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. 2024 Mar 26:8:74.
doi: 10.12688/wellcomeopenres.18854.2. eCollection 2023.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain

Tibebu Habtewold  1 , Martin Wagah  2 , Mgeni Mohamed Tambwe  3 , Sarah Moore  3   4 , Nikolai Windbichler  1 , George Christophides  1 , Harriet Johnson  5 , Haynes Heaton  6 , Joanna Collins  2 , Ksenia Krasheninnikova  2 , Sarah E Pelan  2 , Damon-Lee B Pointon  2 , Ying Sims  2 , James W Torrance  2 , Alan Tracey  2 , Marcela Uliano Da Silva  2 , Jonathan Md Wood  2 , Katharina von Wyschetzki  2 ; Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective; Shane A McCarthy  2 , Daniel E Neafsey  7   8 , Alex Makunin #  2 , Mara K N Lawniczak #  2
Affiliations

A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain

Tibebu Habtewold et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 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 gambiae; 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 An. gambiae assembly idAnoGamb_NW_F1_1.
The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 264,466,745 bp assembly. The distribution of chromosome lengths is shown in dark grey with the plot radius scaled to the longest chromosome present in the assembly (118,196,952 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 chromosome lengths (99,149,756 and 28,097,889 bp), respectively. The pale grey spiral shows the cumulative chromosome 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/idAnoGambNW_F1_1/dataset/CALSDY01.1/snail.
Figure 2.
Figure 2.. Blob plot of base coverage in a subset of idAnoGambNW_F1_1 10x linked reads against GC proportion for An. gambiae assembly idAnoGambNW_F1_1.
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/idAnoGambNW_F1_1/dataset/CALSDY01.1/blob.
Figure 3.
Figure 3.. Cumulative chromosome length for An. gambiae assembly idAnoGambNW_F1_1.
The grey line shows cumulative length for all chromosomes. Coloured lines show cumulative lengths of chromosomes assigned to each phylum using the buscogenes taxrule. The interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/idAnoGambNW_F1_1/dataset/CALSDY01.1/cumulative.
Figure 4.
Figure 4.. Genome assembly of An. gambiae, idAnoGambNW_F1_1: Hi-C contact map.
Visualised in HiGlass. Chromosomes order: 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=Qbx2q2EPRIuiC3qXX8BfFA.
Figure 5.
Figure 5.. Synteny between genome assemblies of An. gambiae, AgamP3 (PEST) and idAnoGambNW_F1_1 (Ifakara).
Grey rectangles on green background represent positions of pericentric and intercalary heterochromatin in AgamP3 . Remaining gaps in idAnoGambNW_F1_1 are indicated with black dots.
Figure 6.
Figure 6.. Genome assembly of An. gambiae, idAnoGambNW_F1_1 sequence similarity heatmap.
Produced with StainedGlass, visualised in HiGlass. Chromosomes order: 2RL, 3RL, X, followed by the unassembled contigs. Darker colours represent higher sequence similarity, notably at pericentric heterochromatin.
See this image and copyright information in PMC

References

    1. Holt RA, Subramanian GM, Halpern A, et al. : The genome sequence of the malaria mosquito Anopheles gambiae. Science. 2002;298(5591):129–149. 10.1126/science.1076181 - DOI - PubMed
    1. Sharakhova MV, Hammond MP, Lobo NF, et al. : Update of the Anopheles gambiae PEST genome assembly. Genome Biol. 2007;8(1): R5. 10.1186/gb-2007-8-1-r5 - DOI - PMC - PubMed
    1. Besansky NJ: Proposal for the Eight Genomes Cluster for Genus Anopheles .2004. Reference Source
    1. Huho BJ, Ng’ habi KR, Killeen GF, et al. : Nature beats nurture: a case study of the physiological fitness of free-living and laboratory-reared male Anopheles gambiae s.l. J Exp Biol. 2007;210(Pt 16):2939–2947. 10.1242/jeb.005033 - DOI - PubMed
    1. Krzywinski J, Sangaré D, Besansky NJ: Satellite DNA from the Y chromosome of the malaria vector Anopheles gambiae. Genetics. 2005;169(1):185–196. 10.1534/genetics.104.034264 - DOI - PMC - PubMed