GEPHE SUMMARY Print
Gephebase Gene
Entry Status
Published
GepheID
GP00001407
Main curator
Prigent
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
Drosophila melanogaster susceptible to nicotine
Trait State in Taxon B
Drosophila melanogaster resistant to nicotine
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Common Name
fruit fly
Synonyms
Sophophora melanogaster; fruit fly; Drosophila melanogaster Meigen, 1830; Sophophora melanogaster (Meigen, 1830); Drosophila melangaster
Rank
species
Lineage
Show more ... Brachycera; Muscomorpha; Eremoneura; Cyclorrhapha; Schizophora; Acalyptratae; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup
NCBI Taxonomy ID
is Taxon A an Infraspecies?
Yes
Taxon A Description
Strain ISO-1
Taxon B
Common Name
fruit fly
Synonyms
Sophophora melanogaster; fruit fly; Drosophila melanogaster Meigen, 1830; Sophophora melanogaster (Meigen, 1830); Drosophila melangaster
Rank
species
Lineage
Show more ... Brachycera; Muscomorpha; Eremoneura; Cyclorrhapha; Schizophora; Acalyptratae; Ephydroidea; Drosophilidae; Drosophilinae; Drosophilini; Drosophila; Sophophora; melanogaster group; melanogaster subgroup
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
Strain A4
GENOTYPIC CHANGE
UniProtKB
Drosophila melanogaster
GenebankID or UniProtKB
Presumptive Null
Molecular Type
Aberration Type
Insertion Size
1-10 kb
Molecular Details of the Mutation
partial 1.5kb Accord element ; possibly a driver of nicotine-sensitive expression ; the resistant strain also has a gene tandem duplication (CNV) that may play complementary role in resistance levels
Experimental Evidence
Authors
Chakraborty M; VanKuren NW; Zhao R; Zhang X; Kalsow S; Emerson JJ
Abstract
Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.
COMMENTS
The QTL harbors a pair of cytochrome P450 genes. According to gene expression Cyp28d1 is the best candidate but Cyp28d2 is also possible. @TE described with nicotine-dependent effect on gene expression in the follow-up article by Chakraborty et al.: Intergenic element between a gene copy is the 5′ end of Accord, a long terminal repeat (LTR) retrotransposon.; Insertion of Accord upstream of another gene called Cyp6g1 has been linked to upregulation of the encoded cytochrome P450 enzyme suggesting that the retrotransposon may be responsible for the upregulated expression of the Cyp28d gene
YOUR FEEDBACK is welcome!