Dataset Information

Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum.

ABSTRACT: Host adaptation is known to occur in Cryptosporidium parvum, with IIa and IId subtype families preferentially infecting calves and lambs, respectively. To improve our understanding of the genetic basis of host adaptation in Cryptosporidium parvum, we sequenced the genomes of two IId specimens and one IIa specimen from China and Egypt using the Illumina technique and compared them with the published IIa IOWA genome. Sequence data were obtained for >99.3% of the expected genome. Comparative genomic analysis identified differences in numbers of three subtelomeric gene families between sequenced genomes and the reference genome, including those encoding SKSR secretory proteins, the MEDLE family of secretory proteins, and insulinase-like proteases. These gene gains and losses compared with the reference genome were confirmed by PCR analysis. Altogether, 5,191-5,766 single nucleotide variants were seen between genomes sequenced in this study and the reference genome, with most SNVs occurring in subtelomeric regions of chromosomes 1, 4, and 6. The most highly polymorphic genes between IIa and IId encode mainly invasion-associated and immunodominant mucin proteins, and other families of secretory proteins. Further studies are needed to verify the biological significance of these genomic differences.

SUBMITTER: Feng Y

PROVIDER: S-EPMC5774651 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum.

Feng Yaoyu Y Li Na N Roellig Dawn M DM Kelley Alyssa A Liu Guangyuan G Amer Said S Tang Kevin K Zhang Longxian L Xiao Lihua L

International journal for parasitology 20170210 5

Host adaptation is known to occur in Cryptosporidium parvum, with IIa and IId subtype families preferentially infecting calves and lambs, respectively. To improve our understanding of the genetic basis of host adaptation in Cryptosporidium parvum, we sequenced the genomes of two IId specimens and one IIa specimen from China and Egypt using the Illumina technique and compared them with the published IIa IOWA genome. Sequence data were obtained for >99.3% of the expected genome. Comparative genomi ...[more]

PMID: 28192123

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Project description:BackgroundCryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome.ResultsAltogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45-767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5' and 3' ends of chromosome 6 and the gp60 region, largely the result of genetic recombination.ConclusionsThe sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to host expansion in C. parvum.

Dataset Information

Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum.

Publications

Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum.

Similar Datasets

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