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. 2024 Sep 26:9:551.
doi: 10.12688/wellcomeopenres.22983.1. eCollection 2024.

Chromosomal reference genome sequences for the malaria mosquito, Anopheles coustani, Laveran, 1900

Lemonde B A Bouafou  1   2 , Diego Ayala  1   3 , Boris K Makanga  4 , Nil Rahola  1   2 , Harriet F Johnson  5 , Haynes Heaton  6 , Martin G Wagah  7 , Joanna C Collins  7 , Ksenia Krasheninnikova  7 , Sarah E Pelan  7 , Damon-Lee B Pointon  7 , Ying Sims  7 , James W Torrance  7 , Alan Tracey  7 , Marcela Uliano-Silva  7 , Jonathan M D Wood  7 , Katharina von Wyschetzki  7 ; Scientific Operations: DNA Pipelines collective; Shane A McCarthy  7   8 , Daniel E Neafsey  9   10 , Alex Makunin  7 , Mara K N Lawniczak  7
Affiliations

Chromosomal reference genome sequences for the malaria mosquito, Anopheles coustani, Laveran, 1900

Lemonde B A Bouafou et al. Wellcome Open Res. .

Abstract

We present genome assembly from individual female An. coustani (African malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 270 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled for both species. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

Keywords: African malaria mosquito; Anopheles coustani; 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 coustani assembly idAnoCousDA_361_x.2.
The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 269,999,061 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 (97,602,170 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 sequence lengths (94,852,749 and 274,232 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/Anopheles%20coustani/dataset/CALSDV01/snail.
Figure 2.
Figure 2.. Blob plot of base coverage in a subset of idAnoCousDA_361_x 10x linked reads against GC proportion for An. coustani assembly idAnoCousDA_361_x.2.
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/Anopheles%20coustani/dataset/CALSDV01/blob.
Figure 3.
Figure 3.. Genome assembly of An. coustani, idAnoCousDA_361_x.2: Hi-C contact map.
Visualised in HiGlass. Chromosomes order: 3RL, 2RL, X, then remaining samples. Off-diagonal signal in 2L indicates a heterozygous inversion in the individual idAnoCousDA-364_x used for Hi-C. The interactive Hi-C map can be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=TOv9LjXMTYKBy8dC3rTKgQ.
Figure 4.
Figure 4.. Alignment dotplot between genome assemblies of An. coustani, idAnoCousDA_361_x.2 and An. atroparvus, AatrE4.
Visualised in D-Genies. Chromosome arms arrangement is the same for these representatives of Anopheles subgenus.
Figure 5.
Figure 5.. Sequence similarity heatmap for genome assembly of An. coustani, idAnoCousDA_361_x.2.
Produced with StainedGlass, visualised in HiGlass. Chromosomes order: 2RL, 3RL, X - followed by the remaining scaffolds. Darker colours represent higher sequence similarity, notably at pericentric and intercalary heterochromatin as well as in unassembled X-linked scaffolds.
See this image and copyright information in PMC

References

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