Arthropod P450 Dokuwiki

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====== Drosophila melanogaster ======
{{ ::drosophila.jpg?200|}}

    Class       : Insecta
    Order       : Diptera
    Suborder    : Brachycera
    Clade       : Cyclorrhapha
    Superfamily : Ephydroidea
    Family      : Drosophilidae

//Common name// : fruit fly

NCBI:txid[[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7227|7227]]

Annotation from assembly GCA_000001215.3

The 88 sequences from [[https://www.sciencedirect.com/science/article/pii/S096517482030179X|Dermauw et al., 2020]] include the two forms of the alternatively spliced CYP4D1 (CYP4D1_v1a /v1b).

A FASTA format file of the CYPome can be downloaded {{ ::drosophila_2020_.fasta |here}}. 

The distribution of genes by CYP clan is tabulated [[CYPfam_by_clan|here]]

The genome of //Drosophila melanogaster// was the first arthropod genome to be sequenced (Adams et al., 2000), and this made the annotation of the first insect CYPome possible ([[https://doi.org/10.1016/S0378-1119(00)00533-3|Tijet et al., 2001]]). 

Many species of the //Drosophila// genus have now been sequenced, and a detailed comparative analysis of 12 //Drosophila// genomes has been published ([[https://doi.org/10.1093/gbe/evu083|Good et al., 2014]]). This paper reports that the CYPome size ranges from 74 (//[[sechellia|D.sechellia]]//) to 94 (//D.willistoni//) genes, with 114 gene gains and 74 gene losses inferred from the phylogeny of these 12 species. 

== P450 pseudogenes in Drosophila melanogaster ==

The Drosophila CYPome paper ([[https://doi.org/10.1016/S0378-1119(00)00533-3|Tijet et al., 2001]]) reported on the genome and transcriptome data available at that time. A sequence gap adjacent to CYP12D1, when filled, revealed a second CYP12D gene with just three (non silent) nucleotide substitutions. Presumably, the very high identity of these two adjacent genes caused a problem in the initial assembly resulting in a gap. These genes are now called CYP12D1p and 12D1d (proximal and distal). 
Seven of the 90 sequences were considered apparent pseudogenes. With improvements of the genome assembly and quality, only four sequences remain as named pseudogenes. CYP307A2, initially thought to be a pseudogene, was later obtained as a full gene when DNA sequence from heterochromatin, not available in the initial release of the genome was annotated.

The four Drosophila melanogaster P450 pseudogenes are analyzed [[Droso_pse|here]].