8th Malaria Genome Meeting

Washington, D.C. December 2-3, 1999

Sequencing Updates

Sanger Centre

For subsequent meeting reports please refer to MFI's Malaria Genome Database page at www.malaria.org/genome.html

Chromosome 1 is in the later stages of gap filling. There are currently 3 almost overlapped YACs being used, and it appears that the centromere has been identified. Chromosome 4 is also in the later stages of gap filling. It has been divided into four subprojects for working purposes. The finished regions of chromosome 4 now stretch more than 200 kB.

Chromosome 13 is in the early stages of finishing and chromosome 5 is also currently in finishing.

Chromosome in finishing
# of contigs >2kb
Total length of contigs
 1
 48
0.55
 4
 52
1.16
 5
180
0.68
13
406
2.11

The Blob (chromosomes 6,7,8, and 9) are now in the shotgun sequencing phase.

Blobpart in shotgun
# of reads
Lower
21,996
Upper
17,795
Chromosome 9
21,200

Stanford

Shotgun sequencing of chromosome 12 is complete, and the chromosome is now in editing and finishing. 21 YACs are being used, with an average coverage of 2x/YAC, yielding greater than 11x coverage of the whole chromosome. While the Stanford group had used YACs from strain B8 to get initial full YAC coverage of the chromosome, now that sequence has been divided into bins, the B8 YAC sequence has been replaced with sequence from 3D7. For the current assembly, there are 70 contigs ranging in size from 2-339 kb. The total assembled size is currently 2.45 Mb. Currently, chromosome 12 is estimated to be approximately 80% AT.

The subtelomeric repeats and telomeres of chromosome 12 have been found, and it is thought that the centromere has also been located.

TIGR/NMRC

Shotgun sequencing of chromosomes 10 and 11 has now been completed, and both chromosomes are concurrently being finished now.

Chromosome4

10

11

Largest contigs

50 kb

85 kb

Largest group of contigs

360 kb

354 kb

Chromosome specific contigs

25

23

% finished

81%

75%

Using Su’s microsattelite primers, Leda has been able to identify about 30 new chromosome 11 microsatellite markers.

Chromosome 14 is currently in closure. There were about 39 physical gaps remaining to be closed at the last assembly. Using PCR products, this has been reduced to about 15 gaps. The remaining few have been significantly challenging. The major hurdle in assembly so far has been A and T homopolymers. Malcolm Gardner requested input from the community in whether there might be new approaches to the homopolymer problem.

Timeline for progress by June, 2000 and expected finish

C'some #

July 2000

Expected Finish

1

Done!

Hope to be done in June

4

Done!

Hope to be done in June

5

Finishing (almost done)

Late 2000

6

Shotgun done

Late 2000

7

Finishing

Late 2000

8

Finishing

Late 2000

9

Finishing

Late 2000

10

In annotation

2000

11

Completing gap closure

Late 2000

12

Gap closure

June 2001

13

Finishing, still mapping as they go

?

14

Hope to be closed

?

2

Done!

Done!

3

Done

Done!

Database development

Ross Coppel, David Roos and Chris Newbold have been laying the groundwork for proposing an integrated plasmodium genome database and presented their recommendations. The database aims to be "usercentric", with outreach efforts and proactive planning in place to make the bench scientist more at ease in the database environment. Meeting participants, both from the sequencing centers and from the general malaria community responded positively to the database plans and offered feedback. A proposal to allow further development will be submitted to BWF for review. Further information about the database planning will be available after submission of the database proposal.

Scientific presentations

Yimin Wu gave an update on the Malaria Reagent Repository at ATTC and invited attendees to register and contribute. Karen Day presented her work on Plasmodium heterogeneity and the epidemiology of malaria. Maria Mota presented some of her recent work on transfection of Plasmodium yoelii. Chris Plowe discussed genetic heterogeneity and drug resistance. John Wootton discussed his group’s recent work on genetic heterogeneity. John Barnwell and Andy Waters summarized the diversity of other malaria parasites. Dan Hartl gave a keynote lecture on evolutionary signal and what it can reveal about the evolution of malaria.

Discussion of genomic work in other plasmodia

Before the meeting, the question "If another plasmodium were to be sequenced, which should it be?" was raised. It was proposed that low level sequencing be done of 4 models, P. knowelsi, P. yoelii, P. chabaudi, and P. bergei. Steve Hoffman discussed 3x or 6x sequencing of P. vivax using funding from DoD. The group left the meeting with the charge to investigate the costs of 3 x and 6x sequencing of a group of organisms: a second strain of falciparum, vivax, knowelsi, bergei, yoelii, chabaudi, and galanaceum. It was generally agreed that obtaining sequence from this wide group was preferable to investing in finished sequence from a single species.

David Schwartz will also identify the cost of doing optical maps across these species. GST projects currently underway in vivax and bergei will interface well with these "lighter" sequencing projects.

Next meeting

The next meeting malaria genome meeting will be hosted by the Wellcome Trust, June 5-6 at Hinxton, Cambridge. Workshops on vaccine development and drug candidates are being planned for 2000.