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Cryptosporidium hominis is the dominant species responsible for human cryptosporidiosis.Within the species,one subtype at the gp60 locus,IbA 10G2,is the most virulent parasite,responsible for all C.Hominisassociated outbreaks in Europe and Australia,and is the dominant outbreak subtype in the United States.In recent years,a newly emerged subtype,IaA28R4,is becoming a dominantC.hominis subtype in both sporadic cases and outbreaks.As the genome of only one C.hominis isolate,TU502 of the IaA25R3 subtype,has been sequenced thus far,the mechanism for the hyper-transmissibility and virulence of IbA 10G2 and IaA28R4 is not clear.In this study,we sequenced the genome of two isolates each of the two subtypes from four waterborne outbreaks in the United States by 454 and Illumina technologies.Altogether,8.61-9.05Mb of Cryptosporidium sequences in 45-831 assembled contigs were obtained from these isolates,representing 94.35-99.47% coverage of the expected genome.The genome of these isolates had96.90-97.01%and 99.78-99.83% nucleotide sequence identity tothe published genomes ofC.parvum and C.hominis,respectively.They also hadan almost complete syntanyin gene organization to the two previously sequenced species; all potential gene re-arrangements were seen around physical gaps in the published C.parvum genome,probably as a results ofmisassembly of scaffolds in the latter.Nevertheless,several major insertions and deletions were seen betweenC,hominis andC.parvum genomes,including two coding regions.The four C.hominis genomes were almost identical to each other and were divergent in nucleotide sequences from the reference IaA25R3 genome atmost highly polymorphic regions examined.The only major sequence differences among the four isolates sequenced in this study were in the 5 and 3 ends and gp60 region of chromosome 6,largely the result of genetic recombination.The sequence similarity among isolates 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 major role in the emergence ofhyper-transmissible C.hominis subtypes,as indicated recently by our population genetic study of chromosome 6 sequences of virulent IbAl 0G2 subtype and other subtypes.Thegene insertions and deletions could be responsible for the major difference in host-specificity between C.hominis and C.Parvum.