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Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.

Anstead CA, Korhonen PK, Young ND, Hall RS, Jex AR, Murali SC, Hughes DS, Lee SF, Perry T, Stroehlein AJ, Ansell BR, Breugelmans B, Hofmann A, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ioannidis P, Waterhouse RM, Zdobnov EM, James PJ, Bagnall NH, Kotze AC, Gibbs RA, Richards S, Batterham P, Gasser RB - Nat Commun (2015)

Bottom Line: Lucilia cuprina is a parasitic fly of major economic importance worldwide.Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina.Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.

ABSTRACT
Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.

No MeSH data available.


Related in: MedlinePlus

Structures of five insecticide-resistance genes in Lucilia cuprina.Diagrams show the genomic structures of L. cuprina genes, which have been implicated in resistance to insecticides used to control L. cuprina — Scl (encoding a transmembrane receptor important for intracellular signalling and proposed to modify phenotypes associated with organophosphorus (OP) insecticide resistance conferred by Rop1), LcaE7 (=Rop1, encoding carboxylesterase E3; associated with OP insecticide resistance), Rdl (resistance to dieldrin), Ace (acetylcholinesterase) and Lcα6 (nAChR α6 subunit). Genes Scl, LcaE7, Rdl and Ace were located to scaffolds nos. 120, 113, 568 and 105, respectively (a–d). It was also noted that the current L. cuprina assembly did not contain Rdl exon 10 compared with the existing Lucilia cDNA sequence (GI: 2565319) (c). The absence of Rdl exon 10 is supported by RNA-seq data. The Lcα6 gene (254 kb) was represented on scaffold nos. 379, 4,253 and 792 (e), and contains 10 exons including four L. cuprina-specific α6 exons (called 3a, 3b, 8a and 8b; all transcribed). The Lcα6 gene is located in a highly repetitive region, and manual sequence analysis of the paired-end reads successfully mapped the scaffold4253 (containing Lcα6 exons 2 and 3b) to a 2.1 kb gap within scaffold379. Gene regions are indicated by blue lines; gaps within gene regions are depicted as dashed lines. Red vertical lines/boxes represent exons.
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f2: Structures of five insecticide-resistance genes in Lucilia cuprina.Diagrams show the genomic structures of L. cuprina genes, which have been implicated in resistance to insecticides used to control L. cuprina — Scl (encoding a transmembrane receptor important for intracellular signalling and proposed to modify phenotypes associated with organophosphorus (OP) insecticide resistance conferred by Rop1), LcaE7 (=Rop1, encoding carboxylesterase E3; associated with OP insecticide resistance), Rdl (resistance to dieldrin), Ace (acetylcholinesterase) and Lcα6 (nAChR α6 subunit). Genes Scl, LcaE7, Rdl and Ace were located to scaffolds nos. 120, 113, 568 and 105, respectively (a–d). It was also noted that the current L. cuprina assembly did not contain Rdl exon 10 compared with the existing Lucilia cDNA sequence (GI: 2565319) (c). The absence of Rdl exon 10 is supported by RNA-seq data. The Lcα6 gene (254 kb) was represented on scaffold nos. 379, 4,253 and 792 (e), and contains 10 exons including four L. cuprina-specific α6 exons (called 3a, 3b, 8a and 8b; all transcribed). The Lcα6 gene is located in a highly repetitive region, and manual sequence analysis of the paired-end reads successfully mapped the scaffold4253 (containing Lcα6 exons 2 and 3b) to a 2.1 kb gap within scaffold379. Gene regions are indicated by blue lines; gaps within gene regions are depicted as dashed lines. Red vertical lines/boxes represent exons.

Mentions: Although there is little detailed knowledge of the molecular basis of insecticide resistance in L. cuprina, numerous studies4 have inferred or proposed a direct or indirect involvement of various genes in such resistance, for both metabolic and target site insensitivity-resistance mechanisms. We have annotated genomic loci for five genes associated with particular resistances, including Ace (acetylcholinesterase, the target for organophosphorus insecticides, OPs), Rdl (resistance to dieldrin), LcaE7 (or Rop1—resistance to OPs; encodes carboxylesterase E3), Scl (transmembrane receptor for intracellular signalling, proposed to be modifier of phenotypes associated with Rop1-mediated OP resistance) and Lcα6 (nAChR α6 subunit) (Fig. 2). Importantly, previously, we had characterized full-length L. cuprina complementary DNA (cDNA) sequences, which assisted direct cDNA–gDNA alignments to support the definition of exon–intron boundaries in the present study. Using the genomic and transcriptomic data sets for L. cuprina, we identified these genes in long genomic scaffolds and established their structures (Fig. 2), which should provide a foundation for functional studies of insecticide resistance in L. cuprina and other pests.


Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.

Anstead CA, Korhonen PK, Young ND, Hall RS, Jex AR, Murali SC, Hughes DS, Lee SF, Perry T, Stroehlein AJ, Ansell BR, Breugelmans B, Hofmann A, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ioannidis P, Waterhouse RM, Zdobnov EM, James PJ, Bagnall NH, Kotze AC, Gibbs RA, Richards S, Batterham P, Gasser RB - Nat Commun (2015)

Structures of five insecticide-resistance genes in Lucilia cuprina.Diagrams show the genomic structures of L. cuprina genes, which have been implicated in resistance to insecticides used to control L. cuprina — Scl (encoding a transmembrane receptor important for intracellular signalling and proposed to modify phenotypes associated with organophosphorus (OP) insecticide resistance conferred by Rop1), LcaE7 (=Rop1, encoding carboxylesterase E3; associated with OP insecticide resistance), Rdl (resistance to dieldrin), Ace (acetylcholinesterase) and Lcα6 (nAChR α6 subunit). Genes Scl, LcaE7, Rdl and Ace were located to scaffolds nos. 120, 113, 568 and 105, respectively (a–d). It was also noted that the current L. cuprina assembly did not contain Rdl exon 10 compared with the existing Lucilia cDNA sequence (GI: 2565319) (c). The absence of Rdl exon 10 is supported by RNA-seq data. The Lcα6 gene (254 kb) was represented on scaffold nos. 379, 4,253 and 792 (e), and contains 10 exons including four L. cuprina-specific α6 exons (called 3a, 3b, 8a and 8b; all transcribed). The Lcα6 gene is located in a highly repetitive region, and manual sequence analysis of the paired-end reads successfully mapped the scaffold4253 (containing Lcα6 exons 2 and 3b) to a 2.1 kb gap within scaffold379. Gene regions are indicated by blue lines; gaps within gene regions are depicted as dashed lines. Red vertical lines/boxes represent exons.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4491171&req=5

f2: Structures of five insecticide-resistance genes in Lucilia cuprina.Diagrams show the genomic structures of L. cuprina genes, which have been implicated in resistance to insecticides used to control L. cuprina — Scl (encoding a transmembrane receptor important for intracellular signalling and proposed to modify phenotypes associated with organophosphorus (OP) insecticide resistance conferred by Rop1), LcaE7 (=Rop1, encoding carboxylesterase E3; associated with OP insecticide resistance), Rdl (resistance to dieldrin), Ace (acetylcholinesterase) and Lcα6 (nAChR α6 subunit). Genes Scl, LcaE7, Rdl and Ace were located to scaffolds nos. 120, 113, 568 and 105, respectively (a–d). It was also noted that the current L. cuprina assembly did not contain Rdl exon 10 compared with the existing Lucilia cDNA sequence (GI: 2565319) (c). The absence of Rdl exon 10 is supported by RNA-seq data. The Lcα6 gene (254 kb) was represented on scaffold nos. 379, 4,253 and 792 (e), and contains 10 exons including four L. cuprina-specific α6 exons (called 3a, 3b, 8a and 8b; all transcribed). The Lcα6 gene is located in a highly repetitive region, and manual sequence analysis of the paired-end reads successfully mapped the scaffold4253 (containing Lcα6 exons 2 and 3b) to a 2.1 kb gap within scaffold379. Gene regions are indicated by blue lines; gaps within gene regions are depicted as dashed lines. Red vertical lines/boxes represent exons.
Mentions: Although there is little detailed knowledge of the molecular basis of insecticide resistance in L. cuprina, numerous studies4 have inferred or proposed a direct or indirect involvement of various genes in such resistance, for both metabolic and target site insensitivity-resistance mechanisms. We have annotated genomic loci for five genes associated with particular resistances, including Ace (acetylcholinesterase, the target for organophosphorus insecticides, OPs), Rdl (resistance to dieldrin), LcaE7 (or Rop1—resistance to OPs; encodes carboxylesterase E3), Scl (transmembrane receptor for intracellular signalling, proposed to be modifier of phenotypes associated with Rop1-mediated OP resistance) and Lcα6 (nAChR α6 subunit) (Fig. 2). Importantly, previously, we had characterized full-length L. cuprina complementary DNA (cDNA) sequences, which assisted direct cDNA–gDNA alignments to support the definition of exon–intron boundaries in the present study. Using the genomic and transcriptomic data sets for L. cuprina, we identified these genes in long genomic scaffolds and established their structures (Fig. 2), which should provide a foundation for functional studies of insecticide resistance in L. cuprina and other pests.

Bottom Line: Lucilia cuprina is a parasitic fly of major economic importance worldwide.Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina.Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.

ABSTRACT
Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.

No MeSH data available.


Related in: MedlinePlus