The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles.
The genome of the Neotropical malaria vector Anopheles albimanus was sequenced as part of the 16 Anopheles Genomes Project published in 2015. The draft assembly of this species consisted of 204 scaffolds with an N50 scaffold size of 18.1 Mb and a total assembly size of 170.5 Mb. It was among the smallest genomes with the longest scaffolds in the 16 Anopheles species cluster, making An. albimanus the logical choice for anchoring the genome assembly to chromosomes. In this study, we developed a high-resolution cytogenetic photomap with completely straightened polytene chromosomes from the salivary glands of the mosquito larvae. Based on this photomap, we constructed a chromosome-based genome assembly using fluorescent in situ hybridization of PCR-amplified DNA probes. Our physical mapping, assisted by an ortholog-based bioinformatics approach, identified and corrected nine misassemblies in five large genomic scaffolds. Misassemblies mostly occurred in junctions between contigs. Our comparative analysis of scaffolds with the An. gambiae genome detected multiple genetic exchanges between pericentromeric regions of chromosomal arms caused by partial-arm translocations. The final map consists of 40 ordered genomic scaffolds and corrected fragments of misassembled scaffolds. The An. albimanus physical map comprises 98.2% of the total genome assembly and represents the most complete genome map among mosquito species. This study demonstrates that physical mapping is a powerful tool for correcting errors in draft genome assemblies and for creating chromosome-anchored reference genomes.
Laboratory for Ecology, Genetics, and Environmental Protection, Tomsk State University, 634050, Russia.
Gleb N
GN
Artemov
Department of Entomology and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
Ashley N
AN
Peery
The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.|Department of Biochemistry and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
Xiaofang
X
Jiang
The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.|Department of Biochemistry and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
Zhijian
Z
Tu
Laboratory for Ecology, Genetics, and Environmental Protection, Tomsk State University, 634050, Russia.
Vladimir N
VN
Stegniy
Laboratory for Ecology, Genetics, and Environmental Protection, Tomsk State University, 634050, Russia msharakh@vt.edu igor@vt.edu.|Department of Entomology and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
Maria V
MV
Sharakhova
Laboratory for Ecology, Genetics, and Environmental Protection, Tomsk State University, 634050, Russia msharakh@vt.edu igor@vt.edu.|Department of Entomology and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.|The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061.
Igor V
0000-0003-0752-3747
IV
Sharakhov
D000818:Animals; D000852:Anopheles / Q000235:genetics* / Q000472:pathogenicity; D002874:Chromosome Mapping / Q000379:methods*; D049750:Genome, Insect; D017404:In Situ Hybridization, Fluorescence; D008288:Malaria / Q000235:genetics* / Q000635:transmission; D059007:Polytene Chromosomes / Q000235:genetics; D012469:Salivary Glands; D014178:Translocation, Genetic
Anopheles albimanus; fluorescence in situ hybridization; mosquito genome; physical mapping; polytene chromosomes