Nucleotide sequence of the genomic region encompassing Adh and Adh-Dup genes of D. lebanonensis (Scaptodrosophila): Gene expression and evolutionary relationships

Abstract

The region of the genome of D. lebanonensis that contains the Adh gene and the downstream Adh-dup gene was sequenced. The structure of the two genes is the same as has been described for D. melanogaster. Adh has two promoters and Adh-dup has only one putative promoter. The levels of expression of the two genes in this species are dramatically different. Hybridizing the same Northern blots with a specific probe for Adh-dup, we did not find transcripts for this gene in D. lebanonensis. The level of Adh distal transcript in adults of D. lebanonensis is five times greater than that of D. melanogaster adults. The maximum levels of proximal transcript are attained at different larval stages in the two species, being three times higher in D. melanogaster late-second-instar larvae than in D. lebanonensis first-instar larvae. The level of Adh transcripts allowed us to determine distal and proximal initiation transcription sites, the position of the first intron, the use of two polyadenylation signals, and the heterogeneity of polyadenylation sites. Temporal and spatial expression profiles of the Adh gene of D. lebanonensis show qualitative differences compared with D. melanogaster. Adh and Adh-dup evolve differently as shown by the synonymous and nonsynonymous substitution rates for the coding region of both genes when compared across two species of the melanogaster group, two of the obscura group of the subgenus Sophophora and D. lebanonensis of the victoria group of the subgenus Scaptodrsophila. Synonymous rates for Adh are approximately half those for Adh-dup, while nonsynonymous rates for Adh are generally higher than those for Adh-dup. Adh shows 76.8% identities at the protein level and 70.2% identities at the nucleotide level while Adh-dup shows 83.7% identities at the protein level and 67.5% identities at the nucleotide level. Codon usage for Adh-dup is shown to be less biased than for Adh, which could explain the higher synonymous rates and the generally lower nonsynonymous substitution rates in Adh-dup compared with Adh. Phylogenetic trees reconstructed by distance matrix and parsimony methods show that Sophophora and Scaptodrosophila subgenera diverged shortly after the separation from the Drosophila subgenus.

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

“…ADH activity and/or transcription has previously been detected in larvae, pupae, and adults of D. lebanonensis but not in embryos (Juan, Papaceit, and Quintana 1994). We detected Adh and Adhr transcripts in D. lebanonensis in embryos, larvae, and adult tissues (data not shown).…”

“…In the subgenus Drosophila, as represented by D. buzzatii, it may be close to Adh but transcribed independently of that gene. In the subgenus Scaptodrosophila, these two genes are very closely linked (just 287 bp apart; Juan, Papaceit, and Quintana 1994), and, as in D. melanogaster Adhr and closely related species, they are transcribed as a dicistronic mRNA. Figure 5 summarizes what is currently known about the distribution and transcription of the Adhr gene in the genus Drosophila.…”

“…Since a monocistronic transcript for Adh has been detected in D. lebanonensis (Albalat and González-Duarte 1993;Juan, Papaceit, and Quintana 1994), we believe that, as in D. melanogaster, there are two transcripts: one monocistronic transcript that encodes ADH and one dicistronic transcript that encodes both ADH and ADHR.…”

“…The primers are given in table 1. (Juan, Papaceit, and Quintana 1994) and Drosophila buzzatii (Shafer [1992] for Adh and this work for Adhr). These figures indicate the positions of the primers used (see Materials and Methods).…”

A statistical analysis of nucleotide substitutions in the Drosophila Adh region reflects irregularities in molecular clocks.

“…Adh Ks values are significantly lower than (in 6 out of 12 comparisons) or equivalent to (in 6 out of 12 comparisons) Adh-dup Ks values (Table 2). Since Adh is more biased than Adh-dup (Albalat et al, 1994;Juan et al, 1994), synonymous substitutions could saturate at a shorter time scale, in which case the Adh Ks values would be underestimated in the D. immigrans and S. lebanonensis comparisons. However, Adh Ks and Adh-dup Ks in Sophophora subgenus comparisons do not show saturation (Moriyama and Powell, 1997a).…”