Mark Blaxter's teaching pages

The C. elegans Physical Map

This is a view of the physical map of the genome as displayed in the genome database ACeDB.

The longer lines at the top are YAC clones (their names start with a Y). The shorter items below are cosmid clones. The bold YACs are ones used in mapping cDNAs to the genome. The yellow boxed cosmids are those sequenced. Cosmids with a following * are ones that are canonical for a set of smaller cosmids, that are not displayed. The yellow bar at the bottom represents the sequenced DNA. The triangles indicate points of transposon insertion in strains of C. elegans.

The C. elegans physical map was constructed in two phases. Firstly approximately 17,000 cosmid clones (insert size 35 kb) were fingerprinted, and contiguated using fingerprint ovelap data. Secondly, selected cosmid clones were mapped to a 3,000 clone yeast artificial chromosome library (insert size >150 kb to 1 Mb) by hybridisation. This served to link and order the cosmid contigs, and has yielded a map which has only a handful of "gaps" (regions not covered by cloned DNAs).

The cosmid fingerprinting was achieved by restricting each with HinD III, labelling the fragment ends with 32-P, and cutting with a second, frequent-cutting enzyme (Sau3A I). The labelled fragments were analysed by acrylamide gel electrophoresis, and the resulting autoradiographs digitised. These digital fingerprints were then examined using custom-written software to identify clones which shared significant overlap, and contigs of overlapping clones were built up. This process resulted in over 600 contigs, some of only a very few clones. These contigs were mapped to the YAC library by selecting marker cosmids spanning each contig and hybridising them to high density YAC library filters. This process resulted in a massive reduction in the number of contigs, to the current position where over 99% of the genome is covered by either YAC and/or cosmid clones. The use of two different host-vector systems appears to have been very succesfull in getting round problems of "unclonable" DNA: segments of the genome which can be propagated only poorly (if at all) in one system appear to be stable in the other.

The physical and genetic maps have been anchored to each other by the molecular cloning of genes defining particular loci. There are over 2,000 genetic loci defined in C. elegans, and a significant proportion of these have been cloned. In addition, many deficiency (large chromosomal deletion) endpoints have been mapped to both genetic and physical maps.

The physical map is continually updated and refined, as ambiguities are resolved and complications sorted out. This process is coordinated by Dr. A. Coulson of the Sanger Institute, Hinxton, Cambridge UK. The physical map is publically available in the C. elegans genome database ACeDB.