Nonfixed duplication containing the Adh gene and a truncated form of the Adhr gene in the Drosophila funebris species group: different modes of evolution of Adh relative to Adhr in Drosophila

Abstract

The sequence of the genomic region that contains the Adh and Adhr genes of Drosophila funebris was used to demonstrate that both genes are present in species of the funebris group. The sequence of this genomic region reveals a 2.9-kb tandem duplication which encompasses 1.6 kb of the 5' flanking region, the entire Adh gene, and two thirds of the first exon of the Adhr gene in D. funebris. This duplication is not fixed in this species since some strains do not carry the duplication. The Adh duplication has also been found in another species of the funebris group, Drosophila macrospina macrospina. The sequence analysis of the 5'-flanking region of the Adh gene indicates a single promoter and shows stretches of high similarity with cis-acting elements responsible for the expression of Adh in Drosophila melanogaster. In confirmation of this indication, the larval and adult transcripts have the same length, which corresponds to the transcription from the promoter proximal to the coding region. The codon bias of the Adh gene of D. funebris is among the lowest reported for any Adh gene in the Drosophilidae species and is very similar to that of the Adhr gene. The Adhr gene evolves slightly faster than Adh at synonymous positions. At nonsynonymous positions, the Adh gene evolves 2.5 times faster than Adhr in the species pair D. funebris-Drosophila immigrans, while in other interspecific comparisons the average is about 1.25. However, in comparisons between some species within the melanogaster and obscura groups, Adh evolves at half the rate of Adhr. The phylogenetic trees constructed with the coding region of the Adh gene cluster D. funebris and D. immigrans and clearly separate them from the clade in which virilis, repleta, and Hawaiian species are grouped. Using the evolutionary synonymous rate estimated for Hawaiian species, the divergence time of D. funebris from the virilis-repleta-Hawaiian clade was estimated as 34.3 Myr, and the divergence time of D. funebris and D. immigrans was estimated as 23.5 Myr.

Duplication, Dicistronic Transcription, and Subsequent Evolution of the Alcohol dehydrogenase and Alcohol dehydrogenase-related Genes in Drosophila

“…The phylogeny supports the view that the ancient organization after Adh/Adhr duplication consisted of two very close genes. (Russo, Takezaki, and Nei 1995;Amador and Juan 1999;this work). Lines indicate species and gene phylogenies.…”

“…The relative level of the two transcripts is controlled by the efficiency of transcriptional read-through of the termination and polyadenylation signals in the intergenic region (Brogna and Ashburner 1997). Quite a lot is known about the distribution of the Adhr gene in the genus Drosophila (Russo, Takezaki, and Nei 1995;Amador and Juan 1999); it has been described in the Scaptodrosophila subgenus and in many species of the Sophophora subgenus, but in two only species of the Drosophila subgenus (in D. immigrans and, recently, in D. funebris). One striking fact is that although the duplication predates the radiation of the genus Drosophila (40-65 Myr;Powell 1997, pp.…”

Partial Characterization and Evolution of Adh-Adhr in Drosophila dunni

“…For the partial sequence of the Adhr gene, low values were also observed: χ 2 /L = 0.24 and ENC = 47.25. This value and the one for Adh of D. funebris (χ 2 /L = 0.26, ENC = 51.80; Amador and Juan, 1999) represent the least biased Adh genes reported so far in the genus.…”

“…With respect to position 421, a transcription error is possible since all genomic sequences from single flies exhibit T at this site. There may be polymorphism (T/C) at position 373, however, since all genomic sequences from single flies showed C at this site, unlike the original DNA genomic sample, which was T. A nonfixed duplication of very recent origin, as reported by Amador and Juan (1999) in some populations of D. funebris of the immigrans-tripunctata radiation, is still a possibility.…”

“…Both are T-C substitutions in the third codon position and did not lead to changes in the amino acid sequence. This is not totally unexpected and may be due to polymorphism for Adh (Kreitman, 1983;Oppentocht et al, 2002), an error that occurred during transcription of mRNA, PCR cloning and/or sequencing, or to a duplication of Adh of very recent origin (Amador and Juan, 1999). In all cases, both strands from cDNA and gDNA were sequenced and a consensus nucleotide sequence was obtained from at least three sequencing reactions, ruling out a sequencing error.…”