The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere

• Main Authors: Austin Compton, Jiangtao Liang, Chujia Chen, Varvara Lukyanchikova, Yumin Qi, Mark Potters, Robert Settlage, Dustin Miller, Stéphane Deschamps, Chunhong Mao, Victor Llaca, Igor V. Sharakhov, Zhijian Tu
• Format: Article
• Language: English
• Published: Oxford University Press 2020-10-01
• Series: G3: Genes, Genomes, Genetics
• Subjects: genome assembly; anopheles albimanus; oxford nanopore; hi-c; bionano
• Online Access: http://g3journal.org/lookup/doi/10.1534/g3.120.401654

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.