Construction and Use of Cosmid Contigs

The application of cosmids to positional cloning strategies has changed over the last several years (1 ). Initially, the construction of genome physical maps, for example, in Caenorhadbitis elegans and Arabidopsis (2 ,3 ), was attempted using cosmid clones randomly selected and analyzed by restriction fingerprinting techniques (2 ). Cosmids were selected as the vector of choice owing to the ease of library construction and, at the time, the relatively large genomic insert size possible. The insert size determines the number of clones required for complete coverage of a given genome. The larger the insert size, the lower the number of clones. Therefore, cosmids offered a real advantage over plasmids and bacteriophage. However, with the advent of yeast artificial chromosome (YAC) (4 ), bacterial artificial chromosome (BAC) (5 ), and P₁ -derived artificial chromsome (PAC) (6 ), cosmids are no longer considered the starting point for long-range genome mapping. The experience of workers who have tried to generate complete genome maps using cosmids has demonstrated that there are areas of genome either underrepresented or absent from the relevant libraries. In fact, several authors have stated that it is easy to start a global physical map with cosmids, but hard or impossible to finish (7 ). Consequently, cosmids are generated and used as resources for further investigation of regions of interest during a mapping project. YACs, because of their cloned insert size, are the best vectors in which to start a physical genome map. However, the number of chimeric YACs and difficulty of subsequent manipulation of YAC DNA owing to the yeast genome background result in cosmids frequently being used as the stepping stones between a global physical map and further investigation of the region of interest. This may be achieved by generating cosmids from a YAC (8 ) or somatic cell hybrids (9 ), or by screening cosmid libraries with either YACs (10 ) or other probes (11 ).