Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species
AuthorsAnsari, Hifzur Rahman
Templeton, Thomas J.
Oguike, Mary C.
Benavente, Ernest Diez
Clark, Taane G.
Sutherland, Colin J.
Barnwell, John W.
KAUST DepartmentPathogen Genomics Laboratory
Biological and Environmental Sciences and Engineering (BESE) Division
Online Publication Date2016-07-05
Print Publication Date2016-10
Permanent link to this recordhttp://hdl.handle.net/10754/617088
MetadataShow full item record
AbstractMalaria in humans is caused by six species of Plasmodium parasites, of which the nuclear genome sequences for the two Plasmodium ovale spp., P. ovale curtisi and P. ovale wallikeri, and Plasmodium malariae have not yet been analyzed. Here we present an analysis of the nuclear genome sequences of these three parasites, and describe gene family expansions therein. Plasmodium ovale curtisi and P. ovale wallikeri are genetically distinct but morphologically indistinguishable and have sympatric ranges through the tropics of Africa, Asia and Oceania. Both P. ovale spp. show expansion of the surfin variant gene family, and an amplification of the Plasmodium interspersed repeat (pir) superfamily which results in an approximately 30% increase in genome size. For comparison, we have also analyzed the draft nuclear genome of P. malariae, a malaria parasite causing mild malaria symptoms with a quartan life cycle, long-term chronic infections, and wide geographic distribution. Plasmodium malariae shows only a moderate level of expansion of pir genes, and unique expansions of a highly diverged transmembrane protein family with over 550 members and the gamete P25/27 gene family. The observed diversity in the P. ovale wallikeri and P. ovale curtisi surface antigens, combined with their phylogenetic separation, supports consideration that the two parasites be given species status.
CitationGenome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species 2016 International Journal for Parasitology
SponsorsTJT was supported by a visiting professorship to the Institute of Tropical Medicine, Nagasaki University, Japan. JC was supported by grants from the National Natural Science Foundation of China (No. 81271870) and the National Natural Science Foundation of Jiangsu Province, China (No. BK20150001). AP is supported by faculty baseline funding from the King Abdullah University of Science and Technology (KAUST), Saudi Arabia and the Global Institute for Collaborative Research and Education (GI-CoRE) at the Center for Disease Control, Hokkaido University, Japan. RC is supported by Japanese Society of Parasitology (JSPS), Japan Grant-in-Aid for Scientific Research Nos. 24255009, 25870525 and 16K21233. MCO, EDB, TGC and CJS are supported by UK Medical Research Council Project Grant MR/L008661/1 to CJS. The authors thank the staff of the Bioscience Core Laboratory in KAUST for sequencing the DNA libraries. Osamu Kaneko is thanked for discussions and critical reading of the manuscript.
- Plasmodium malariae and Plasmodium ovale infections in the China-Myanmar border area.
- Authors: Li P, Zhao Z, Xing H, Li W, Zhu X, Cao Y, Yang Z, Sattabongkot J, Yan G, Fan Q, Cui L
- Issue date: 2016 Nov 15
- Evidence of non-Plasmodium falciparum malaria infection in Kédougou, Sénégal.
- Authors: Daniels RF, Deme AB, Gomis JF, Dieye B, Durfee K, Thwing JI, Fall FB, Ba M, Ndiop M, Badiane AS, Ndiaye YD, Wirth DF, Volkman SK, Ndiaye D
- Issue date: 2017 Jan 3
- Polymorphisms analysis of the Plasmodium ovale tryptophan-rich antigen gene (potra) from imported malaria cases in Henan Province.
- Authors: Zhou R, Liu Y, Li S, Zhao Y, Huang F, Yang C, Qian D, Lu D, Deng Y, Zhang H, Xu B
- Issue date: 2018 Mar 23
- Persistent Parasitism: The Adaptive Biology of Malariae and Ovale Malaria.
- Authors: Sutherland CJ
- Issue date: 2016 Oct
- Plasmodium ovale curtisi and Plasmodium ovale wallikeri in North-West Ethiopia.
- Authors: Alemu A, Fuehrer HP, Getnet G, Tessema B, Noedl H
- Issue date: 2013 Sep 28
Showing items related by title, author, creator and subject.
A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolatesSubudhi, Amit; Boopathi, P.A.; Middha, Sheetal; Acharya, Jyoti; Rao, Sudha Narayana; Mugasimangalam, Raja C.; Sirohi, Paramendra; Kochar, Sanjay K.; Kochar, Dhanpat K.; Das, Ashis (Genomics Data, Elsevier BV, 2016-07-21) [Article]Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3 MB nuclear genome and encodes ~ 5600 transcripts. The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and prognostics. Here, we describe the strategy involved in designing a custom P. falciparum 15K array using the Agilent platform and Genotypic's Right Design methodology to study the transcriptome of Indian field isolates for which genome sequence information is limited. The array contains probes representing genome sequences of two distinct geographical isolates (i.e. 3D7 and HB3) and sub-telomeric var gene sequences of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts through a 244K array experimentation. Array performance for the 15K array, was evaluated and validated using RNA materials from P. falciparum clinical isolates. A large percentage (91%) of the represented transcripts was detected from Indian P. falciparum patient isolates. Replicated probes and multiple probes representing the same gene showed perfect correlation between them suggesting good probe performance. Additional transcripts could be detected due to inclusion of unique probes representing HB3 strain transcripts. Variant surface antigen (VSA) transcripts were detected by optimized probes representing the VSA genes of three geographically distinct strains. The 15K cross strain P. falciparum array has shown good efficiency in detecting transcripts from P. falciparum parasite samples isolated from patients. The low parasite loads and presence of host RNA makes arrays a preferred platform for gene expression studies over RNA-Seq.
Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulationsDiez Benavente, Ernest; Florez de Sessions, Paola; Moon, Robert W.; Holder, Anthony A.; Blackman, Michael J.; Roper, Cally; Drakeley, Christopher J.; Pain, Arnab; Sutherland, Colin J.; Hibberd, Martin L.; Campino, Susana; Clark, Taane G. (PLOS Genetics, Public Library of Science (PLoS), 2017-09-18) [Article]The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.
Phenomics, Genomics and Genetics in Plasmodium vinckeiRamaprasad, Abhinay (2017-11) [Dissertation]
Advisors: Pain, Arnab; Culleton, Richard
Committee members: Gojobori, Takashi; Gao, Xin; Carter, RichardRodent malaria parasites (RMPs) serve as tractable models for experimental genetics, and as valuable tools to study malaria parasite biology and host-parasitevector interactions. Plasmodium vinckei, one of four RMPs adapted to laboratory mice, is the most geographically widespread species and displays considerable phenotypic and genotypic diversity amongst its subspecies and strains. The phenotypes and genotypes of P. vinckei isolates have been relatively less characterized compared to other RMPs, hampering its use as an experimental model for malaria. Here, we have studied the phenotypes and sequenced the genomes and transcriptomes of ten P. vinckei isolates including representatives of all five subspecies, all of which were collected from wild thicket rats (Thamnomys rutilans) in sub-Saharan Central Africa between the late 1940s and mid 1960s. We have generated a comprehensive resource for P. vinckei comprising of five high-quality reference genomes, growth profiles and genotypes of P. vinckei isolates, and expression profiles of genes across the intra-erythrocytic developmental stages of the parasite. We observe significant phenotypic and genotypic diversity among P. vinckei isolates, making them particularly suitable for classical genetics and genomics-driven studies on malaria parasite biology. As part of a proof of concept study, we have shown that experimental genetic crosses can be performed between P. vinckei parasites to potentially identify genotype-phenotype relationships. We have also shown that they are amenable to genetic manipulation in the laboratory.