Worm Breeder's Gazette 10(3): 67
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.
contigs= 251 mean contig size= 340kb proportion of genome in mapped contigs= 60% Since our previous report, 260 joins have been made. Mostly, we have been probing cosmid grids with YAC clones taken at random from a new bank of median insert size 250kb. The genetic cluster on each chromosome is now represented fairly completely by seven contigs on average. As well as providing linkage, the random probing has led to almost continuous coverage of the larger contigs by YACs (shown by the histogram under the chromosome plots); thus, selected YACs can one day be used to make 'polytene filters' for mapping unknown probes. Although this progress is satisfactory, we must emphasize once again that the genome map is necessarily tentative. The great majority of joins deduced by YAC hybridization are correct, but some, particularly those involving a single YAC overlapping a single cosmid, may turn out to be wrong. Furthermore, the orientation and positioning of contigs often depends upon very limited molecular genetic data which is also subject to revision. But what are we to do? Obviously you expect, and are entitled to, the latest information. However, before investing research time in a project that depends on a particular linkage, please look at the relevant contig with a jaundiced eye, and consult us about the status of any doubtful joins. GENOMIC COMMUNICATION The map is entering the electronic age. Two secondary databases have been established in the U.S.; both are kept up to date with respect to the database at MRC by regular electronic mail messages. All three databases are on Vax computers (in order to avoid our having to rewrite software), but they can be accessed by microcomputers equipped with suitable terminal emulators and modems. Terminal emulators that have worked so far are Smarterm 240 (Persoft, Inc.) for the IBM PC, and VersaTerm Pro (Abelbeck Software) for the MacIntosh. Both can store contig plots and produce hardcopy on a local printer. Access via certain computer networks may also be possible, and we leave that to your ingenuity. Smarterm 240 should be set up to run in Tektronix 4014 mode. We haven't encountered any serious problems with Smarterm, probably because we haven't much experience with it yet. VersaTerm Pro users should have version 2.10 or later. Version 2.00 has a bug that prevents proper switching between windows (annoying, but not fatal). In the 'settings' menu under 'Extras', set 'auto tek', 'auto wraparound', 'text scrolled on clear page', 'ignore vt100 answerback', and 'signal end of file transfer'. 'Retain cleared graphics' must be off. To prevent the text window from blocking your view of the contig plot, use the mouse to shrink it and move it to the bottom of the screen. The St Louis database has been successfully accessed from St Paul and from MIT, so distance seems no problem. However, if anyone with a Vax on the West Coast would like to operate a third database we will set it up. MRC Operator: John Sulston (Bitnet: JES@UK.AC.CAM.MRC-LMB) 1200 baud modems: 223-242096, 223-243981, 223-213285, 223- 213299 St Louis Operator: Bob Waterston (Bitnet: WATERSTON@WUMS) 2400 baud modems: 314-367-1604, 314-367-2281, 314-361- 1200 baud modems: 314-361-0863, 314-361- 0918 MIT Operator: Stuart Kim (Bitnet: KIM@MITUCCF) 2400 baud modems: 617-258-8657; 1200 baud: 617-258- 6181 When you are connected, you will be prompted for Username:. Enter <C_ELEGANS>. You will next be prompted for Password:. Enter <WORMS>. The program starts automatically. When finished, quit the program with <*> and answer <N> to the prompt asking you if you want to run the program again. You will automatically be logged off. GENOME SIZE The time has come to revise the estimated size of the genome. The original estimate, of 80 Mb, was based on a Cot comparison between C. elegans and E. coli (Sulston and Brenner, Genetics, 77, 95-104, (1974) ). The size of the E. coli genome was then believed to be 4 Mb. Yuji Kohara (Cell 50, 495-508 (1987)) has now shown that E. coli actually contains 4.7 Mb. So C. elegans is predicted to contain some 95 Mb. The new estimate fits better with a measurement of the size of the ribosomal cluster, by Bob Waterston using pulse field gel electrophoresis. He found a 700 kb BglI fragment; this size must be corrected down by an unknown amount to allow for non-ribosomal end sequences. The old hybridization figure of 0.44%, corrected for the proportion of the tandem repeat occupied by 18s+26s coding sequence ( Ellis et al, NAR, 14, 2345-2364 (1986)), indicates that the ribosomal cluster occupies 0.60% of the genome. On this basis, an upper limit for the size of the genome is about 115 Mb. Overall, then, our current best estimate for the size of the genome is about 100Mb. [See Figures 1 & 2]