PT  - JOURNAL ARTICLE
AU  - Compton, Austin
AU  - Liang, Jiangtao
AU  - Chen, Chujia
AU  - Lukyanchikova, Varvara
AU  - Qi, Yumin
AU  - Potters, Mark
AU  - Settlage, Robert
AU  - Miller, Dustin
AU  - Deschamps, Stéphane
AU  - Mao, Chunhong
AU  - Llaca, Victor
AU  - Sharakhov, Igor V.
AU  - Tu, Zhijian
TI  - The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere
AID  - 10.1534/g3.120.401654
DP  - 2020 Oct 01
TA  - G3: Genes|Genomes|Genetics
PG  - 3811--3819
VI  - 10
IP  - 10
4099  - http://www.g3journal.org/content/10/10/3811.short
4100  - http://www.g3journal.org/content/10/10/3811.full
AB  - Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. 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.