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