IRGSP Interim Meeting Higlights
November 22, 2003
Shanghai Institute for Biological Research
Shanghai, PRC
Sequencing Progress
The following table shows IRGSP progress
in finishing BAC/PAC clones as of November 16, 2003.
| Site |
Total |
PHASE1 |
PHASE2 |
PLN |
BAC/month |
| ASPGC |
287
|
2 |
223 |
80 |
19 |
| CSHL |
109
|
3 |
1 |
105 |
0 |
| Genoscope |
286
|
1 |
64 |
220 |
14 |
| KRGRP |
16
|
9 |
22 |
0 |
0 |
| NCGR |
297
|
0 |
115 |
216 |
0 |
| PGIR |
40
|
0 |
6 |
34 |
22 |
| TIGR |
387
|
15 |
147 |
223 |
9 |
| RGP |
1810
|
41 |
601 |
1168 |
88 |
| IIRGS |
115
|
0 |
88 |
29 |
10 |
| AGI |
132
|
1 |
3 |
129 |
2 |
| BRIGI |
2
|
0 |
0 |
2 |
0 |
| Total |
3483 |
72 |
1270 |
2206 |
164 |
It is evident that at the current rate
the IRGSP is on schedule to finish 1277 clones by the self imposed deadline
of December, 2004.
Chromosomes 1, 4, 7, and 10 have been finished, as well as complete centromeres
on chromosomes 4 and 8.
Physical Map
The summary of the current physical map,
prepared by Jianzhong Wu (RGP), indicates 56 physical gaps remain. Gap
size is estimated based on Fiber FISH technology, BAC finger printing, the
YAC physical map, and the genetic map. About 30% of the total length of
remaining gaps are in centromes.
| Chr
No. |
cM |
PAC/BAC
clones |
Tile
length (Mb) |
Gap
No. |
Full
length (Mb) |
Coverage
(%)* |
Unmapped
(Mb) |
| 1 |
181.8 |
392 |
43.6 |
7 |
45.2 |
96.5 |
1.6 |
| 2 |
157.9 |
359 |
36.5 |
4 |
38.7 |
94.3 |
2.2 |
| 3 |
166.4 |
332 |
36.7 |
7 |
39.3 |
93.4 |
2.6 |
| 4 |
129.6 |
296 |
35.2 |
3 |
36.0 |
97.8 |
0.8 |
| 5 |
122.3 |
287 |
29.7 |
5 |
31.8 |
93.4 |
2.1 |
| 6 |
126.3 |
282 |
31.3 |
2 |
34.3 |
91.3 |
3.0 |
| 7 |
118.6 |
294 |
29.9 |
2 |
31.2 |
95.8 |
1.3 |
| 8 |
121.2 |
283 |
29.2 |
2 |
30.7 |
95.1 |
1.5 |
| 9 |
93.5 |
221 |
23.0 |
5 |
24.6 |
93.5 |
1.6 |
| 10 |
83.8 |
208 |
23.0 |
5 |
23.8 |
96.6 |
0.8 |
| 11 |
119.5 |
262 |
28.5 |
6 |
32.2 |
88.5 |
3.7 |
| 12 |
109.5 |
277 |
27.2 |
8 |
30.5 |
89.2 |
3.3 |
| Total |
1530.4 |
3493 |
373.8 |
56 |
398.3 |
93.8 |
24.5 |
*The region containing rice rDNA sequence
on chromosome 9 is not included.
The estimate for total genome size of
398.3 Mb comes very close to 400.5 Mb obtained by Chen et al. (Plant Cell
14: 537, 2002).
The members have used Syngenta sequence, multiple BAC/PAC libraries, and
a new 40-50 kb random sheared fosmid library, to close the gaps and extend
boundaries. Thirty two gaps have been closed using these resources in the
last eight months.
The members agreed to explore means to measure all remaining gaps by fiber
FISH.
In another effort to close the remaining
gaps, Rod Wing noted that there are 80 unanchored contigs on the AGI map
covering about 12 Mb. In collaboration with the RGP, he proposes to map
these contigs and to perform survey sequencing on the potentially interesting
contigs to identify clones that are not on the current sequence-based map.
Sequence Quality
Members measure band size from in silico
as compared with empirical digests of each finished clone with three to six
enzymes. It was agreed to use two additional approaches to check sequence
quality:
Cari Soderlund (AGI) has developed simulated
digest software which automatically does in silico digests on finished BACs and PACs
as they are posted. Clones with matching digests are automatically brought
into the AGI physical map.
The simulated digest software will be rewritten so that all submitted finished clones can be checked by this method.
Dick McCombie proposed, and members accepted,
a mechanism that would allow CSHL and Genoscope to request trace files for
five randomly chosen finished clones for each group where they will be reassembled
at both sites to verify that submitted sequence meets phase 3 quality. McCombie
noted that CSHL and TIGR had traded trace files for a similar exercise in
the past.
Finishing Workshop
A workshop, conducted by finishers from
CSHL will be held in Tsukuba, Japan on February 2-3, 2004, so that IRGSP
finishers can compare notes and exchange ideas on finishing methods and how
to approach problem clones.
Future Meetings
The next IRGSP meeting will be held in
Tsukuba, Japan on February 4, 2004.
The next interim meeting will be held in
Tucson, Arizona in conjunction with the 2nd International Symposium
on Rice Functional Genomics, probably in October, 2004.
It was agreed to have monthly conference
calls beginning March, 2004.
Posted by Takuji Sasaki and Ben Burr,
25 November 2003
RICE GENOME RESEARCH PROGRAM (RGP) HOME PAGE
webmaster@staff.or.jp
Copyright (C) The International Rice Genome Sequencing Project (IRGSP). 2005 All rights reserved.
|
|
|