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Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes.

Tang K, Guo Y, Zhang L, Rowe LA, Roellig DM, Frace MA, Li N, Liu S, Feng Y, Xiao L - Parasit Vectors (2015)

Bottom Line: The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships.Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences.

View Article: PubMed Central - PubMed

Affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. kht7@cdc.gov.

ABSTRACT

Background: Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.

Methods: The genome of one Chinese C. cayetanensis isolate was sequenced using Roche 454 and Illumina technologies. The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships. Sequence variations in the mitochondrial genome were identified by comparison of two C. cayetanensis nucleotide sequences from this study and a recent publication.

Results: The apicoplast and mitochondrial genomes of C. cayetanensis are 34,155 and 6,229 bp in size and code for 65 and 5 genes, respectively. Comparative genomic analysis showed high similarities between C. cayetanensis and Eimeria tenella in both genomes; they have 85.6% and 90.4% nucleotide sequence similarities, respectively, and complete synteny in gene organization. Phylogenetic analysis of the genomic sequences confirmed the genetic similarities between cecum-infecting avian Eimeria spp. and C. cayetanensis. Like in other coccidia, both genomes of C. cayetanensis are transcribed bi-directionally. The apicoplast genome is circular, codes for the complete machinery for protein biosynthesis, and contains two inverted repeats that differ slightly in LSU rRNA gene sequences. In contrast, the mitochondrial genome has a linear concatemer or circular mapping topology. Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.

Conclusions: The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences. The availability of sequence data beyond rRNA and heat shock protein genes could facilitate studies of C. cayetanensis biology and development of genotyping tools for investigations of cyclosporiasis outbreaks.

No MeSH data available.


Related in: MedlinePlus

Map of the apicoplast genome of Cyclospora cayetanensis
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Fig1: Map of the apicoplast genome of Cyclospora cayetanensis

Mentions: The apicoplast genome is 34,155 bp in size with the following base composition: A (40.28 %), T (37.76 %), C (10.79 %) and G (11.16 %), with an overall AT content of 78.04 %. It contained two inverted repeats (IR). Each IR unit is 5,244 bp in length and contains genes coding for an SSU rRNA, an LSU rRNA, and nine tRNAs (Fig. 1). PCR with one primer in the repeat and the other primer in the non-repeat part of the apicoplast sequence amplified the two regions joining the IR to the main body of the apicoplast (Fig. 2). The joint sequences were confirmed by Sanger sequencing, which yielded sequences identical to those from the whole genome sequencing. PCR amplification of the sequence between the closer ends of the two IRs was not successful probably because of the inverted nature of the repeat units. However, a search of reads from Roche 454 sequencing revealed that there are 33 bp between the closer ends of the two IRs. This allowed the construction of the full circular apicoplast genome of C. cayetanensis. The presence of two IRs was also confirmed by mapping of sequence reads to the assembled contigs, as the two IRs differed by eight nucleotides in a 58-bp region of the LSU rRNA gene (Table 1). The relative placement of the two slightly different IR units in the circular apicoplast genome was not clear.Fig. 1


Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes.

Tang K, Guo Y, Zhang L, Rowe LA, Roellig DM, Frace MA, Li N, Liu S, Feng Y, Xiao L - Parasit Vectors (2015)

Map of the apicoplast genome of Cyclospora cayetanensis
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4495940&req=5

Fig1: Map of the apicoplast genome of Cyclospora cayetanensis
Mentions: The apicoplast genome is 34,155 bp in size with the following base composition: A (40.28 %), T (37.76 %), C (10.79 %) and G (11.16 %), with an overall AT content of 78.04 %. It contained two inverted repeats (IR). Each IR unit is 5,244 bp in length and contains genes coding for an SSU rRNA, an LSU rRNA, and nine tRNAs (Fig. 1). PCR with one primer in the repeat and the other primer in the non-repeat part of the apicoplast sequence amplified the two regions joining the IR to the main body of the apicoplast (Fig. 2). The joint sequences were confirmed by Sanger sequencing, which yielded sequences identical to those from the whole genome sequencing. PCR amplification of the sequence between the closer ends of the two IRs was not successful probably because of the inverted nature of the repeat units. However, a search of reads from Roche 454 sequencing revealed that there are 33 bp between the closer ends of the two IRs. This allowed the construction of the full circular apicoplast genome of C. cayetanensis. The presence of two IRs was also confirmed by mapping of sequence reads to the assembled contigs, as the two IRs differed by eight nucleotides in a 58-bp region of the LSU rRNA gene (Table 1). The relative placement of the two slightly different IR units in the circular apicoplast genome was not clear.Fig. 1

Bottom Line: The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships.Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences.

View Article: PubMed Central - PubMed

Affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. kht7@cdc.gov.

ABSTRACT

Background: Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.

Methods: The genome of one Chinese C. cayetanensis isolate was sequenced using Roche 454 and Illumina technologies. The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships. Sequence variations in the mitochondrial genome were identified by comparison of two C. cayetanensis nucleotide sequences from this study and a recent publication.

Results: The apicoplast and mitochondrial genomes of C. cayetanensis are 34,155 and 6,229 bp in size and code for 65 and 5 genes, respectively. Comparative genomic analysis showed high similarities between C. cayetanensis and Eimeria tenella in both genomes; they have 85.6% and 90.4% nucleotide sequence similarities, respectively, and complete synteny in gene organization. Phylogenetic analysis of the genomic sequences confirmed the genetic similarities between cecum-infecting avian Eimeria spp. and C. cayetanensis. Like in other coccidia, both genomes of C. cayetanensis are transcribed bi-directionally. The apicoplast genome is circular, codes for the complete machinery for protein biosynthesis, and contains two inverted repeats that differ slightly in LSU rRNA gene sequences. In contrast, the mitochondrial genome has a linear concatemer or circular mapping topology. Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.

Conclusions: The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences. The availability of sequence data beyond rRNA and heat shock protein genes could facilitate studies of C. cayetanensis biology and development of genotyping tools for investigations of cyclosporiasis outbreaks.

No MeSH data available.


Related in: MedlinePlus