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Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z - Genome Biol. (2014)

Bottom Line: RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism.Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution.RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range.

Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism.

Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

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Genome landscape. Density of genes (black vertical lines), transposable elements (TEs; green vertical lines), and short tandem repeats (STRs; red vertical lines) in 100 kb windows of mapped scaffolds. Based on the physical map, scaffolds were ordered and oriented respective to their position in the chromosomes and then 100 kb non-overlapping windows were generated for each scaffold (X-axis). The density of genes and TEs (Y-axis) was determined using coverageBed. Satellite sequences were identified using TandemRepeatFinder. The short tandem repeats track is a combination of the number of microsatellites, minisatellites, and satellites per 100 kb window.
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Fig4: Genome landscape. Density of genes (black vertical lines), transposable elements (TEs; green vertical lines), and short tandem repeats (STRs; red vertical lines) in 100 kb windows of mapped scaffolds. Based on the physical map, scaffolds were ordered and oriented respective to their position in the chromosomes and then 100 kb non-overlapping windows were generated for each scaffold (X-axis). The density of genes and TEs (Y-axis) was determined using coverageBed. Satellite sequences were identified using TandemRepeatFinder. The short tandem repeats track is a combination of the number of microsatellites, minisatellites, and satellites per 100 kb window.

Mentions: The density of genes, TEs, and short tandem repeats (STRs) for each chromosome were determined based on the physical map (Figure 4). The average numbers of genes for each chromosome arm are consistent with those in An. gambiae. The X had the lowest number of genes per 100 kb, and the highest densities of genes per 100 kb were seen on 2R and 3 L (Figure 5; Additional file 1: Tables S2 and S3). Chromosomes 2R and 3 L also contain the greatest numbers of polymorphic inversions [44]. Genes functioning as drivers of adaptation could be expected to occur in greater densities on chromosome arms with higher numbers of polymorphic inversions [45].Figure 4


Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, Tu Z - Genome Biol. (2014)

Genome landscape. Density of genes (black vertical lines), transposable elements (TEs; green vertical lines), and short tandem repeats (STRs; red vertical lines) in 100 kb windows of mapped scaffolds. Based on the physical map, scaffolds were ordered and oriented respective to their position in the chromosomes and then 100 kb non-overlapping windows were generated for each scaffold (X-axis). The density of genes and TEs (Y-axis) was determined using coverageBed. Satellite sequences were identified using TandemRepeatFinder. The short tandem repeats track is a combination of the number of microsatellites, minisatellites, and satellites per 100 kb window.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4195908&req=5

Fig4: Genome landscape. Density of genes (black vertical lines), transposable elements (TEs; green vertical lines), and short tandem repeats (STRs; red vertical lines) in 100 kb windows of mapped scaffolds. Based on the physical map, scaffolds were ordered and oriented respective to their position in the chromosomes and then 100 kb non-overlapping windows were generated for each scaffold (X-axis). The density of genes and TEs (Y-axis) was determined using coverageBed. Satellite sequences were identified using TandemRepeatFinder. The short tandem repeats track is a combination of the number of microsatellites, minisatellites, and satellites per 100 kb window.
Mentions: The density of genes, TEs, and short tandem repeats (STRs) for each chromosome were determined based on the physical map (Figure 4). The average numbers of genes for each chromosome arm are consistent with those in An. gambiae. The X had the lowest number of genes per 100 kb, and the highest densities of genes per 100 kb were seen on 2R and 3 L (Figure 5; Additional file 1: Tables S2 and S3). Chromosomes 2R and 3 L also contain the greatest numbers of polymorphic inversions [44]. Genes functioning as drivers of adaptation could be expected to occur in greater densities on chromosome arms with higher numbers of polymorphic inversions [45].Figure 4

Bottom Line: RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism.Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution.RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range.

Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism.

Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

Show MeSH
Related in: MedlinePlus