Author Correction: Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly

Chakraborty, Mahul; Ramaiah, Arunachalam; Adolfi, Adriana; Halas, Paige; Kaduskar, Bhagyashree; Ngo, Luna Thanh; Jayaprasad, Suvratha; Paul, Kiran; Whadgar, Saurabh; Srinivasan, Subhashini; Subramani, Suresh; Bier, Ethan; James, Anthony A.; Emerson, J. J.

doi:10.1186/s12915-022-01314-2

Cited by 9 publications

(17 citation statements)

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“…We found an eiger homolog, g22826, which is within the 3L i region of IndInt and is missing in the reported list of 361 genes with immune repertoire in An. stephensi [4]. A crystal structure of the complex of eiger and its receptor from Drosophila has revealed that eiger belongs to the TNF superfamily and its two receptors, wengen and grnd, are members of the TNFR superfamily(6ZT0 [33]).…”

Section: Resultsmentioning

confidence: 99%

“…These forms are identifiable based on the number of ridges on eggs[3]. The genomes of three strains of the type-form have been reported recently[4][5][6]. A comparison of these three genomes revealed the presence of all three genotypes of the 2R b inversion among the various strains of the type-form.…”

Section: Introductionmentioning

confidence: 99%

“…Of these, more recently, homologs of 361 genes were reported in An. stephensi [4] (https://github.com/mahulchak/stephensi_genome/blob/master/immune.gff), which is in the same range (285, 338, and 353, respectively) of immune-repertoire genes reported for D. melanogaster ( Dm ), An. gambiae ( Ag ), and Ae.…”

Section: Introductionmentioning

confidence: 99%

“…This is especially important in the identification of cytokines and lymphokine homologs, which are notorious for exhibiting low or undetectable homology at the sequence level (https://www.amazon.com/Homology-Folding-Proteins-Biotechnology-Intelligence/dp/3540636056 ) . For example, members of TNF and TNFR superfamilies, recently identified and characterized in Drosophila , are missing in the collation of genes implicated in innate immunity in flies and in mosquito vectors[4][15].…”

Section: Introductionmentioning

confidence: 99%

“…stephensi , we have sequenced and assembled the genome of an isofemale line from a strain of intermediate-form from Bangalore (IndInt) displaying diminished susceptibility to Plasmodium . We present the assembly of this strain and report an inversion not found in the genomes of the three strains of the type-form[4][5][6][18]. Comparative genomics with other Anopheles vectors and deep annotation of genes within this inversion, using fold-prediction algorithms, revealed missed or hidden genes likely to be relevant in Plasmodium resistance.…”

Section: Introductionmentioning

confidence: 99%

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Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Srinivasan

Ghosh

Das

et al. 2022

Preprint

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Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. An. stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, have been reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a TNF-like gene, which is the homolog of the eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of wengen (wgn) and grindelwald (grnd) genes in IndInt, which are known to be the receptors for eiger in Drosophila. We have identified all the genes in IndInt required for eiger-mediated signaling by analogy to TNF-TNFR system, suggesting the presence of a functionally active eiger signaling pathway present in IndInt. Comparative genomics of high-quality genome assemblies of the three type-forms with that of IndInt, reveals structurally disruptive mutations in eiger gene in all three strains of the type-form, alluding to compromised innate immunity in the type-form as the cause of high vectorial capacity in these strains. This is the first report of the presence of an intact evolutionarily-conserved TNF-TNFR signaling system in malaria vectors, with a potential role in Plasmodium resistance.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Srinivasan

Ghosh

Das

et al. 2022

Preprint

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Unraveling the genomic complexity of sylvatic mosquitoes in changing Neotropical environments

Loaiza

Bennett

Miller

et al. 2023

Current Opinion in Biotechnology

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Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Srinivasan

Ghosh

Das

et al. 2022

Sci Rep

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Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. Anopheles stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, were reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in the IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a tumor necrosis factor-alpha (TNF-alpha) like gene, which is the homolog of the Eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of Wengen (Wgn) and Grindelwald (Grnd) genes, which are known to be the receptors for Eiger in Drosophila. We have identified all the genes in IndInt required for Eiger-mediated signaling by analogy to the TNF-alpha system, suggesting the presence of a functionally-active Eiger signaling pathway in IndInt. Comparative genomics of the three type-forms with that of IndInt, reveals structurally disruptive mutations in Eiger gene in all three strains of the type-form, suggesting compromised innate immunity in the type-form as the likely cause of high vectorial capacity in these strains. This is the first report of the presence of a homolog of Eiger in malaria vectors, known to be involved in cell death in Drosophila, within an inversion region in IndInt syntenic to an inversion associated with Plasmodium resistance in An. gambiae.

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Author Correction: Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly

Cited by 9 publications

References 1 publication

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Unraveling the genomic complexity of sylvatic mosquitoes in changing Neotropical environments

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

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