Simultaneous population genomics of hosts and their parasites with selective whole genome amplification
Date
2025-11-05
Journal Title
Journal ISSN
Volume Title
Publisher
Parasites & Vectors
Abstract
Background Generating parasite genomes is challenging when little of the DNA in infected host tissue is from the parasite. We used selective whole genome amplification (SWGA) to generate genomic data from wildlife samples of the avian haemosporidian Haemoproteus majoris (lineage PARUS1) and its host, the blue tit (Cyanistes caeruleus). Methods We used SWGA to amplify the parasite DNA in nine avian blood samples collected between 1996 and 2021, and subsequently performed short-read sequencing and bioinformatically separated the host and parasite reads in each sample. Results SWGA increased the percentage of parasite reads significantly. Sequencing to a depth of about 56 million reads (forward and reverse) per sample resulted on average (± standard error [SE]) in 11.3X ± 1.85 for the host genome and 1.17X ± 0.446 mean depth of coverage for the host and parasite, respectively, after SWGA. Furthermore, about 74% of the host genome (genome size approx. 1.2 Gb) and 33% of the parasite genome (approx. 23.9 Mb) had at least 1X coverage on average; two samples had 1X coverage of approximately 60% of the parasite genome. Parasite sequencing success was positively correlated with parasitemia. When comparing the parasite sequences in the four best samples, we identified 9895 sites (minimum 5X coverage) that varied among the infections. When filtering the full dataset to at least six samples per variant, we identified 14,512,339 and 7068 sites that varied among samples in the host and parasite populations, respectively, revealing variation among samples and years. Conclusions SWGA facilitates dual host-parasite population genomics in this system and will greatly expand our understanding of host-parasite interactions over space and time.
Description
This article was originally published in Parasites & Vectors. The version of record is available at: https://doi.org/10.1186/s13071-025-07087-1
© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line
to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Keywords
Avian malaria, Coevolution, Host genomics, Parasite evolution, Pathogen genomics
Citation
Ellis, V.A., Theodosopoulos, A., Sharma, I. et al. Simultaneous population genomics of hosts and their parasites with selective whole genome amplification. Parasites Vectors 18, 448 (2025). https://doi.org/10.1186/s13071-025-07087-1