Biology
Document Type
Article
Abstract
Background: Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. Methods: We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. Results: Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. Conclusions: The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS. Graphical Abstract: (Figure presented.) © The Author(s) 2024.
Publication Title
Parasites and Vectors
Publication Date
12-2024
Volume
17
Issue
1
ISSN
1756-3305
DOI
10.1186/s13071-024-06158-z
Keywords
Aedes albopictus, population genomics, SNP chip, validation
Repository Citation
Cosme, Luciano Veiga; Corley, Margaret; Johnson, Thomas; Severson, Dave W.; Yan, Guiyun; Wang, Xiaoming; Beebe, Nigel; Maynard, Andrew; Bonizzoni, Mariangela; Khorramnejad, Ayda; Martins, Ademir Jesus; Lima, José Bento Pereira; and Livdahl, Todd P., "A genotyping array for the globally invasive vector mosquito, Aedes albopictus" (2024). Biology. 21.
https://commons.clarku.edu/faculty_biology/21
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright
Publisher source must be acknowledged with citation:
Cosme, L. V., Corley, M., Johnson, T., Severson, D. W., Yan, G., Wang, X., ... & Caccone, A. (2024). A genotyping array for the globally invasive vector mosquito, Aedes albopictus. Parasites & Vectors, 17(1), 106.
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