{"id":364,"date":"2020-08-28T20:56:00","date_gmt":"2020-08-29T00:56:00","guid":{"rendered":"http:\/\/www.briggsae.org\/?page_id=364"},"modified":"2023-03-21T21:07:16","modified_gmt":"2023-03-22T01:07:16","slug":"genetics-genomics","status":"publish","type":"page","link":"https:\/\/www.briggsae.org\/?page_id=364","title":{"rendered":"Genetics & Genomics"},"content":{"rendered":"\n

LINKAGE MAPS<\/strong><\/h3>\n\n\n\n

Polymorphis-based linkage map<\/strong> – CURRENT<\/a>
Source: <\/strong>Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD and Gupta BP(2010). A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae<\/em>. BMC Genomics 11:236 (http:\/\/www.biomedcentral.com\/1471-2164\/11\/236<\/a>).<\/p>\n\n\n\n

<\/div>\n\n\n\n

Tables from the paper (Koboldt et al. 2010) – Table 2<\/a> (SNPs), Table 3<\/a> (medium Indels), Table 4<\/a> (small indels)<\/p>\n\n\n\n

List of polymorphisms<\/a> (SNPs and indels) – text files<\/p>\n\n\n\n

Old <\/a>w<\/a>e<\/a>b<\/a>page listing polymorphisms<\/a><\/p>\n\n\n\n

<\/div>\n\n\n\n

Phenotypic marker-based linkage map<\/strong> – CURRENT (v10.1)<\/a>
In this update new loci\/genes have been added. The order of genes is based 3-factor mapping and\/or physical locations in the CB3 assembly. Linkage distance, where mentioned, is based on 2-factor mapping experiments. The C. elegans<\/em> orthologs (indicated by a ‘Cbr’ prefix) were validated by transgenic rescue experiments. Some of the mutations have been sequenced. Genes and integrants that are linked but not precisely mapped are listed next to LGI to LGX groups. Question marked (?) loci require validation. <\/p>\n\n\n\n

Older versions of maps can be found here<\/a>.<\/p>\n\n\n\n

Genetic mutations<\/a><\/p>\n\n\n\n

Linkage data<\/a><\/p>\n\n\n\n

<\/div>\n\n\n\n

GENOME SEQUENCE<\/strong><\/p>\n\n\n\n

Download CB4 assembly – WormBase FTP<\/a>  (see ReadMe<\/a> file) <\/p>\n\n\n\n

<\/div>\n\n\n\n

GENES AND CONTIGS<\/strong><\/p>\n\n\n\n

Assembled contigs (Hillier et al. 2007)<\/a>
Browse all<\/a>
Search Wormbase<\/a><\/p>\n\n\n\n

<\/div>\n\n\n\n

PROCESS-SPECIFIC GENES<\/strong>
(gene sets are not updated!)<\/em>
Vulva<\/a>
Dauer<\/a>
Sex-determination<\/a>
Body morphology<\/a> <\/p>\n\n\n\n

<\/div>\n\n\n\n

MESCELLANEOUS<\/strong>
(information not up to date)<\/em><\/p>\n\n\n\n

Non-coding <\/a>R<\/a>NA<\/a>
Most common InterPro domains<\/a>
Genome sizes of organisms<\/a> <\/p>\n\n\n\n

<\/div>\n\n\n\n

SELECTED PUBLICATIONS<\/strong><\/p>\n\n\n\n

Review (Wormbook)<\/a><\/p>\n\n\n\n

Genome sequence (Stein et al. 2003)<\/a>
Partial text of the C. briggsae whole-genome shotgun assembly announcement on July 12, 2002 (Sanger Institute website). <\/em><\/p>\n\n\n\n

The Washington University Genome Sequencing Center (St. Louis) has already sequenced approximately 13 Mb of the C. briggsae<\/em> genome in bacterial clones. During the second half of 2001 the GSC and the Sanger Institute have each sequenced approximately 1,000,000 whole genome shotgun reads from plasmids and BAC and fosmid ends. These give a greater than 10x coverage of the genome. We have made preliminary assemblies using the PHUSION assembler of Jim Mullikin.<\/p>\n\n\n\n

This C. briggsae<\/em> sequence (version cb25.agp8) was assembled from 2.05 million whole genome shotgun reads, of which 88.2% are in read pairs. Using the Phusion assembler, reads were first assembled into contigs on the basis of overlap information, and then into supercontigs using read pair information to cross gaps. The supercontigs were then assembled into mapped ultracontigs on the basis of FPC fingerprint mapping, adding in some material from the previously finished clones to bridge gaps. Because of the absence of dense chromosomal maps for C. briggsae<\/em>, we can not assign these ultracontigs to chromosomal locations, and so can not give draft chromosome sequences. <\/p>\n\n\n\n

Chromosome assembly of C. briggsae genome (Hillier et al. 2007)<\/a><\/p>\n\n\n\n

Other genome sequence-related articles<\/a><\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

LINKAGE MAPS Polymorphis-based linkage map – CURRENTSource: Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD and Gupta BP(2010). A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics 11:236 (http:\/\/www.biomedcentral.com\/1471-2164\/11\/236). Tables from the paper (Koboldt et al. 2010) – Table 2 (SNPs), Table 3 … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","footnotes":""},"class_list":["post-364","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.briggsae.org\/index.php?rest_route=\/wp\/v2\/pages\/364","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.briggsae.org\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.briggsae.org\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.briggsae.org\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/www.briggsae.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=364"}],"version-history":[{"count":59,"href":"https:\/\/www.briggsae.org\/index.php?rest_route=\/wp\/v2\/pages\/364\/revisions"}],"predecessor-version":[{"id":806,"href":"https:\/\/www.briggsae.org\/index.php?rest_route=\/wp\/v2\/pages\/364\/revisions\/806"}],"wp:attachment":[{"href":"https:\/\/www.briggsae.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=364"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}