Genomic sequence capture of Plasmodium relictum in experimentally infected birds
Abstract Background Sequencing parasite genomes in the presence of host DNA is challenging. Sequence capture can overcome this problem by using RNA probes that hybridize with the parasite DNA and then are removed from solution, thus isolating the parasite DNA for efficient sequencing. Methods Here w...
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| Format: | Article |
| Language: | English |
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BMC
2022-07-01
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| Series: | Parasites & Vectors |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13071-022-05373-w |
| _version_ | 1828375001397460992 |
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| author | Vincenzo A. Ellis Victor Kalbskopf Arif Ciloglu Mélanie Duc Xi Huang Abdullah Inci Staffan Bensch Olof Hellgren Vaidas Palinauskas |
| author_facet | Vincenzo A. Ellis Victor Kalbskopf Arif Ciloglu Mélanie Duc Xi Huang Abdullah Inci Staffan Bensch Olof Hellgren Vaidas Palinauskas |
| author_sort | Vincenzo A. Ellis |
| collection | DOAJ |
| description | Abstract Background Sequencing parasite genomes in the presence of host DNA is challenging. Sequence capture can overcome this problem by using RNA probes that hybridize with the parasite DNA and then are removed from solution, thus isolating the parasite DNA for efficient sequencing. Methods Here we describe a set of sequence capture probes designed to target 1035 genes (c. 2.5 Mbp) of the globally distributed avian haemosporidian parasite, Plasmodium relictum. Previous sequence capture studies of avian haemosporidians from the genus Haemoproteus have shown that sequencing success depends on parasitemia, with low-intensity, chronic infections (typical of most infected birds in the wild) often being difficult to sequence. We evaluate the relationship between parasitemia and sequencing success using birds experimentally infected with P. relictum and kept under laboratory conditions. Results We confirm the dependence of sequencing success on parasitemia. Sequencing success was low for birds with low levels of parasitemia (< 1% infected red blood cells) and high for birds with higher levels of parasitemia. Plasmodium relictum is composed of multiple lineages defined by their mitochondrial DNA haplotype including three that are widespread (SGS1, GRW11, and GRW4); the probes successfully isolated DNA from all three. Furthermore, we used data from 25 genes to describe both among- and within-lineage genetic variation. For example, two samples of SGS1 isolated from different host species differed by 11 substitutions across those 25 genes. Conclusions The sequence capture approach we describe will allow for the generation of genomic data that will contribute to our understanding of the population genetic structure and evolutionary history of P. relictum, an extreme host generalist and widespread parasite. Graphical Abstract |
| first_indexed | 2024-04-14T07:41:35Z |
| format | Article |
| id | doaj.art-a1de9cad74d6469480d6e10e18f91f04 |
| institution | Directory Open Access Journal |
| issn | 1756-3305 |
| language | English |
| last_indexed | 2024-04-14T07:41:35Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Parasites & Vectors |
| spelling | doaj.art-a1de9cad74d6469480d6e10e18f91f042022-12-22T02:05:29ZengBMCParasites & Vectors1756-33052022-07-0115111210.1186/s13071-022-05373-wGenomic sequence capture of Plasmodium relictum in experimentally infected birdsVincenzo A. Ellis0Victor Kalbskopf1Arif Ciloglu2Mélanie Duc3Xi Huang4Abdullah Inci5Staffan Bensch6Olof Hellgren7Vaidas Palinauskas8Molecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityMolecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityMolecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityMolecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityMolecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityDepartment of Parasitology, Faculty of Veterinary Medicine, Erciyes UniversityMolecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityMolecular Ecology and Evolution Laboratory, Department of Biology, Lund UniversityNature Research CentreAbstract Background Sequencing parasite genomes in the presence of host DNA is challenging. Sequence capture can overcome this problem by using RNA probes that hybridize with the parasite DNA and then are removed from solution, thus isolating the parasite DNA for efficient sequencing. Methods Here we describe a set of sequence capture probes designed to target 1035 genes (c. 2.5 Mbp) of the globally distributed avian haemosporidian parasite, Plasmodium relictum. Previous sequence capture studies of avian haemosporidians from the genus Haemoproteus have shown that sequencing success depends on parasitemia, with low-intensity, chronic infections (typical of most infected birds in the wild) often being difficult to sequence. We evaluate the relationship between parasitemia and sequencing success using birds experimentally infected with P. relictum and kept under laboratory conditions. Results We confirm the dependence of sequencing success on parasitemia. Sequencing success was low for birds with low levels of parasitemia (< 1% infected red blood cells) and high for birds with higher levels of parasitemia. Plasmodium relictum is composed of multiple lineages defined by their mitochondrial DNA haplotype including three that are widespread (SGS1, GRW11, and GRW4); the probes successfully isolated DNA from all three. Furthermore, we used data from 25 genes to describe both among- and within-lineage genetic variation. For example, two samples of SGS1 isolated from different host species differed by 11 substitutions across those 25 genes. Conclusions The sequence capture approach we describe will allow for the generation of genomic data that will contribute to our understanding of the population genetic structure and evolutionary history of P. relictum, an extreme host generalist and widespread parasite. Graphical Abstracthttps://doi.org/10.1186/s13071-022-05373-wAvian malariaParasitemiaHaemosporidaHybrid enrichmentParasite genomics |
| spellingShingle | Vincenzo A. Ellis Victor Kalbskopf Arif Ciloglu Mélanie Duc Xi Huang Abdullah Inci Staffan Bensch Olof Hellgren Vaidas Palinauskas Genomic sequence capture of Plasmodium relictum in experimentally infected birds Parasites & Vectors Avian malaria Parasitemia Haemosporida Hybrid enrichment Parasite genomics |
| title | Genomic sequence capture of Plasmodium relictum in experimentally infected birds |
| title_full | Genomic sequence capture of Plasmodium relictum in experimentally infected birds |
| title_fullStr | Genomic sequence capture of Plasmodium relictum in experimentally infected birds |
| title_full_unstemmed | Genomic sequence capture of Plasmodium relictum in experimentally infected birds |
| title_short | Genomic sequence capture of Plasmodium relictum in experimentally infected birds |
| title_sort | genomic sequence capture of plasmodium relictum in experimentally infected birds |
| topic | Avian malaria Parasitemia Haemosporida Hybrid enrichment Parasite genomics |
| url | https://doi.org/10.1186/s13071-022-05373-w |
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