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However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step toward the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp Telomeric Repeat Unit (TRU) and are confirmed by analyzing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step toward resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.<\/jats:p>","DOI":"10.1534\/g3.120.401654","type":"journal-article","created":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T22:35:42Z","timestamp":1599172542000},"page":"3811-3819","source":"Crossref","is-referenced-by-count":25,"title":["The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere"],"prefix":"10.1093","volume":"10","author":[{"given":"Austin","family":"Compton","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Virginia Tech, Blacksburg, VA24061"},{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangtao","family":"Liang","sequence":"additional","affiliation":[{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"},{"name":"Department of Entomology, Virginia Tech, Blacksburg, VA24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chujia","family":"Chen","sequence":"additional","affiliation":[{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"},{"name":"Genetics Bioinformatics and Computational Biology PhD program, Virginia Tech, Blacksburg, VA 24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Varvara","family":"Lukyanchikova","sequence":"additional","affiliation":[{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"},{"name":"Department of Entomology, Virginia Tech, Blacksburg, VA24061"},{"name":"Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumin","family":"Qi","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Virginia Tech, Blacksburg, VA24061"},{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Potters","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Virginia Tech, Blacksburg, VA24061"},{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Settlage","sequence":"additional","affiliation":[{"name":"Advanced Research Computing, Virginia Tech, Blacksburg, VA24061"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dustin","family":"Miller","sequence":"additional","affiliation":[{"name":"MR4 Program, Center for Disease Control Foundation CDCF, Atlanta, GA30329"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Deschamps","sequence":"additional","affiliation":[{"name":"Corteva Agriscience, Johnston, IA 50131"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunhong","family":"Mao","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA 22911"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Llaca","sequence":"additional","affiliation":[{"name":"Corteva Agriscience, Johnston, IA 50131"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Igor V","family":"Sharakhov","sequence":"additional","affiliation":[{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"},{"name":"Department of Entomology, Virginia Tech, Blacksburg, VA24061"},{"name":"Genetics Bioinformatics and Computational Biology PhD program, Virginia Tech, Blacksburg, VA 24061"},{"name":"Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhijian","family":"Tu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Virginia Tech, Blacksburg, VA24061"},{"name":"Fralin Life Science Institute, Virginia Tech, Blacksburg, VA24061"},{"name":"Genetics Bioinformatics and Computational Biology PhD program, Virginia Tech, Blacksburg, VA 24061"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,1]]},"reference":[{"key":"2021042107464581300_bib1","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1186\/s12936-016-1421-4","article-title":"Spatial distributions of Anopheles species in relation to malaria incidence at 70 localities in the highly endemic Northwest and South Pacific coast regions of Colombia.","volume":"15","author":"Ahumada","year":"2016","journal-title":"Malar. 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