Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly

In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology

Mitotic-chromosome-based physical mapping of the Culex quinquefasciatus genome

The genome assembly of southern house mosquito Cx. quinquefasciatus is represented by a high number of supercontigs with no order or orientation on the chromosomes. Although cytogenetic maps for the polytene chromosomes of this mosquito have been developed, their utilization for the genome mapping remains difficult because of the low number of high-quality spreads in chromosome preparations. Therefore, a simple and robust mitotic-chromosome-based approach for the genome mapping of Cx. quinquefasciatus still needs to be developed. In this study, we performed physical mapping of 37 genomic supercontigs using fluorescent in situ hybridization on mitotic chromosomes from imaginal discs of 4th instar larvae. The genetic linkage map nomenclature was adopted for the chromosome numbering based on the direct positioning of 58 markers that were previously genetically mapped. The smallest, largest, and intermediate chromosomes were numbered as 1, 2, and 3, respectively. For idiogram development, we analyzed and described in detail the morphology and proportions of the mitotic chromosomes. Chromosomes were subdivided into 19 divisions and 72 bands of four different intensities. These idiograms were used for mapping the genomic supercontigs/genetic markers. We also determined the presence of length polymorphism in the q arm of sex-determining chromosome 1 in Cx. quinquefasciatus related to the size of ribosomal locus. Our physical mapping and previous genetic linkage mapping resulted in the chromosomal assignment of 13% of the total genome assembly to the chromosome bands. We provided the first detailed description, nomenclature, and idiograms for the mitotic chromosomes of Cx. quinquefasciatus. Further application of the approach developed in this study will help to improve the quality of the southern house mosquito genome

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

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.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.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

Multicolor FISH on mitotic and polytene chromosomes of <i>Aedes aegypti</i>.

<p>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 <i>Amyl</i> (C) are obtained on prophase and polytene chromosomes, respectively.</p

Chromosome locations of genetic markers and genomic supercontigs.

<p>Major signals are indicated by asterisks, NA – not applicable, LG – Linkage Group.</p

Localization of QTLs to various pathogens on linkage and chromosome maps of <i>Aedes aegypti</i>.

<p>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.</p

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

<p>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).</p

Integrated linkage, chromosome, and genome map–iMap of <i>Ae. aegypti</i>.

<p>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.</p

The construction of idiograms for mitotic chromosome of <i>Aedes aegypti</i>.

<p>Early metaphase chromosomes of <i>Ae. aegypti</i> 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.</p

Mitotic-chromosome-based physical mapping of the Culex quinquefasciatus genome

The genome assembly of southern house mosquito Cx. quinquefasciatus is represented by a high number of supercontigs with no order or orientation on the chromosomes. Although cytogenetic maps for the polytene chromosomes of this mosquito have been developed, their utilization for the genome mapping remains difficult because of the low number of high-quality spreads in chromosome preparations. Therefore, a simple and robust mitotic-chromosome-based approach for the genome mapping of Cx. quinquefasciatus still needs to be developed. In this study, we performed physical mapping of 37 genomic supercontigs using fluorescent in situ hybridization on mitotic chromosomes from imaginal discs of 4th instar larvae. The genetic linkage map nomenclature was adopted for the chromosome numbering based on the direct positioning of 58 markers that were previously genetically mapped. The smallest, largest, and intermediate chromosomes were numbered as 1, 2, and 3, respectively. For idiogram development, we analyzed and described in detail the morphology and proportions of the mitotic chromosomes. Chromosomes were subdivided into 19 divisions and 72 bands of four different intensities. These idiograms were used for mapping the genomic supercontigs/genetic markers. We also determined the presence of length polymorphism in the q arm of sex-determining chromosome 1 in Cx. quinquefasciatus related to the size of ribosomal locus. Our physical mapping and previous genetic linkage mapping resulted in the chromosomal assignment of 13% of the total genome assembly to the chromosome bands. We provided the first detailed description, nomenclature, and idiograms for the mitotic chromosomes of Cx. quinquefasciatus. Further application of the approach developed in this study will help to improve the quality of the southern house mosquito genome