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

Abstract

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 towards 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 analysing 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 towards 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.

Sequence, Chromatin and Evolution of Satellite DNA

“…Telomeres of lower Diptera, Anopheles , Rhynchosciara, and Chironomus are different from both microsatellite telomeres of most eukaryotes and retrotransposon telomeres of Drosophila . Lower Diptera telomeres carry long tandem repeats (satellites) and telomere elongation and maintenance has been suggested to take place by unequal crossover during homologous recombination [ 147 , 148 , 149 , 150 ].…”

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly

“…gambiae (AgamP4) genome (BUSCO 97.4%, contig N50 = 85 kb, scaffold N50 = 49 Mb), arguably the best characterized genome among malaria vectors ( Fig. 1a, Table 1, Additional file 1: Table S1, Additional file 1: Figures S3 and S5) [7,20,[24][25][26][27]. Furthermore, the concordance of short reads mapped to the assembly suggests that assembly errors are rare (short read consensus quality value or QV = 49.2, or~1 discrepancy per 83 kb), which is further supported by uniformly mapping long reads and a high-resolution Hi-C contact map (Fig.…”

Chromatin Structure and Function in Mosquitoes

“…Until recently, the application of Hi-C had been limited to the improvement of the genome assembly of several mosquito species: Culex quinquefasciatus ( Dudchenko et al, 2017 ), Aedes aegypti ( Dudchenko et al, 2017 ; Matthews et al, 2018 ), Ae. albopictus ( Palatini et al, 2020 ), Anopheles albimanus ( Compton et al, 2020a ), An. funestus ( Ghurye et al, 2019a , b ), An.…”