The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Publication Date
November 17, 2003
Journal
PLOS Biology
Authors
Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, et al
Volume
1
Issue
2
Pages
e45
DOI
https://dx.plos.org/10.1371/journal.pbio.0000045
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.0000045
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/14624247
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC261899
Europe PMC
http://europepmc.org/abstract/MED/14624247
Web of Science
000188835200010
Scopus
4243088097
Mendeley
http://www.mendeley.com/research/genome-sequence-caenorhabditis-briggsae-platform-comparative-genomics
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{"title"=>"The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics", "type"=>"journal", "authors"=>[{"first_name"=>"Lincoln D.", "last_name"=>"Stein", "scopus_author_id"=>"7202575097"}, {"first_name"=>"Zhirong", "last_name"=>"Bao", "scopus_author_id"=>"7202908421"}, {"first_name"=>"Darin", "last_name"=>"Blasiar", "scopus_author_id"=>"6507309485"}, {"first_name"=>"Thomas", "last_name"=>"Blumenthal", "scopus_author_id"=>"7004852462"}, {"first_name"=>"Michael R.", "last_name"=>"Brent", "scopus_author_id"=>"7003506985"}, {"first_name"=>"Nansheng", "last_name"=>"Chen", "scopus_author_id"=>"55573104300"}, {"first_name"=>"Asif", "last_name"=>"Chinwalla", "scopus_author_id"=>"6602374635"}, {"first_name"=>"Laura", "last_name"=>"Clarke", "scopus_author_id"=>"55201640600"}, {"first_name"=>"Chris", "last_name"=>"Clee", "scopus_author_id"=>"6602582295"}, {"first_name"=>"Avril", "last_name"=>"Coghlan", "scopus_author_id"=>"7005018591"}, {"first_name"=>"Alan", "last_name"=>"Coulson", "scopus_author_id"=>"7101637792"}, {"first_name"=>"Peter", "last_name"=>"D'Eustachio", "scopus_author_id"=>"7007005764"}, {"first_name"=>"David H.A.", "last_name"=>"Fitch", "scopus_author_id"=>"56269749600"}, {"first_name"=>"Lucinda A.", "last_name"=>"Fulton", "scopus_author_id"=>"56439179500"}, {"first_name"=>"Robert E.", "last_name"=>"Fulton", "scopus_author_id"=>"55419308300"}, {"first_name"=>"Sam", "last_name"=>"Griffiths-Jones", "scopus_author_id"=>"6603579163"}, {"first_name"=>"Todd W.", "last_name"=>"Harris", "scopus_author_id"=>"7402723183"}, {"first_name"=>"La Deana W.", "last_name"=>"Hillier", "scopus_author_id"=>"35351976400"}, {"first_name"=>"Ravi", "last_name"=>"Kamath", "scopus_author_id"=>"55397380000"}, {"first_name"=>"Patricia E.", "last_name"=>"Kuwabara", "scopus_author_id"=>"6701363143"}, {"first_name"=>"Elaine R.", "last_name"=>"Mardis", "scopus_author_id"=>"7003499321"}, {"first_name"=>"Marco A.", "last_name"=>"Marra", "scopus_author_id"=>"55553154800"}, {"first_name"=>"Tracie L.", "last_name"=>"Miner", "scopus_author_id"=>"21834097000"}, {"first_name"=>"Patrick", "last_name"=>"Minx", "scopus_author_id"=>"6603432098"}, {"first_name"=>"James C.", "last_name"=>"Mullikin", "scopus_author_id"=>"6603704418"}, {"first_name"=>"Robert W.", "last_name"=>"Plumb", "scopus_author_id"=>"8759317700"}, {"first_name"=>"Jane", "last_name"=>"Rogers", "scopus_author_id"=>"9742279400"}, {"first_name"=>"Jacqueline E.", "last_name"=>"Schein", "scopus_author_id"=>"35351155100"}, {"first_name"=>"Marc", "last_name"=>"Sohrmann", "scopus_author_id"=>"6602849408"}, {"first_name"=>"John", "last_name"=>"Spieth", "scopus_author_id"=>"7003503606"}, {"first_name"=>"Jason E.", "last_name"=>"Stajich", "scopus_author_id"=>"7003427286"}, {"first_name"=>"Chaochun", "last_name"=>"Wei", "scopus_author_id"=>"55470612000"}, {"first_name"=>"David", "last_name"=>"Willey", "scopus_author_id"=>"7006214811"}, {"first_name"=>"Richard K.", "last_name"=>"Wilson", "scopus_author_id"=>"56713341900"}, {"first_name"=>"Richard", "last_name"=>"Durbin", "scopus_author_id"=>"7102868950"}, {"first_name"=>"Robert H.", "last_name"=>"Waterston", "scopus_author_id"=>"7006420348"}], "year"=>2003, "source"=>"PLoS Biology", "identifiers"=>{"sgr"=>"4243088097", "doi"=>"10.1371/journal.pbio.0000045", "pui"=>"39112161", "pmid"=>"14624247", "scopus"=>"2-s2.0-4243088097", "issn"=>"15449173", "isbn"=>"1545-7885 (Electronic)\\r1544-9173 (Linking)"}, "id"=>"993d9d1f-604d-3b76-b85c-3f7c39c4e8b6", "abstract"=>"The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.", "link"=>"http://www.mendeley.com/research/genome-sequence-caenorhabditis-briggsae-platform-comparative-genomics", "reader_count"=>363, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>40, "Researcher"=>90, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>94, "Student > Postgraduate"=>13, "Student > Master"=>44, "Other"=>11, "Student > Bachelor"=>20, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>23}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>40, "Researcher"=>90, "Student > Doctoral Student"=>15, "Student > Ph. D. 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Figshare 12001 May 20:57 UTC

Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/4786315"], "description"=>"<p>Differential Sizes of Chemosensory Receptor Subfamilies in C. elegans and C. briggsae</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079756, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Differential_Sizes_of_Chemosensory_Receptor_Subfamilies_in_C_elegans_and_C_briggsae/3079756", "title"=>"Differential Sizes of Chemosensory Receptor Subfamilies in C. elegans and C. briggsae", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786318"], "description"=>"<p>ncRNA Gene Predictions Present in C. elegans and C. briggsae Genome Assemblies</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079759, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/ncRNA_Gene_Predictions_Present_in_C_elegans_and_C_briggsae_Genome_Assemblies/3079759", "title"=>"ncRNA Gene Predictions Present in C. elegans and C. briggsae Genome Assemblies", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786279"], "description"=>"<p>When annotating the C. briggsae and <i>C. elegans acy-4</i> orthologs, we chose the Genefinder <i>ce-acy-4</i> prediction and the Genefinder <i>cb-acy-4</i> prediction because, out of the 12 possible combinations of a C. briggsae and a C. elegans prediction, this pair shows the most similarity to each other. Coding sequence (CDS) conservation between <i>cb-acy-4</i> and <i>ce-acy-4</i> provides evidence for as many as 12 additional N-terminal exons in the Genefinder <i>ce-acy-4</i> prediction, as compared to <i>T01C2.1</i>, the WS77 <i>ce-acy-4</i> prediction. Subsequently, four of the additional N-terminal exons that were predicted by FGENESH and Genefinder were confirmed by new EST data (marked with asterisks).</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>634512, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0000045.g001"], "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Joint_Refinement_of_C_elegans_and_C_briggsae_Gene_Models_acy_4_/634512", "title"=>"Joint Refinement of C. elegans and C. briggsae Gene Models: <i>acy-4</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786321"], "description"=>"<p>Top Ten Most Abundant Repeat Element Families in C. briggsae</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079762, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Top_Ten_Most_Abundant_Repeat_Element_Families_in_C_briggsae/3079762", "title"=>"Top Ten Most Abundant Repeat Element Families in C. briggsae", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786324"], "description"=>"<p>Top Ten Most Abundant Repeat Element Families in C. elegans</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079765, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Top_Ten_Most_Abundant_Repeat_Element_Families_in_C_elegans/3079765", "title"=>"Top Ten Most Abundant Repeat Element Families in C. elegans", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786327"], "description"=>"<p>Bases Covered by Aligned WABA Blocks, Stratified by Relationship to Annotated C. elegans Genes</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079768, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Bases_Covered_by_Aligned_WABA_Blocks_Stratified_by_Relationship_to_Annotated_C_elegans_Genes/3079768", "title"=>"Bases Covered by Aligned WABA Blocks, Stratified by Relationship to Annotated C. elegans Genes", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786330"], "description"=>"<p>Chromosomal Partners at Colinearity Breakpoints</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079771, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Chromosomal_Partners_at_Colinearity_Breakpoints/3079771", "title"=>"Chromosomal Partners at Colinearity Breakpoints", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4747972", "https://ndownloader.figshare.com/files/4747984", "https://ndownloader.figshare.com/files/4747996", "https://ndownloader.figshare.com/files/4748002", "https://ndownloader.figshare.com/files/4748008", "https://ndownloader.figshare.com/files/4748014", "https://ndownloader.figshare.com/files/4786273", "https://ndownloader.figshare.com/files/4786276"], "description"=>"<div><p>The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.</p></div>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>153402, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0000045.sd001", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd002", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd003", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd004", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd005", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd006", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd007", "https://dx.doi.org/10.1371/journal.pbio.0000045.sd008"], "stats"=>{"downloads"=>10, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Genome_Sequence_of_Caenorhabditis_briggsae_A_Platform_for_Comparative_Genomics/153402", "title"=>"The Genome Sequence of <i>Caenorhabditis briggsae:</i> A Platform for Comparative Genomics", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786333"], "description"=>"<p>Chromosomal Arms at Colinearity Breakpoints</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079774, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t010", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Chromosomal_Arms_at_Colinearity_Breakpoints/3079774", "title"=>"Chromosomal Arms at Colinearity Breakpoints", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786336"], "description"=>"<p>Updating the C. elegans Gene Set Using C. briggsae Similarity</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079777, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t011", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Updating_the_C_elegans_Gene_Set_Using_C_briggsae_Similarity/3079777", "title"=>"Updating the C. elegans Gene Set Using C. briggsae Similarity", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786306"], "description"=>"<p>Classification of Predicted C. briggsae and C. elegans Proteins into GOslim Categories</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079750, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Classification_of_Predicted_C_briggsae_and_C_elegans_Proteins_into_GOslim_Categories/3079750", "title"=>"Classification of Predicted C. briggsae and C. elegans Proteins into GOslim Categories", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786285"], "description"=>"<p>C. elegans is shown in white background and C. briggsae in light blue background. The arrows indicate regions of C. elegans-specific expansion of the family. The inset shows a schematic of the region of C. elegans chromosome I corresponding to the sra expansion in the upper right of the tree. C. briggsae genes are named using the prefix CBG, while C. elegans genes are numbered consecutively across the cosmid on which they were first identified. The root of this tree is arbitrary.</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>634666, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0000045.g003"], "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tree_View_of_All_Chemosensory_Receptor_Genes_in_the_Sra_Subfamily_/634666", "title"=>"Tree View of All Chemosensory Receptor Genes in the Sra Subfamily", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786288"], "description"=>"<p>WABA coding segments are shown as dark blue, strong alignments as medium blue, and weak alignments as grey. Regions that do not align are shown as dotted lines. The alignments of three sequenced C. elegans mRNA sequences are also shown for comparison.</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>634718, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0000045.g004"], "stats"=>{"downloads"=>16, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_WABA_Alignment_over_a_Known_C_elegans_Gene_snt_1_/634718", "title"=>"A WABA Alignment over a Known C. elegans Gene <i>(snt-1)</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786291"], "description"=>"<p>C. briggsae supercontigs are shown on the <i>y-</i>axis, and C. elegans chromosomes from WS77 are shown on the <i>x-</i>axis. Red dots and lines indicate regions of colinearity identified by WABA alignments between the two genomes. Blue dots are the positions of protein orthologs. Green areas show where blue and red intersect, indicating concordance between the positions of ortholog pairs and colinearity blocks.</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079735, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Representation_of_the_C_briggsae_WGS_Assembly_on_a_C_elegans_Scaffold_Using_Colinearity_Relationships/3079735", "title"=>"Representation of the C. briggsae WGS Assembly on a C. elegans Scaffold Using Colinearity Relationships", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786294"], "description"=>"<p>Each panel corresponds to a C. elegans chromosome, and the individual tracks show different measurements of evolutionary divergence.</p> <p>(A) Regions of synteny (colinearity) between C. elegans and C. briggsae. White areas correspond to areas where the two genomes could not be aligned owing to divergence and are more abundant in the chromosome arms.</p> <p>(B) C. elegans gene density and genetic map position. Gene density is plotted as a histogram, showing a relatively uniform distribution of genes across each chromosome. The relationship of the position of genes on the genetic map to their position on the sequence is superimposed on the <i>y-</i>axis. Steeper slopes in this plot indicate higher rates of meiotic recombination. Inflection points in the genetic map plot reflect the division of the chromosomes into recombinationally active “arms” and recombinationally slow “centers.”</p> <p>(C) <i>C. briggsae/C. elegans</i> orthologs normalized for gene density in 100 kbp sliding windows. Prominent regions of low ortholog density are seen on chromosome arms.</p> <p>(D) C. elegans “orphans,” genes with no significant protein similarity in C. briggsae or the non-C. elegans portion of SwissProt. This histogram has been normalized for gene density in 100 kbp sliding windows. Spikes in orphan density seem to correlate with regions of low ortholog density.</p> <p>(E) C. elegans genes that mutate to lethality or are lethal in RNAi screens, in 100 kbp sliding windows normalized to overall gene density. This track shows the distribution of essential genes and demonstrates their tendency to cluster in the chromosome centers.</p> <p>(F) Repetitive elements, binned in 100 kbp sliding windows. Repeat-rich regions correlate with both the absence of significant syntenic coverage and ortholog-poor regions.</p> <p>(G) The K<sub>A</sub>/K<sub>S</sub> ratio in ortholog pairs. Lower values indicate greater levels of purifying selection.</p> <p>(H) The rate of K<sub>S</sub> within ortholog pairs, in 100 kbp sliding windows.</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079738, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evolutionary_Divergence_across_C_elegans_Chromosome_V/3079738", "title"=>"Evolutionary Divergence across C. elegans Chromosome V", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2003-11-17 08:27:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/4786297"], "description"=>"<p>Inversions have broken the syntenic region into three conserved segments. Genes that do not have an ortholog in this syntenic region are in grey; orthologs are joined by lines. In C. elegans, genes that differ substantially in structure between the WS77 and hybrid gene sets are marked with an asterisk.</p>", "links"=>[], "tags"=>["soil nematodes Caenorhabditis briggsae", "briggsae gene families", "briggsae draft sequence", "RNA", "mold nematode genomes", "briggsae genome", "Caenorhabditis elegans diverged", "elegans genome"], "article_id"=>3079741, "categories"=>["Biochemistry", "Microbiology", "Genetics", "Molecular Biology", "Biotechnology", "Evolutionary Biology", "Biological Sciences not elsewhere classified", "Developmental Biology", "Cancer", "Statistics", "Infectious Diseases", "Plant Biology", "Virology"], "users"=>["Lincoln D Stein", "Zhirong Bao", "Darin Blasiar", "Thomas Blumenthal", "Michael R Brent", "Nansheng Chen", "Asif Chinwalla", "Laura Clarke", "Chris Clee", "Avril Coghlan", "Alan Coulson", "Peter D'Eustachio", "David H. A Fitch", "Lucinda A Fulton", "Robert E Fulton", "Sam Griffiths-Jones", "Todd W Harris", "LaDeana W Hillier", "Ravi Kamath", "Patricia E Kuwabara", "Elaine R Mardis", "Marco A Marra", "Tracie L Miner", "Patrick Minx", "James C Mullikin", "Robert W Plumb", "Jane Rogers", "Jacqueline E Schein", "Marc Sohrmann", "John Spieth", "Jason E Stajich", "Chaochun Wei", "David Willey", "Richard K Wilson", "Richard Durbin", "Robert H Waterston"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0000045.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Region_on_C_elegans_Chromosome_III_Containing_33_Genes_and_the_Syntenic_C_briggsae_Region_Which_Has_38_Genes/3079741", "title"=>"A Region on C. elegans Chromosome III Containing 33 Genes, and the Syntenic C. briggsae Region, Which Has 38 Genes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2003-11-17 08:27:06"}
PMC Usage Stats 623617 Mar 12:26 UTC

PMC Usage Stats | Further Information

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Relative Metric 462782810 May 16:07 UTC

Relative Metric

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