Mitotic-Chromosome-Based Physical Mapping of the Culex quinquefasciatus Genome

Abstract

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.

Comparative Transcriptomics Reveals Key Gene Expression Differences between Diapausing and Non-Diapausing Adults of Culex pipiens

“…quinquefasciatus genome (N50 = 476 kb) and low chromosomal assignment of the total genome assembly (13%) emphasize the need for further investigation of the Cx . pipiens complex [ 64 , 65 ]. Furthermore, the absence of a full physical map limits the prospect of genome-wide association studies, and many transcripts are hypothetical proteins of unknown ontology.…”

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

“…In total, 12 matches to the genetic linkage groups were established. Also, 12 matches were made to the mitotic chromosomes physical map described recently [ 7 ]. Locations of 13 supercontigs and 2cDNA probes were previously unknown for polytene chromosomes, but were found either for genetic linkage groups [ 6 ] or mitotic chromosomes [ 7 ], which enabled the integration of the data.…”

“…However, genetic linkage mapping reveals only the relative positions of these supercontigs in each of three linkage groups. Recently reported mitotic chromosomes based physical mapping [ 7 ] reveals physical location of 37 supercontigs, but this method lacks resolution, reporting, for example two supercontigs 3.205 and 3.99 belonging to the same location. Also, due to the short length of mitotic chromosomes it is impossible to infer the supercontig orientation within the chromosome, which is important for advancing genome assembly.…”

“…Chromosome images were completely straightened and robust landmarks to distinguish chromosome arms were established. This map adopted a chromosome nomenclature of the genetic linkage map developed for the C. pipiens complex [ 6 ] and for mitotic chromosomes of Culex quinquefasciatus [ 7 ]. The polytene and linkage maps were matched by placement of two genetic markers and 10 supercontigs carrying genetic markers to the chromosomes, based on fluorescent in situ hybridization (FISH) results.…”

Chromatin Structure and Function in Mosquitoes

“…aegypti ( Sharakhova et al, 2011 ; Timoshevskiy et al, 2013 , 2014 ), Cx. quinquefasciatus ( Naumenko et al, 2015 ), Cx. tarsalis ( Little, 2020 ), and several Anopheles species ( Cornel and Collins, 2000 ; Sharakhov et al, 2002 , 2004 , 2016 ; Sharakhova et al, 2010 ; George et al, 2010 , 2020 ; Xia et al, 2010 ; Jiang et al, 2014 ; Artemov et al, 2015 , 2017 , 2018 ; Neafsey et al, 2015 ; Wei et al, 2017 ; Lukyanchikova et al, 2020 ; Waterhouse et al, 2020 ), and they contributed not only to the improvement of the genomes annotation, by assessing the ordering and orientation of the contigs and scaffolds, but also to the study of the organization of centromeres in different cell types ( Sharakhova et al, 2019 ; Lukyanchikova et al, 2020 ).…”