A standard cytogenetic map of Culex quinquefasciatus polytene chromosomes in application for fine-scale physical mapping

Abstract

BackgroundSouthern house mosquito Culex quinquefasciatus belongs to the C. pipiens cryptic species complex, with global distribution and unclear taxonomy. Mosquitoes of the complex can transmit human and animal pathogens, such as filarial worm, West Nile virus and avian malarial Plasmodium. Physical gene mapping is crucial to understanding genome organization, function, and systematic relationships of cryptic species, and is a basis for developing new vector control strategies. However, physical mapping was not established previously for Culex due to the lack of well-structured polytene chromosomes.MethodsInbreeding was used to diminish inversion polymorphism and asynapsis of chromosomal homologs. Identification of larvae of the same developmental stage using the shape of imaginal discs allowed achievement of uniformity in chromosomal banding pattern. This together with high-resolution phase-contrast photography enabled the development of a cytogenetic map. Fluorescent in situ hybridization was used for gene mapping.ResultsA detailed cytogenetic map of C. quinquefasciatus polytene chromosomes was produced. Landmarks for chromosome recognition and cytological boundaries for two inversions were identified. Locations of 23 genes belonging to 16 genomic supercontigs, and 2 cDNA were established. Six supercontigs were oriented and one was found putatively misassembled. The cytogenetic map was linked to the previously developed genetic linkage groups by corresponding positions of 2 genetic markers and 10 supercontigs carrying genetic markers. Polytene chromosomes were numbered according to the genetic linkage groups.ConclusionsThis study developed a new standard cytogenetic photomap of the polytene chromosomes for C. quinquefasciatus and was applied for the fine-scale physical mapping. It allowed us to infer chromosomal position of 1333 of annotated genes belonging to 16 genomic supercontigs and find orientation of 6 of these supercontigs; the new cytogenetic and previously developed genetic linkage maps were integrated based on 12 matches. The map will further assist in finding chromosomal position of the medically important and other genes, contributing into improvement of the genome assembly. Better assembled C. quinquefasciatus genome can serve as a reference for studying other vector species of C. pipiens complex and will help to resolve their taxonomic relationships. This, in turn, will contribute into future development of vector and disease control strategies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-0912-4) contains supplementary material, which is available to authorized users.

The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes

“…This inversion was previously identified in a cytogenetic study of Cx. quinquefasciatus and was called the 3Rb inversion [ 45 ].…”

“…Because the complexity of the Culex genome affects the quality of its polytene chromosomes, the identification of chromosomal rearrangements in this genus is difficult. Few inversions have been described in Culex [ 45 , 71 , 72 ]. In this study, Hi-C scaffolding led to identification of a polymorphic chromosomal inversion 3qB in the long arm of this chromosome in Cx.…”

“…Previously, the development of a cytogenetic map for the salivary gland polytene chromosomes of the JHB strain of Cx. quinquefasciatus demonstrated the presence of two distinct paracentric chromosomal inversions [ 45 ]. One of them was 3Rb in subdivisions 58C–59C.…”