Worm Breeder's Gazette 12(1): 16 (September 1, 1991)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Sequencing and mapping C. elegans cDNA's

R. Ainscough[1], A. Coulson[1], M. Craxton[1], R. Durbin[1], P. Green[2], L. Hillier[2], N. Halloran[2], C. Huynh[2], C. Lee[1], C. Martin[3], M. Metzstein[1], J. Sulston[1], K. Thomas[1], R. Waterston[2], R. Wilson[2]

Figure 1

[1]M.R.C. Laboratory of Molecular Biology,Cambridge CB2 2QH,England
[2]Dept of Genetics, Washington University School of Medicine, St.Louis, MO 63110, USA
[3]Human Genome Center, Lawrence Berkely Laboratory, Berkely, CA 94720

As an adjunct to our genomic sequencing project we are taking advantage of a sorted cDNA library (generated by Chris Martin) consisting of 1743 cDNA clones, estimated to contain 1400 different cDNAs.This would represent 10% or so of the mRNAs currently thought to exist in C. elegans. Sorting was achieved by probing the library with pools of previously isolated clones, to avoid repeatedly re-isolating clones already represented in the selected subset.

ABI 373A sequencers have been used to obtain sequence from the 5' end of the cDNAs. Both double-stranded plasmid DNA and PCR amplified inserts have been used as templates; the latter is faster but the former provides better quality sequence data. To date we have sequenced 550 clones.

Each sequence has been analyzed by BLAST against the NCBI nonredundant database GENINFO. About one in three shows significant (BLAST score of >100) similarity to known genes (see listing).

Taking advantage of the almost complete physical map we are able to rapidly map the cDNA's by hybridization to the genomically ordered array of YAC clones ('polytene' filters). On average,this locates mapped cDNAs to a resolution of about 100kb.

The sequence and mapping data generated by this project are being rapidly made available to the C. elegans community through the database acedb and the sequences are being submitted to the EMBL and GENBANK databases. The tagged and mapped cDNA's should prove useful and they should also provide a resource for checking predicted genes obtained in the genomic sequencing effort. The clones are available on request from the St. Louis lab.

[See Figure 1]

Figure 1