Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

Abstract

Background Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. Findings In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis. Conclusion The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

Anopheles mosquitoes reveal new principles of 3D genome organization in insects

“…Our dot plot alignment of the AcolN2 genome assembly with the AgamP4 assembly and with the recently sequenced genome AcolMOP1 of the An. coluzzii MOPTI strain 38 demonstrated that all these assemblies have the standard arrangement with respect to the 2Ru inversion (Supplementary Fig. 1A, B ).…”

“…While this work was in preparation, several Anopheles genome assemblies were generated using Hi-C and complementary approaches 36 , 38 , 55 – 57 . Further comparisons of these assemblies may reveal even strain-specific features of the linear and spatial genome organization.…”

plotsr: Visualising structural similarities and rearrangements between multiple genomes

“…plotsr is highly adjustable and allows additional visualisation of genomic features as well as zoom-in views on specific regions. It generates publication-quality visualisations (Zamyatin et al, 2021;Zhang et al, 2021;Li et al, 2021) and will help towards a better understanding of differences within genomes. Given the great importance of genomic analysis in many research fields, we are continuously developing plotsr to add more useful parameters allowing for more control and customisation.…”

The chromosome-level genome assembly of Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae)

“…GeMoMa predicted genes using protein homology, intron conservation, and transcripts. GeMoMa was used with the parameters “GeMoMa.c = 0.5 GeMoMa.p = 8” and protein sequences from five species, namely Contarinia nasturtii 42 (GCF_009176525.2), Bradysia coprophila 57 (GCF_014529535.1), Anopheles arabiensis 58 (GCF_016920715.1), Drosophila melanogaster 59 (GCF_000001215.4), and Bombyx mori 60 (GCF_014905235.1). In addition, the protein sequences obtained from the same set of five species used in the GeMoMa analysis were included in the MAKER pipeline as supporting evidence for protein homology.…”