Genomic Sequence around Butterfly Wing Development Genes: Annotation and Comparative Analysis
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{"title"=>"Genomic sequence around butterfly wing development genes: Annotation and comparative analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Inês C.", "last_name"=>"ConceiçãoInê", "scopus_author_id"=>"23970252000"}, {"first_name"=>"Anthony D.", "last_name"=>"Long", "scopus_author_id"=>"36523530800"}, {"first_name"=>"Jonathan D.", "last_name"=>"Gruber", "scopus_author_id"=>"36058869900"}, {"first_name"=>"Patrícia", "last_name"=>"Beldade", "scopus_author_id"=>"6603236733"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21909358", "doi"=>"10.1371/journal.pone.0023778", "sgr"=>"84855389479", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84855389479", "issn"=>"19326203", "pui"=>"362471912"}, "id"=>"1351855d-453a-3b4a-a102-1a0a05b44471", "abstract"=>"BACKGROUND: Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations) and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes).\\n\\nCONCLUSIONS: The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1) the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2) the high conservation of non-coding sequence around the genes wingless and Ecdysone receptor, both involved in multiple developmental processes including wing pattern formation.", "link"=>"http://www.mendeley.com/research/genomic-sequence-around-butterfly-wing-development-genes-annotation-comparative-analysis", "reader_count"=>46, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>39, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>39}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Finland"=>1, "United Kingdom"=>2, "Italy"=>1, "Switzerland"=>1}, "group_count"=>0}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/740440"], "description"=>"<p>General characteristics observed for each BAC clone, including a summary of the annotation parameters discussed in the text.</p>1<p>BAC ID including NCBI accession number, BAC clone name from library at CUGI <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-CUGI1\" target=\"_blank\">[27]</a>, and BAC sequence name from assembly by JGI. The CUGI and JGI names are used in the custom database <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-Bicyclus1\" target=\"_blank\">[47]</a>;</p>2<p>Genes used to select the BACs for sequencing (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#s1\" target=\"_blank\">Introduction</a> for abbreviations);</p>3<p><i>B. anynana</i> linkage group based on mapping of the target genes (LG; <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-Beldade5\" target=\"_blank\">[26]</a>);</p>4<p>% repetitive sequence corresponding to single repeats (S) and low complexity (LC) regions as identified by RepeatMasker <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-Smit1\" target=\"_blank\">[41]</a>;</p>5<p>type of TEs, according to CENSOR <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-Jurka1\" target=\"_blank\">[74]</a> classification;</p>6<p>predicted peptides by Kaikogaas: number and (average aminoacid length);</p>7<p>predicted peptides after manual validation: number and (average aminoacid length);</p>8<p>Number of <i>B. anynana</i> UniGenes matching each BAC, and number corresponding to the validated predicted genes in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone-0023778-g001\" target=\"_blank\">Figure 1</a>, cf. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-Bicyclus1\" target=\"_blank\">[47]</a>;</p>9<p>Percent sequence annotated as corresponding to protein-coding, intronic and intergenic DNA. Details in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778-Bicyclus1\" target=\"_blank\">[47]</a> and the supplementary files.</p>", "links"=>[], "tags"=>["characteristics", "bacs"], "article_id"=>410820, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Inês C. Conceição", "Anthony D. Long", "Jonathan D. Gruber", "Patrícia Beldade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023778.t001", "stats"=>{"downloads"=>3, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_characteristics_of_the_B_anynana_BACs_analyzed_/410820", "title"=>"Main characteristics of the <i>B. anynana</i> BACs analyzed.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-08-31 00:13:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/740140"], "description"=>"<p>Each <i>B. anynana</i> BAC sequence is represented, with the corresponding scaffold in <i>B. mori</i> (including information on chromosomal location). Each putative gene is represented by a different color: <i>B. anynana</i> gene names in bold correspond to those on which BAC selection was based (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone-0023778-t001\" target=\"_blank\">Table 1</a>), and <i>B. mori</i> gene names reflect SilkDB annotation (e.g., <b>010572</b> is SilkDB gene BGIBMGA<b>010572</b>). Exons are explicitly annotated for <i>B. anynana</i> as stripes of the same color (darker shade for duplicated exons). Arrows indicate the direction of transcription of each gene, and fine lines are used for highlighting chromosomal rearrangements. The figure contains a legend for the representation of sequence length, and for the protein-coding genes, repetitive sequence, transposable elements, and microRNA identified in this study. Details on all <i>B. anynana</i> predicted peptides can be found in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778.s003\" target=\"_blank\">Table S3</a>.</p>", "links"=>[], "tags"=>["genomic", "regions", "fine-scale", "synteny"], "article_id"=>410514, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Inês C. Conceição", "Anthony D. Long", "Jonathan D. Gruber", "Patrícia Beldade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023778.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_of_B_anynana_genomic_regions_and_fine_scale_synteny_with_B_mori_/410514", "title"=>"Annotation of <i>B. anynana</i> genomic regions and fine-scale synteny with <i>B. mori</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-31 00:08:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/740321"], "description"=>"<p>Neighbour-joining, unrooted tree reconstructed with MEGA 4 using the aminoacid sequence of the putative <i>Adh</i> genes in <i>B. anynana</i> (<i>Bany</i>, in green), together with the corresponding paralogs from chromosome 10 in <i>B. mori</i> (<i>Bmori</i>, in red, showing Silkdb gene accessions and BLAST results) and <i>D. melanogaster</i> (<i>Dmel</i>, in blue, showing FlyBase gene accessions). Numbers are bootstrap values for 1000 replicates.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>410700, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Inês C. Conceição", "Anthony D. Long", "Jonathan D. Gruber", "Patrícia Beldade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023778.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_Adh_genes_/410700", "title"=>"Phylogenetic tree of <i>Adh</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-31 00:11:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/740248"], "description"=>"<p>VISTA plots of all BAC sequences against <i>B. mori</i> and, when available, other lepidopterans (moths <i>Bombyx mori</i>, <i>Helicoverpa armigera</i>, <i>Spodoptera frugipera</i>, and butterflies <i>Papilio dardanus</i>, <i>Heliconius melpomene</i>). Regions more than 70% conserved in a 100 bp window (VISTA default settings) appear as peaks with blue corresponding to annotated protein-coding regions and red to conserved non-coding sequence. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023778#pone.0023778.s005\" target=\"_blank\">Figure S2</a> shows close-up and extended analysis of regions around genes <i>wingless</i> and <i>Ecdysone receptor</i>.</p>", "links"=>[], "tags"=>["dna"], "article_id"=>410622, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Inês C. Conceição", "Anthony D. Long", "Jonathan D. Gruber", "Patrícia Beldade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023778.g002", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conservation_of_DNA_sequence_in_relation_to_other_lepidopterans_/410622", "title"=>"Conservation of DNA sequence in relation to other lepidopterans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-31 00:10:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/373452", "https://ndownloader.figshare.com/files/373501", "https://ndownloader.figshare.com/files/373553", "https://ndownloader.figshare.com/files/373568", "https://ndownloader.figshare.com/files/373635", "https://ndownloader.figshare.com/files/373684"], "description"=>"<div><h3>Background</h3><p>Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including <em>Bicyclus anynana</em>, where a whole-genome BAC library allows targeted access to large genomic regions.</p> <h3>Methodology/Principal Findings</h3><p>We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in <em>B. anynana</em> developing wings. Extensive manual curation of <em>in silico</em> predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of <em>Alcohol dehydrogenase</em> genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations) and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes).</p> <h3>Conclusions</h3><p>The general properties and organization of the available <em>B. anynana</em> genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1) the <em>Alcohol dehydrogenase</em> expansion with higher similarity between the five tandemly-repeated <em>B. anynana</em> paralogs than with the corresponding <em>B. mori</em> orthologs, and 2) the high conservation of non-coding sequence around the genes <em>wingless</em> and <em>Ecdysone receptor</em>, both involved in multiple developmental processes including wing pattern formation.</p> </div>", "links"=>[], "tags"=>["genomic", "annotation", "comparative"], "article_id"=>133758, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Inês C. Conceição", "Anthony D. Long", "Jonathan D. Gruber", "Patrícia Beldade"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023778.s001", "https://dx.doi.org/10.1371/journal.pone.0023778.s002", "https://dx.doi.org/10.1371/journal.pone.0023778.s003", "https://dx.doi.org/10.1371/journal.pone.0023778.s004", "https://dx.doi.org/10.1371/journal.pone.0023778.s005", "https://dx.doi.org/10.1371/journal.pone.0023778.s006"], "stats"=>{"downloads"=>9, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Sequence_around_Butterfly_Wing_Development_Genes_Annotation_and_Comparative_Analysis/133758", "title"=>"Genomic Sequence around Butterfly Wing Development Genes: Annotation and Comparative Analysis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-08-31 01:02:38"}

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