BibTex format
@article{Cosme:2024:10.1186/s13071-024-06158-z,
author = {Cosme, LV and Corley, M and Johnson, T and Severson, DW and Yan, G and Wang, X and Beebe, N and Maynard, A and Bonizzoni, M and Khorramnejad, A and Martins, AJ and Lima, JBP and Munstermann, LE and Surendran, SN and Chen, C-H and Maringer, K and Wahid, I and Mukherjee, S and Xu, J and Fontaine, MC and Estallo, EL and Stein, M and Livdahl, T and Scaraffia, PY and Carter, BH and Mogi, M and Tuno, N and Mains, JW and Medley, KA and Bowles, DE and Gill, RJ and Eritja, R and González-Obando, R and Trang, HTT and Boyer, S and Abunyewa, A-M and Hackett, K and Wu, T and Nguyn, J and Shen, J and Zhao, H and Crawford, JE and Armbruster, P and Caccone, A},
doi = {10.1186/s13071-024-06158-z},
journal = {Parasites and Vectors},
title = {A genotyping array for the globally invasive vector mosquito, Aedes albopictus},
url = {http://dx.doi.org/10.1186/s13071-024-06158-z},
volume = {17},
year = {2024}
}
RIS format (EndNote, RefMan)
TY - JOUR
AB - BackgroundAlthough 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.MethodsWe 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.ResultsProbes 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 > 2
AU - Cosme,LV
AU - Corley,M
AU - Johnson,T
AU - Severson,DW
AU - Yan,G
AU - Wang,X
AU - Beebe,N
AU - Maynard,A
AU - Bonizzoni,M
AU - Khorramnejad,A
AU - Martins,AJ
AU - Lima,JBP
AU - Munstermann,LE
AU - Surendran,SN
AU - Chen,C-H
AU - Maringer,K
AU - Wahid,I
AU - Mukherjee,S
AU - Xu,J
AU - Fontaine,MC
AU - Estallo,EL
AU - Stein,M
AU - Livdahl,T
AU - Scaraffia,PY
AU - Carter,BH
AU - Mogi,M
AU - Tuno,N
AU - Mains,JW
AU - Medley,KA
AU - Bowles,DE
AU - Gill,RJ
AU - Eritja,R
AU - González-Obando,R
AU - Trang,HTT
AU - Boyer,S
AU - Abunyewa,A-M
AU - Hackett,K
AU - Wu,T
AU - Nguyn,J
AU - Shen,J
AU - Zhao,H
AU - Crawford,JE
AU - Armbruster,P
AU - Caccone,A
DO - 10.1186/s13071-024-06158-z
PY - 2024///
SN - 1756-3305
TI - A genotyping array for the globally invasive vector mosquito, Aedes albopictus
T2 - Parasites and Vectors
UR - http://dx.doi.org/10.1186/s13071-024-06158-z
VL - 17
ER -