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.

The Genome Map

Alan Coulson, John Sulston, Yuji Kohara, Donna Albertson, Rita Fishpool, Leon Avery, Robert Waterston, Humaira Ameer

Figure 1

Figure 2

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]

Figure 1

Figure 2