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. 2024 Oct 16:9:599.
doi: 10.12688/wellcomeopenres.23198.1. eCollection 2024.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles nili, Theobald, 1904

Sandrine Eveline Nsango  1 , Diego Ayala  2   3 , Jean-Pierre Agbor  1 , Harriet F Johnson  4 , Haynes Heaton  5 , Martin G Wagah  6 , Joanna C Collins  6 , Ksenia Krasheninnikova  6 , Sarah E Pelan  6 , Damon-Lee B Pointon  6 , Ying Sims  6 , James W Torrance  6 , Alan Tracey  6 , Marcela Uliano-Silva  6 , Jonathan M D Wood  6 , Katharina von Wyschetzki  6 ; Wellcome Sanger Institute Scientific Operations: Sequencing Operations; Shane A McCarthy  6   7 , Daniel E Neafsey  8   9 , Alex Makunin  6 , Mara K N Lawniczak  6
Affiliations

A chromosomal reference genome sequence for the malaria mosquito, Anopheles nili, Theobald, 1904

Sandrine Eveline Nsango et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual male Anopheles nili (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 195 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

Keywords: African malaria mosquito; Anopheles nili; chromosomal; genome sequence.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Snail plot summary of assembly statistics for Anopheles nili assembly idAnoNiliSN_F5_01.
The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 195,236,048 bp assembly. The distribution of sequence lengths is shown in dark grey with the plot radius scaled to the longest sequence present in the assembly (78,106,464 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 sequence lengths (75,938,266 and 1,265,936 bp), respectively. The pale grey spiral shows the cumulative sequence count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the diptera_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idAnoNiliSN_F5_01/dataset/CALSGA01/snail.
Figure 2.
Figure 2.. Blob plot of base coverage in a subset of idAnoNiliSN_F5_01 10x linked reads against GC proportion for An. nili assembly idAnoNiliSN_F5_01.
Chromosomes are coloured by phylum. Circles are sized in proportion to chromosome length. Histograms show the distribution of chromosome length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idAnoNiliSN_F5_01/dataset/CALSGA01/blob.
Figure 3.
Figure 3.. Hi-C contact map for genome assembly of An. nili, idAnoNiliSN_F5_01.
Visualised in HiGlass. Chromosomes order: 2RL, 3RL, X, then remaining scaffolds. Signal from Y-linked scaffolds is weak because while the individual used for PacBio was male, the individual used for Hi-C was female. The white regions in the autosomes are caused by repetitive regions with lower read mapping. The interactive Hi-C map can be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=JFXN0-4tSx6yNkF8v9PnSg.
Figure 4.
Figure 4.. Alignment dotplot between genome assemblies of An. nili (idAnoNiliSN_F5_01) and An. gambiae, AgamP4 (PEST).
Visualised in DGenies. Chromosome arms correspondence (nili-gambiae): 2R-2R, 2L-3L, 3R-3R, 3L-2L in agreement with .
Figure 5.
Figure 5.. Sequence similarity heatmap for genome assembly of An. nili, idAnoNiliSN_F5_01.
Produced with StainedGlass, visualised in HiGlass. Chromosomes order: 3RL, 2RL, X, followed by the remaining scaffolds. Darker colours represent higher sequence similarity, notably at pericentric and intercalary heterochromatin as well as in unassembled scaffolds.
See this image and copyright information in PMC

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