Category Archive: Genomics of Apicomplexa

Dec 16

Genetic diversity of avian haemosporidians in Malaysia: cytochrome b lineages of the genera Plasmodium and Haemoproteus (Haemosporida) from Selangor.

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Genetic diversity of avian haemosporidians in Malaysia: cytochrome b lineages of the genera Plasmodium and Haemoproteus (Haemosporida) from Selangor.
Infect Genet Evol. 2015 Apr;31:33-9
Authors: Iv…

Dec 16

Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

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Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

Infect Genet Evol. 2015 Apr;31:53-60

Authors: Terao M, Akter S, Yasin MG, Nakao R, Kato H, Alam MZ, Katakura K

Abstract
Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh.

PMID: 25620376 [PubMed – indexed for MEDLINE]

Oct 29

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains.

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A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains.

Nat Commun. 2014;5:4052

Authors: Preston MD, Campino S, Assefa SA, Echeverry DF, Ocholla H, Amambua-Ngwa A, Stewart LB, Conway DJ, Borrmann S, Michon P, Zongo I, Ouédraogo JB, Djimde AA, Doumbo OK, Nosten F, Pain A, Bousema T, Drakeley CJ, Fairhurst RM, Sutherland CJ, Roper C, Clark TG

Abstract
Malaria is a major public health problem that is actively being addressed in a global eradication campaign. Increased population mobility through international air travel has elevated the risk of re-introducing parasites to elimination areas and dispersing drug-resistant parasites to new regions. A simple genetic marker that quickly and accurately identifies the geographic origin of infections would be a valuable public health tool for locating the source of imported outbreaks. Here we analyse the mitochondrion and apicoplast genomes of 711 Plasmodium falciparum isolates from 14 countries, and find evidence that they are non-recombining and co-inherited. The high degree of linkage produces a panel of relatively few single-nucleotide polymorphisms (SNPs) that is geographically informative. We design a 23-SNP barcode that is highly predictive (~92%) and easily adapted to aid case management in the field and survey parasite migration worldwide.

PMID: 24923250 [PubMed – indexed for MEDLINE]

Oct 11

Cryptosporidium parvum IId family: clonal population and dispersal from Western Asia to other geographical regions.

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Cryptosporidium parvum IId family: clonal population and dispersal from Western Asia to other geographical regions.

Sci Rep. 2014;4:4208

Authors: Wang R, Zhang L, Axén C, Bjorkman C, Jian F, Amer S, Liu A, Feng Y, Li G, Lv C, Zhao Z, Qi M, Dong H, Wang H, Sun Y, Ning C, Xiao L

Abstract
In this study, 111 Cryptosporidium parvum IId isolates from several species of animals in China, Sweden, and Egypt were subtyped by multilocus sequence typing (MLST). One to eleven subtypes were detected at each of the 12 microsatellite, minisatellite, and single nucleotide polymorphism (SNP) loci, forming 25 MLST subtypes. Host-adaptation and significant geographical segregation were both observed in the MLST subtypes. A clonal population structure was seen in C. parvum IId isolates from China and Sweden. Three ancestral lineages and the same RPGR sequence were shared by these isolates examined. Therefore, the present genetic observations including the higher nucleotide diversity of C. parvum IId GP60 sequences in Western Asia, as well as the unique distribution of IId subtypes (almost exclusively found in Asia, Europe, and Egypt) and in combination with the domestication history of cattle, sheep, and goats, indicated that C. parvum IId subtypes were probably dispersed from Western Asia to other geographical regions. More population genetic structure studies involving various C. parvum subtype families using high-resolution tools are needed to better elucidate the origin and dissemination of C. parvum in the world.

PMID: 24572610 [PubMed – indexed for MEDLINE]

Sep 01

The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium.

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The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium.
Genome. 2014 Sep;57(9):507-11
Authors: Nikbakht H, Xia X, Hickey DA
Abstract
The genome …

Aug 16

NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii.

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NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii.
BMC Genomics. 2014;15:1168
Authors: Khan A, Shaik JS, Behnke M, Wang Q, …

Jul 17

Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile.

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Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile.

Eukaryot Cell. 2014 Dec;13(12):1507-18

Authors: Walzer KA, Wier GM, Dam RA, Srinivasan AR, Borges AL, English ED, Herrmann DC, Schares G, Dubey JP, Boyle JP

Abstract
Toxoplasma gondii and its nearest extant relative, Hammondia hammondi, are phenotypically distinct despite their remarkable similarity in gene content, synteny, and functionality. To begin to identify genetic differences that might drive distinct infection phenotypes of T. gondii and H. hammondi, in the present study we (i) determined whether two known host-interacting proteins, dense granule protein 15 (GRA15) and rhoptry protein 16 (ROP16), were functionally conserved in H. hammondi and (ii) performed the first comparative transcriptional analysis of H. hammondi and T. gondii sporulated oocysts. We found that GRA15 and ROP16 from H. hammondi (HhGRA15 and HhROP16) modulate the host NF-κB and STAT6 pathways, respectively, when expressed heterologously in T. gondii. We also found the transcriptomes of H. hammondi and T. gondii to be highly distinct. Consistent with the spontaneous conversion of H. hammondi tachyzoites into bradyzoites both in vitro and in vivo, H. hammondi high-abundance transcripts are enriched for genes that are of greater abundance in T. gondii bradyzoites. We also identified genes that are of high transcript abundance in H. hammondi but are poorly expressed in multiple T. gondii life stages, suggesting that these genes are uniquely expressed in H. hammondi. Taken together, these data confirm the functional conservation of known T. gondii virulence effectors in H. hammondi and point to transcriptional differences as a potential source of the phenotypic differences between these species.

PMID: 25280815 [PubMed – indexed for MEDLINE]

Jul 08

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

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Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Genome Res. 2014 Oct;24(10):1676-85
Authors: Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M,…

Jul 08

The genome of Eimeria falciformis–reduction and specialization in a single host apicomplexan parasite.

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The genome of Eimeria falciformis–reduction and specialization in a single host apicomplexan parasite.

BMC Genomics. 2014;15:696

Authors: Heitlinger E, Spork S, Lucius R, Dieterich C

Abstract
BACKGROUND: The phylum Apicomplexa comprises important unicellular human parasites such as Toxoplasma and Plasmodium. Eimeria is the largest and most diverse genus of apicomplexan parasites and some species of the genus are the causative agent of coccidiosis, a disease economically devastating in poultry. We report a complete genome sequence of the mouse parasite Eimeria falciformis. We assembled and annotated the genome sequence to study host-parasite interactions in this understudied genus in a model organism host.
RESULTS: The genome of E. falciformis is 44 Mb in size and contains 5,879 predicted protein coding genes. Comparative analysis of E. falciformis with Toxoplasma gondii shows an emergence and diversification of gene families associated with motility and invasion mainly at the level of the Coccidia. Many rhoptry kinases, among them important virulence factors in T. gondii, are absent from the E. falciformis genome. Surface antigens are divergent between Eimeria species. Comparisons with T. gondii showed differences between genes involved in metabolism, N-glycan and GPI-anchor synthesis. E. falciformis possesses a reduced set of transmembrane transporters and we suggest an altered mode of iron uptake in the genus Eimeria.
CONCLUSIONS: Reduced diversity of genes required for host-parasite interaction and transmembrane transport allow hypotheses on host adaptation and specialization of a single host parasite. The E. falciformis genome sequence sheds light on the evolution of the Coccidia and helps to identify determinants of host-parasite interaction critical for drug and vaccine development.

PMID: 25142335 [PubMed – indexed for MEDLINE]

May 13

Mitochondrial genome of Babesia orientalis, apicomplexan parasite of water buffalo (Bubalus babalis, Linnaeus, 1758) endemic in China.

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Mitochondrial genome of Babesia orientalis, apicomplexan parasite of water buffalo (Bubalus babalis, Linnaeus, 1758) endemic in China.
Parasit Vectors. 2014;7:82
Authors: He L, Zhang Y, Zhang QL, …

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