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Naming & shaming
& sequencing
the ‘Apicomplexans’
Outline of the presentation
• Eukaryotic pathogen sequencing in Sanger
• ‘Apicomplexans’ – ‘the culprits’!
• Sequencing Plasmodium in Sanger
• Plasmodium biology: what makes P. falciparum unique
• Comparitive genomics
• Insights from other Apicomplexan genomes (theileria)
Eukaryotic Pathogen Sequencing in PSU
Why ‘Apicomplexans’?
The Apical Complex
The Apicoplast
Algae forms symbiotic relationship with host
eukaryote
Ancient algae
chloroplast
Eukaryote cell
cyanobacterium
Modern plasmodiumApicoplast
DNA from apicoplast migrates to nucleus
Naming & shaming the ‘Apicomplexans’
The World of Apicomplexans!
Intestinal disease in mammals
Parasitise brain/ kidney of rodent
Malaria
Tropical theileriosis
Babesiosis
Periph. eosinophilia (30%)
Brain infection (Chinchila)
Parasitises heart muscle/brain
Toxoplasmosis
parasitic disease of falcolns
bowel diease in human
Coccidiosis
Insect gut parasites
Cryptosporidiosis
Insect gut parasites
Dog parasites
Oyster parasite
Euk. pathogen sequencing projects in PSUApicomplexan sequencing projects in PSU
X 3
The PlasmodiaP. falciparum (Gardner et al 2002)
P. reichenowi (3x shotgun in progress)
P. vivax (full sequencing in progress)
P. cynomolgi
P. knowlesi (8x shotgun, complete)
P. gallinaceum (3x shotgun in progress)
P. berghei (Complete sequencing in progress)
P. yoelii (5.6x, Carlton et al 2002)
P. chabaudi (8x shotgun, in progress)
X 3
One child die of P. falciparum malaria in sub-Saharan Africa every 30 seconds
Comparitive genomics: P. falciparum & rodent malarias
(Neil Hall)
The Chromosomes of P. falciparum
Rep20
TARE2-5
antigenic variation
House-keeping antigenicvariation
telomere Subtelomericrepeats
VAR genes RIFIN / STEVOR genes Other gene families
VAR genes Rifin
P. falciparum & P. vivax: sub-telomeric species-specific gene families
P. falciparum
P. vivax
Rings Mature Trophs
Erythrocytic forms of P. falciparum
Adhesive domains of pfEMP-1 (var gene)
Extracellular TM Intracellular
DBL-1 DBL-2 DBL-3 DBL-4 ATS
DBL-5
Blood Group A antigenCR1GAG’s CD36
IgM
ICAM-1 CD31 CSA
CIDR C2 CIDR TM
pfEMP-1 (250-350 kDa)
var (8-15 kb) Exon IIExon I
Whole genome domain organisation of pfEMP1 proteins
• 59 var genes in total.• Expressed on red cell
surface and involved in sequestration
• 3 types of domain.– DBL- duffy binding like– CIDR- cystine rich
interdomain region– C2 - constant2
Telomeric var gene organisation
• Telomeric var genes tend to be type 1
• All internal var clusters tend to be type 1
• Three upstream conserved sequences present– UPSa – 11 members- Inverted vars– UPSb -35 members - telomeric vars– UPSc 13 members - Internal vars
Internal var clusters• Five chromosomes have
internal var genes
• All internal var clusters tend to be type 1
• GC-rich elements (202 bp) associated with all internal var gene clusters (42 % G+C)
– No GC-rich element in telomeric var genes
– Form secondary structure?– Function?
Comparitive genomics: synteny breaks
P. falciparum
P. knowlesi
P. yoelii
EBL-1 (erythrocyte invasion)
Subtelomeric gene families in malaria
falciparum reichenowi gallinaceum chabaudi berghei yoelii
yir/cir/bir 0 0 0 138 180 838
pyst-a 1 - - 108 45 168
pyst-b 0 - - 10 34 57
pyst-c 0 - - 5 4 21
pyst-d 0 - - 0 1 17
pcst-f 0 - - 10 2 1
pcst-g 0 - - 75 11 7
pcst-h 1 - - 5 6 4
Var 59 >100* 0 0 0 0
Rifin/stevor 177 >100 0 0 0 0
Summary
Analysis & DatabasesMartin AslettAndrew BerryUlrike BöhmeAna Cerdeño Lisa CrossmanChristiane FowlerMatthew HoldenArnab PainChris Peacock Hubert RenauldMohammed Sebaihia Valerie Wood
ProgrammingDavid HarperRob DaviesArnaud KerhornouPaul Mooney Kim RutherfordEllen ScofieldAdrian Tivey Ed Zuiderwijk
Karen MungallIan GoodheadZahra HanceHeidi HauserMandy SandersMark SimmondsDanielle Walker
Barbara HarrisAndrew BarronLouise ClarkCraig CortonJonathan DoggettNicola LennardAlexandra LineDoug Ormond
David HarrisNigel FoskerArlette GobleLee MurphySusan O’NeilSimon RutterDavid SaundersKathy SeegerRobert Squares
Carol ChurcherBecky AtkinKaren Brooks Inna CherevachTracey ChillingworthPaul DavisNancy HamlinKay JagelsSharon MouleBrian WhiteSally Whitehead
SubcloningMike Quail Angela LordHalina NorbertczakClaire PriceEster Rabbinowitsch John Woodward
AdministrationYvonne ShawSarah L.ocke
Sequencing
MicroarraysCeline CarretTheresa FeltwellMaria FookesNefeli Nikolaidou- KatsaridouMatloob QureshiJason Skelton Comparative
GenomicsAlison DennisEmily KayHelena Seth-Smith
Project ManagementBart BarrellJulian ParkhillNeil HallStephen Bentley Matthew Berriman Al IvensMarie-Adèle Rajandream Nick Thomson