A genotyping array for the globally invasive vector mosquito, Aedes albopictus
Authors: 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 , Munstermann Leonard E. , Surendran Sinnathamby N. , Chen Chun-Hong , Maringer Kevin , Wahid Isra , Mukherjee Shomen , Xu Jiannon , Fontaine Michael C. , Estallo Elizabet L. , Stein Marina , Livdahl Todd , Scaraffia Patricia Y. , Carter Brendan H. , Mogi Motoyoshi , Tuno Nobuko , Mains James W. , Medley Kim A. , Bowles David E. , Gill Richard J. , Eritja Roger , González-Obando Ranulfo , Trang Huynh T. T. , Boyer Sébastien , Abunyewa Ann-Marie , Hackett Kayleigh , Wu Tina , Nguyễn Justin , Shen Jiangnan , Zhao Hongyu , Crawford Jacob E. , Armbruster Peter , Caccone Adalgisa 
Published: March 2024

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