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A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number.

Mok BW, Ribacke U, Sherwood E, Wahlgren M - Malar. J. (2008)

Bottom Line: The n-gene transcription levels were found to correlate to the number of n-gene copies.Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome.In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden. bobo.mok@ki.se

ABSTRACT

Background: Segmental duplications (SD) have been found in genomes of various organisms, often accumulated at the ends of chromosomes. It has been assumed that the sequence homology in-between the SDs allow for ectopic interactions that may contribute to the emergence of new genes or gene variants through recombinatorial events.

Methods: In silico analysis of the 3D7 Plasmodium falciparum genome, conducted to investigate the subtelomeric compartments, led to the identification of subtelomeric SDs. Sequence variation and copy number polymorphisms of the SDs were studied by DNA sequencing, real-time quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The levels of transcription and the developmental expression of copy number variant genes were investigated by qPCR.

Results: A block of six genes of >10 kilobases in size, including var, rif, pfmc-2tm and three hypothetical genes (n-, o- and q-gene), was found duplicated in the subtelomeric regions of chromosomes 1, 2, 3, 6, 7, 10 and 11 (SD1). The number of SD1 per genome was found to vary from 4 to 8 copies in between different parasites. The intragenic regions of SD1 were found to be highly conserved across ten distinct fresh and long-term cultivated P. falciparum. Sequence variation was detected in a approximately 23 amino-acid long hypervariable region of a surface-exposed loop of PFMC-2TM. A hypothetical gene within SD1, the n-gene, encoding a PEXEL/VTS-containing two-transmembrane protein was found expressed in ring stage parasites. The n-gene transcription levels were found to correlate to the number of n-gene copies. Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome. In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

Conclusion: Plasmodium falciparum carries multiple sequence conserved SDs in the otherwise highly variable subtelomeres of its chromosomes. The uniqueness of the SDs amongst plasmodium species, and the conserved nature of the genes within, is intriguing and suggests an important role of the SD to P. falciparum.

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Copy number polymorphisms of the n-gene in different P. falciparum strains and isolates. (A) Copy numbers of the n-gene in different parasite lines relative to 3D7 detected by qPCR. (B) Visualization of copy numbers and localization of n-gene (green) in 3D7, FCR3 and 7G8. Distribution of fluorescent signals at the rim of the parasite nuclei (blue) confirms the position of the SD at the chromosomal ends.
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Figure 4: Copy number polymorphisms of the n-gene in different P. falciparum strains and isolates. (A) Copy numbers of the n-gene in different parasite lines relative to 3D7 detected by qPCR. (B) Visualization of copy numbers and localization of n-gene (green) in 3D7, FCR3 and 7G8. Distribution of fluorescent signals at the rim of the parasite nuclei (blue) confirms the position of the SD at the chromosomal ends.

Mentions: Using the n-gene as a representative member of SD1, the SD1 copy number in different P. falciparum strains relative to the 3D7 parasite was estimated using qPCR. The genomes of HB3 and the clinical isolate (UAM25) were found to contain the same number of SD1 copies as 3D7 (n = 8), whereas Dd2 was found to carry ≤ 4 (Figure 4A). Comparable numbers of pfmc-2tm was previously reported for HB3 relative to 3D7 [40], signifying a copy number association between the n-gene and pfmc-2tm.


A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number.

Mok BW, Ribacke U, Sherwood E, Wahlgren M - Malar. J. (2008)

Copy number polymorphisms of the n-gene in different P. falciparum strains and isolates. (A) Copy numbers of the n-gene in different parasite lines relative to 3D7 detected by qPCR. (B) Visualization of copy numbers and localization of n-gene (green) in 3D7, FCR3 and 7G8. Distribution of fluorescent signals at the rim of the parasite nuclei (blue) confirms the position of the SD at the chromosomal ends.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279139&req=5

Figure 4: Copy number polymorphisms of the n-gene in different P. falciparum strains and isolates. (A) Copy numbers of the n-gene in different parasite lines relative to 3D7 detected by qPCR. (B) Visualization of copy numbers and localization of n-gene (green) in 3D7, FCR3 and 7G8. Distribution of fluorescent signals at the rim of the parasite nuclei (blue) confirms the position of the SD at the chromosomal ends.
Mentions: Using the n-gene as a representative member of SD1, the SD1 copy number in different P. falciparum strains relative to the 3D7 parasite was estimated using qPCR. The genomes of HB3 and the clinical isolate (UAM25) were found to contain the same number of SD1 copies as 3D7 (n = 8), whereas Dd2 was found to carry ≤ 4 (Figure 4A). Comparable numbers of pfmc-2tm was previously reported for HB3 relative to 3D7 [40], signifying a copy number association between the n-gene and pfmc-2tm.

Bottom Line: The n-gene transcription levels were found to correlate to the number of n-gene copies.Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome.In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden. bobo.mok@ki.se

ABSTRACT

Background: Segmental duplications (SD) have been found in genomes of various organisms, often accumulated at the ends of chromosomes. It has been assumed that the sequence homology in-between the SDs allow for ectopic interactions that may contribute to the emergence of new genes or gene variants through recombinatorial events.

Methods: In silico analysis of the 3D7 Plasmodium falciparum genome, conducted to investigate the subtelomeric compartments, led to the identification of subtelomeric SDs. Sequence variation and copy number polymorphisms of the SDs were studied by DNA sequencing, real-time quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The levels of transcription and the developmental expression of copy number variant genes were investigated by qPCR.

Results: A block of six genes of >10 kilobases in size, including var, rif, pfmc-2tm and three hypothetical genes (n-, o- and q-gene), was found duplicated in the subtelomeric regions of chromosomes 1, 2, 3, 6, 7, 10 and 11 (SD1). The number of SD1 per genome was found to vary from 4 to 8 copies in between different parasites. The intragenic regions of SD1 were found to be highly conserved across ten distinct fresh and long-term cultivated P. falciparum. Sequence variation was detected in a approximately 23 amino-acid long hypervariable region of a surface-exposed loop of PFMC-2TM. A hypothetical gene within SD1, the n-gene, encoding a PEXEL/VTS-containing two-transmembrane protein was found expressed in ring stage parasites. The n-gene transcription levels were found to correlate to the number of n-gene copies. Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome. In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

Conclusion: Plasmodium falciparum carries multiple sequence conserved SDs in the otherwise highly variable subtelomeres of its chromosomes. The uniqueness of the SDs amongst plasmodium species, and the conserved nature of the genes within, is intriguing and suggests an important role of the SD to P. falciparum.

Show MeSH
Related in: MedlinePlus