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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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Gene content and organization of the segmental duplicon SD1. (A) Example of a typical SD1 containing six complete genes. Genes encoding PEXEL-containing proteins are depicted in black. A red arrow indicates the position of the hypervariable loop in pfmc2tm. (B) The SD1 exists in eight copies in the 3D7 genome with a slight variation in respect to the rif gene. Homologous rif copies, with > 95% sequence homology, in between the SD1s are shown with the same color. Crosses indicate breakpoints of each SD1.
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Figure 2: Gene content and organization of the segmental duplicon SD1. (A) Example of a typical SD1 containing six complete genes. Genes encoding PEXEL-containing proteins are depicted in black. A red arrow indicates the position of the hypervariable loop in pfmc2tm. (B) The SD1 exists in eight copies in the 3D7 genome with a slight variation in respect to the rif gene. Homologous rif copies, with > 95% sequence homology, in between the SD1s are shown with the same color. Crosses indicate breakpoints of each SD1.

Mentions: Comparative analysis of the P. falciparum genome with rodent plasmodium species has disclosed synteny breaks at the boundaries of the subtelomeric compartments [18]. Here, we have analysed the subtelomeric gene content of the 3D7 genome by grouping the genes into families as shown in Figure 1. Eight homologous regions were found, all sharing the same genomic organization being located on seven chromosomes (Chromosomes 1, 2, 3, 6, 7, 10 and 11). This duplicated DNA segment (named SD1) was found to contain six genes: rif, pfmc-2tm, a var pseudogene and three hypothetical genes (n-, o- and q-gene) (Figure 2A). The breakpoints of these segmental duplicons vary slightly, with the 5' break point being either within or downstream with respect to the rif gene and the 3' break point being either upstream or downstream of the var pseudogene. The most extended duplicated loci (approximately 32 kb in size) are both located on chromosome 6, but on opposite chromosomal ends. Although the rif genes are not identical in-between the SD1, homologous rif copies can be found within all SD1 (Figure 2B). Most of the genes within SD1 encode PEXEL-containing export proteins, with the exception of the q-gene and the var pseudogenes (Additional File 2). SD1-fragments harbouring only two or three of the SD1- genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome (Additional File 1).


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)

Gene content and organization of the segmental duplicon SD1. (A) Example of a typical SD1 containing six complete genes. Genes encoding PEXEL-containing proteins are depicted in black. A red arrow indicates the position of the hypervariable loop in pfmc2tm. (B) The SD1 exists in eight copies in the 3D7 genome with a slight variation in respect to the rif gene. Homologous rif copies, with > 95% sequence homology, in between the SD1s are shown with the same color. Crosses indicate breakpoints of each SD1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Gene content and organization of the segmental duplicon SD1. (A) Example of a typical SD1 containing six complete genes. Genes encoding PEXEL-containing proteins are depicted in black. A red arrow indicates the position of the hypervariable loop in pfmc2tm. (B) The SD1 exists in eight copies in the 3D7 genome with a slight variation in respect to the rif gene. Homologous rif copies, with > 95% sequence homology, in between the SD1s are shown with the same color. Crosses indicate breakpoints of each SD1.
Mentions: Comparative analysis of the P. falciparum genome with rodent plasmodium species has disclosed synteny breaks at the boundaries of the subtelomeric compartments [18]. Here, we have analysed the subtelomeric gene content of the 3D7 genome by grouping the genes into families as shown in Figure 1. Eight homologous regions were found, all sharing the same genomic organization being located on seven chromosomes (Chromosomes 1, 2, 3, 6, 7, 10 and 11). This duplicated DNA segment (named SD1) was found to contain six genes: rif, pfmc-2tm, a var pseudogene and three hypothetical genes (n-, o- and q-gene) (Figure 2A). The breakpoints of these segmental duplicons vary slightly, with the 5' break point being either within or downstream with respect to the rif gene and the 3' break point being either upstream or downstream of the var pseudogene. The most extended duplicated loci (approximately 32 kb in size) are both located on chromosome 6, but on opposite chromosomal ends. Although the rif genes are not identical in-between the SD1, homologous rif copies can be found within all SD1 (Figure 2B). Most of the genes within SD1 encode PEXEL-containing export proteins, with the exception of the q-gene and the var pseudogenes (Additional File 2). SD1-fragments harbouring only two or three of the SD1- genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome (Additional File 1).

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