An integrated linkage, chromosome, and genome map for the yellow fever mosquito Aedes aegypti

Abstract

Background: Aedes aegypti, the yellow fever mosquito, is an efficient vector of arboviruses and a convenient model system for laboratory research. Extensive linkage mapping of morphological and molecular markers localized a number of quantitative trait loci (QTLs) related to the mosquito's ability to transmit various pathogens. However, linking the QTLs to Ae. aegypti chromosomes and genomic sequences has been challenging because of the poor quality of polytene chromosomes and the highly fragmented genome assembly for this species.

Methodology/principal findings: Based on the approach developed in our previous study, we constructed idiograms for mitotic chromosomes of Ae. aegypti based on their banding patterns at early metaphase. These idiograms represent the first cytogenetic map developed for mitotic chromosomes of Ae. aegypti. One hundred bacterial artificial chromosome clones carrying major genetic markers were hybridized to the chromosomes using fluorescent in situ hybridization. As a result, QTLs related to the transmission of the filarioid nematode Brugia malayi, the avian malaria parasite Plasmodium gallinaceum, and the dengue virus, as well as sex determination locus and 183 Mbp of genomic sequences were anchored to the exact positions on Ae. aegypti chromosomes. A linear regression analysis demonstrated a good correlation between positions of the markers on the physical and linkage maps. As a result of the recombination rate variation along the chromosomes, 12 QTLs on the linkage map were combined into five major clusters of QTLs on the chromosome map.

Conclusion: This study developed an integrated linkage, chromosome, and genome map-iMap-for the yellow fever mosquito. Our discovery of the localization of multiple QTLs in a few major chromosome clusters suggests a possibility that the transmission of various pathogens is controlled by the same genomic loci. Thus, the iMap will facilitate the identification of genomic determinants of traits responsible for susceptibility or refractoriness of the mosquito to diverse pathogens.

Figure 1. The construction of idiograms for mitotic chromosome of Aedes aegypti.

Early metaphase chromosomes of Ae. aegypti stained with YOYO-1 iodide (A) were utilized for idiogram (B) development. Chromosome numbers are shown on the top of each chromosome. Chromosomal arms p and q and numbered divisions and subdivisions are shown on the left side of the idiograms. Landmarks are indicated by asterisks.

Figure 2. FISH on early metaphase chromosomes of Aedes aegypti.

BAC DNA probes labeled by CY3 (red) and Cy5 (blue) were hybridized to the chromosomes stained with YOYO-1 iodide. Positions of the BAC clones on chromosomes 1 (A), 2 (B), and 3 (C) are indicated by arrows.

Figure 3. Multicolor FISH on mitotic and polytene chromosomes of Aedes aegypti.

DNA probes labeled with fluorescein, Cy3, Cy5, and combinations of these dyes were hybridized to the prophase (A, B, C) and polytene chromosomes (D) stained by DAPI. The maximum resolutions of ∼0.5 Mb between markers LF179 and LF314 (A) and 300 kb between markers LF407 and Amyl (C) are obtained on prophase and polytene chromosomes, respectively.

Figure 4. Integrated linkage, chromosome, and genome map–iMap of Ae. aegypti.

Chromosome divisions and subdivisions are indicated on the left sides of the idiograms. The positions of genetic markers are shown on the right sides of the idiograms. The numbers of supercontigs in brackets are indicated by last 2–4 digits of supercontig ID. Anchor markers for dengue virus 2 (DEN2) midgut infection barrier (MIB) QTL are in purple; for DEN2 midgut escape barrier (MEB) QTL – in brown; filarial worm QTL - in blue; malaria parasite QTL – in green; for sex determination locus - in red. LF 98 is QTL anchor marker for both filarial worm and malaria parasite pathogens. The orientations of 4 supercontigs are demonstrated by arrows. Major locations of the BAC clones with multiple signals on the chromosomes are indicated by asterisks. Two BAC clones and 3 supercontigs in conflict with previous genetic mapping/genome assembly are in bold.

Figure 5. Linear regression analyses of the physical position of a gene as a function of its cM position.

For chromosomes 1 (A), 2 (B), and 3 (C), the linear regression model is provided along with the probability that the slope is zero and the proportion of the total variance accounted for by the linear model (R²).

Figure 6. Localization of QTLs to various pathogens on linkage and chromosome maps of Aedes aegypti.

The linkage positions of QTLs in cM on linkage groups I, II, and III are indicated on the left side. QTLs to dengue virus 2 (DEN2), midgut infection barrier (MIB), DEN2 midgut escape barrier (MEB), malaria parasite, and filarial worm are shown on the right sides of chromosomes 1, 2, and 3.