Drosophila melanogaster"], "article_id"=>1382642, "categories"=>["Uncategorised"], "users"=>["Beatriz Vicoso", "Doris Bachtrog"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1002078.s001", "https://dx.doi.org/10.1371/journal.pbio.1002078.s002", "https://dx.doi.org/10.1371/journal.pbio.1002078.s003", "https://dx.doi.org/10.1371/journal.pbio.1002078.s004", "https://dx.doi.org/10.1371/journal.pbio.1002078.s005", "https://dx.doi.org/10.1371/journal.pbio.1002078.s006", "https://dx.doi.org/10.1371/journal.pbio.1002078.s007", "https://dx.doi.org/10.1371/journal.pbio.1002078.s008", "https://dx.doi.org/10.1371/journal.pbio.1002078.s009", "https://dx.doi.org/10.1371/journal.pbio.1002078.s010", "https://dx.doi.org/10.1371/journal.pbio.1002078.s011", "https://dx.doi.org/10.1371/journal.pbio.1002078.s012", "https://dx.doi.org/10.1371/journal.pbio.1002078.s013", "https://dx.doi.org/10.1371/journal.pbio.1002078.s014", "https://dx.doi.org/10.1371/journal.pbio.1002078.s015", "https://dx.doi.org/10.1371/journal.pbio.1002078.s016", "https://dx.doi.org/10.1371/journal.pbio.1002078.s017", "https://dx.doi.org/10.1371/journal.pbio.1002078.s018"], "stats"=>{"downloads"=>51, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Numerous_Transitions_of_Sex_Chromosomes_in_Diptera_/1382642", "title"=>"Numerous Transitions of Sex Chromosomes in Diptera", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-16 03:38:29"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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