Giardia duodenalis (syn. Giardia intestinalis or Giardia lamblia) infSAects over 280 million people each year and numerous animals. G. duodenalis can be subdivided into eight assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study, we isolated single and pooled cysts of assemblages C and D from dog faeces by FACS, and sequenced them using multiple displacement amplification and Illumina paired-end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99 % marker genes observed) and the allelic sequence heterozygosity (ASH) values of assemblages C and D were 0.89 and 0.74 %, respectively. These ASH values were slightly higher than for assemblage B (>0.43 %) and much higher than for assemblages A and E, which ranged from 0.002 to 0.037 %. The flavohaemoglobin and 4Fe-4S binding domain family encoding genes involved in O2 and NO detoxification were only present in assemblages A, B and E. Cathepsin B orthologs were found in all genomes. Six clades of cathepsin B orthologs contained one gene of each genome, while in three clades not all assemblages were represented. We conclude that whole-genome sequencing from a single Giardia cyst results in complete draft genomes, making the genomes of unculturable Giardia assemblages accessible. Observed differences between the genomes of assemblages C and D on one hand and the assemblages A, B and E on the other hand are possibly associated with host specificity.
SprongH,
CacciòSM,
van der GiessenJWB.
ZOOPNET Network and Partners Identification of zoonotic genotypes of Giardia duodenalis
. PLoS Negl Trop Dis2009; 3:e558
FranzénO,
Jerlström-HultqvistJ,
CastroE,
SherwoodE,
AnkarklevJ et al. Draft genome sequencing of Giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?. PLoS Pathog2009; 5:e1000560 [View Article]
MonisPT,
AndrewsRH,
MayrhoferG,
EyPL.
Genetic diversity within the morphological species Giardia intestinalis and its relationship to host origin. Infect Genet Evol2003; 3:29–38 [View Article]
PoxleitnerMK,
CarpenterML,
MancusoJJ,
WangC-JR,
DawsonSC et al. Evidence for karyogamy and exchange of genetic material in the binucleate intestinal parasite Giardia intestinalis
. Science2008; 319:1530–1533 [View Article]
AdamRD,
DahlstromEW,
MartensCA,
BrunoDP,
BarbianKD et al. Genome sequencing of Giardia lamblia genotypes A2 and B isolates (DH and Gs) and comparative analysis with the genomes of genotypes A1 and E (WB and pig). Genome Biol Evol2013; 5:2498–2511 [View Article]
Jerlström-HultqvistJ,
FranzénO,
AnkarklevJ,
XuF,
NohýnkováE et al. Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate. BMC Genomics2010; 11:e543 [View Article]
DubourgA,
XiaD,
WinpennyJP,
Al NaimiS,
BouzidM et al.Giardia secretome highlights secreted tenascins as a key component of pathogenesis. Gigascience2018; 7:giy003 [View Article]
TroellK,
HallströmB,
DivneA-M,
AlsmarkC,
ArrighiR et al.Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics2016; 17:471 [View Article]
UiterwijkM,
NijsseR,
KooymanFNJ,
WagenaarJA,
Mughini-GrasL et al. Comparing four diagnostic tests for Giardia duodenalis in dogs using latent class analysis. Parasit Vectors2018; 11:439 [View Article]
CacciòSM,
BeckR,
LalleM,
MarinculicA,
PozioE.
Multilocus genotyping of Giardia duodenalis reveals striking differences between assemblages A and B. Int J Parasitol2008; 38:1523–1531 [View Article]
TsengYC,
HoGD,
Chen TTW,
HuangBF,
ChengPC et al. Prevalence and genotype of Giardia duodenalis from faecal samples of stray dogs in Hualien city of eastern Taiwan. Trop Biomed2014; 31:305–311
BankevichA,
NurkS,
AntipovD,
GurevichAA,
DvorkinM et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol2012; 19:455–477 [View Article]
EnrightAJ,
Van DongenS,
OuzounisCA.
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res2002; 30:1575–1584 [View Article]
NguyenL-T,
SchmidtHA,
von HaeselerA,
MinhBQ.
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol2015; 32:268–274 [View Article]
JainC,
Rodriguez-RLM,
PhillippyAM,
KonstantinidisKT,
AluruS.
High throughput ani analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun2018; 9:
AnsellBRE,
BakerL,
EmerySJ,
McConvilleMJ,
SvärdSG et al. Transcriptomics indicates active and passive metronidazole resistance mechanisms in three seminal Giardia lines. Front Microbiol2017; 8:e00398 [View Article]
Ma'ayehSY,
KnörrL,
SvärdSG.
Transcriptional profiling of Giardia intestinalis in response to oxidative stress. Int J Parasitol2015; 45:925–938 [View Article]
MastronicolaD,
TestaF,
ForteE,
BordiE,
PucilloLP et al. Flavohemoglobin and nitric oxide detoxification in the human protozoan parasite Giardia intestinalis
. Biochem Biophys Res Commun2010; 399:654–658 [View Article]
MonisP,
ThompsonRCA.
Giardia – from genome to proteome. In
RollinsonD,
HaySI.
(editors) Advances in Parasitology78 London and Amsterdam: Elsevier; 2012 pp 57–95
PallantL,
BarutzkiD,
SchaperR,
ThompsonRCA.
The epidemiology of infections with Giardia species and genotypes in well cared for dogs and cats in Germany. Parasit Vectors2015; 8:2 [View Article]
XuF,
Jerlström-HultqvistJ,
EinarssonE,
ÁstvaldssonA,
SvärdSG et al. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PLoS Genet2014; 10:e1004053 [View Article]