Annotated draft genome sequences of three species ofCryptosporidium:Cryptosporidium meleagridisisolate UKMEL1,C. baileyiisolate TAMU-09Q1 andC. hominisisolates TU502_2012 and UKH1

Ifeonu, Olukemi O.; Chibucos, Marcus C.; Orvis, Joshua; Su, Qi; Elwin, Kristin; Guo, Feng; Zhang, Haili; Xiao, Lihua; Sun, Mingfei; Chalmers, Rachel M.; Fraser, Claire M.; Zhu, Guangxi; Kissinger, Jessica C.; Widmer, Giovanni; Silva, Joana C.

doi:10.1093/femspd/ftw080

Cited by 35 publications

(32 citation statements)

References 23 publications

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“…However, the vast majority of such studies compare data between limited numbers of genomes, which makes the task of identifying new markers even more problematic. Cryptosporidium genomes are being sequenced at a pace (17)(18)(19)(20)(21)37) that is increasing our general knowledge of Cryptosporidium spp. Subsequent sequencing of additional genomes, especially from clinical samples, will increase the likelihood of facilitating the identification of new genetic markers in order to improve the classification of species status, as well as increasing the genotyping resolution of C. parvum and C. hominis subtype population genetics and epidemiology.…”

Section: Discussionmentioning

confidence: 99%

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

et al. 2017

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In order to improve genotyping and epidemiological analysis of Cryptosporidium spp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 different Cryptosporidium hominis patient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17ϫ and 490ϫ coverage. Sequence homologybased functional annotation identified several genes of interest, including the gene encoding Cryptosporidium oocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to the Cryptosporidium parvum reference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in the C. hominis tree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencing Cryptosporidium directly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes of Cryptosporidium from human fecal samples, while alluding to the potential for a higher degree of genotyping within Cryptosporidium epidemiology.

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Section: Discussionmentioning

confidence: 99%

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

et al. 2017

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“…In this study, to improve our understanding of potential genetic determinants of the host range and pathogenicity in Cryptosporidium species, we sequenced the genomes of C. bovis and C. ryanae and performed a comparative genomics analysis of the three intestinal species infecting cattle and available whole genome sequence data from other Cryptosporidium species [10,11,[20][21][22]. mETHODS Specimen collection and whole-genome sequencing C. bovis isolate 42482 and C. ryanae isolate 45019 were collected from dairy calves in Shanghai and Guangdong, China, respectively.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species

Guo

et al. 2020

Microbial Genomics

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The three common intestinal Cryptosporidium species in cattle differ significantly in host range, pathogenicity and public health significance. While Cryptosporidium parvum is pathogenic in pre-weaned calves and has a broad host range, C. bovis and C. ryanae are largely non-pathogenic and bovine-specific species in post-weaned calves. Thus far, only the genome of C. parvum has been sequenced. To improve our understanding of the genetic determinants of biological differences among Cryptosporidium spcies, we sequenced the genomes of C. bovis and C. ryanae and conducted a comparative genomics analysis. The genome of C. bovis has a gene content and organization more similar to C. ryanae than to other Cryptosporidium species sequenced to date; the level of similarity in amino acid and nucleotide sequences between the two species is 75.2 and 69.4 %, respectively. A total of 3723 and 3711 putative protein-encoding genes were identified in the genomes of C. bovis and C. ryanae, respectively, which are fewer than the 3981 in C. parvum. Metabolism is similar among the three species, although energy production pathways are further reduced in C. bovis and C. ryanae. Compared with C. parvum, C. bovis and C. ryanae have lost 14 genes encoding mucin-type glycoproteins and three for insulinase-like proteases. Other gene gains and losses in the two bovine-specific and non-pathogenic species also involve the secretory pathogenesis determinants (SPDs); they have lost all genes encoding MEDLE, FLGN and SKSR proteins, and two of the three genes for NFDQ proteins, but have more genes encoding secreted WYLE proteins, secreted leucine-rich proteins and GPI-anchored adhesin PGA18. The only major difference between C. bovis and C. ryanae is in nucleotide metabolism. In addition, half of the highly divergent genes between C. bovis and C. ryanae encode secreted or membrane-bound proteins. Therefore, C. bovis and C. ryanae have gene organization and metabolic pathways similar to C. parvum, but have lost some invasion-associated mucin glycoproteins, insulinase-like proteases, MEDLE secretory proteins and other SPDs. The multiple gene families under positive selection, such as helicase-associated domains, AMP-binding domains, protein kinases, mucins, insulinases and TRAPs could contribute to differences in host specificity and pathogenicity between C. parvum and C. bovis. Biological studies should be conducted to assess the contribution of these copy number variations to the narrow host range and reduced pathogenicity of C. bovis and C. ryanae.

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“…The availability of new sequencing technologies has made it possible to perform genome-wide profiling of genetic polymorphisms in a large number of species including several protozoan parasites2728293031. These analyses have significantly improved our understanding of the diversity and evolution of these pathogens, provided insights into their virulence, host modulation and the genetic basis of drug resistance phenotypes, and helped to develop novel approaches for disease control and prevention, and informed public health policy323334353637.…”

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confidence: 99%

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

Silva

Cornillot

McCracken

et al. 2016

Sci Rep

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Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution.

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Annotated draft genome sequences of three species ofCryptosporidium:Cryptosporidium meleagridisisolate UKMEL1,C. baileyiisolate TAMU-09Q1 andC. hominisisolates TU502_2012 and UKH1

Cited by 35 publications

References 23 publications

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

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