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. 2024 Sep 26:9:553.
doi: 10.12688/wellcomeopenres.22988.1. eCollection 2024.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles maculipalpis, Giles, 1902

Nil Rahola  1   2 , Diego Ayala  1   3 , Lemonde B A Bouafou  1   2 , Boris K Makanga  4 , 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 ; Wellcome Sanger Institute Scientific Operations: Sequencing Operations; Shane A McCarthy  7 , Daniel E Neafsey  7 , Alex Makunin  7 , Mara K N Lawniczak  7
Affiliations

A chromosomal reference genome sequence for the malaria mosquito, Anopheles maculipalpis, Giles, 1902

Nil Rahola et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual female Anopheles maculipalpis (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 224 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 maculipalpis; 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 maculipalpis assembly.
The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 224,074,805 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 (98,751,411 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 sequence lengths (92,548,589 and 21,651,475 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/idAnoMacuDA_375_x/dataset/CALSDU01/snail.
Figure 2.
Figure 2.. Blob plot of base coverage in a subset of idAnoMacuDA-375_x 10x linked reads against GC proportion for An. maculipalpis assembly idAnoMacuDA_375_x.
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/idAnoMacuDA_375_x/dataset/CALSDU01/blob.
Figure 3.
Figure 3.. Genome assembly of An. maculipalpis, idAnoMacuDA_375_x: Hi-C contact map.
Visualised in HiGlass. Chromosomes are ordered as 2RL, 3RL, X, then remaining scaffolds. The interactive Hi-C map can be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=LR0ErKCBRiyLbpoq-qAnnw.
Figure 4.
Figure 4.. Alignment dotplot between genome assemblies of An. maculipalpis idAnoMacuDA_375_x and An. gambiae, AgamP4 (PEST).
Chromosome arms correspondence (maculipalpus-gambiae): 2R-2R, 2L-3L, 3R-3R, 3L-2L in agreement with .
Figure 5.
Figure 5.. Sequence similarity heatmap for genome assembly of An. maculipalpis, idAnoMacuDA_375_x.
Produced with StainedGlass, visualised in HiGlass. CChromosomes are ordered as 2RL, 3RL, X, then remaining scaffolds. Darker colours represent higher sequence similarity, notably at putative centromeres and terminal part of X.
See this image and copyright information in PMC

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