A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number
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 va...
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ftdoajarticles:oai:doaj.org/article:9bcd982b88f4429092feb969a7cf8839 2023-05-15T15:17:11+02:00 A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number Ribacke Ulf Mok Bobo W Sherwood Ellen Wahlgren Mats 2008-03-01T00:00:00Z https://doi.org/10.1186/1475-2875-7-46 https://doaj.org/article/9bcd982b88f4429092feb969a7cf8839 EN eng BMC http://www.malariajournal.com/content/7/1/46 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-7-46 1475-2875 https://doaj.org/article/9bcd982b88f4429092feb969a7cf8839 Malaria Journal, Vol 7, Iss 1, p 46 (2008) Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2008 ftdoajarticles https://doi.org/10.1186/1475-2875-7-46 2022-12-31T01:45:04Z 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 ≈ 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 ≈ 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 ... Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Rif ENVELOPE(-16.172,-16.172,66.526,66.526) Malaria Journal 7 1 46 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Ribacke Ulf Mok Bobo W Sherwood Ellen Wahlgren Mats A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
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 ≈ 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 ≈ 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 ... |
format |
Article in Journal/Newspaper |
author |
Ribacke Ulf Mok Bobo W Sherwood Ellen Wahlgren Mats |
author_facet |
Ribacke Ulf Mok Bobo W Sherwood Ellen Wahlgren Mats |
author_sort |
Ribacke Ulf |
title |
A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number |
title_short |
A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number |
title_full |
A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number |
title_fullStr |
A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number |
title_full_unstemmed |
A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number |
title_sort |
highly conserved segmental duplication in the subtelomeres of plasmodium falciparum chromosomes varies in copy number |
publisher |
BMC |
publishDate |
2008 |
url |
https://doi.org/10.1186/1475-2875-7-46 https://doaj.org/article/9bcd982b88f4429092feb969a7cf8839 |
long_lat |
ENVELOPE(-16.172,-16.172,66.526,66.526) |
geographic |
Arctic Rif |
geographic_facet |
Arctic Rif |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 7, Iss 1, p 46 (2008) |
op_relation |
http://www.malariajournal.com/content/7/1/46 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-7-46 1475-2875 https://doaj.org/article/9bcd982b88f4429092feb969a7cf8839 |
op_doi |
https://doi.org/10.1186/1475-2875-7-46 |
container_title |
Malaria Journal |
container_volume |
7 |
container_issue |
1 |
container_start_page |
46 |
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1766347457642364928 |