Molecular phylogeny and evolution of alcohol dehydrogenase (Adh) genes in legumes

Abstract

Background: Nuclear genes determine the vast range of phenotypes that are responsible for the adaptive abilities of organisms in nature. Nevertheless, the evolutionary processes that generate the structures and functions of nuclear genes are only now be coming understood. The aim of our study is to isolate the alcohol dehydrogenase (Adh) genes in two distantly related legumes, and use these sequences to examine the molecular evolutionary history of this nuclear gene.

Results: We isolated the expressed Adh genes from two species of legumes, Sophora flavescens Ait. and Wisteria floribunda DC., by a RT-PCR based approach and found a new Adh locus in addition to homologues of the Adh genes found previously in legumes. To examine the evolution of these genes, we compared the species and gene trees and found gene duplication of the Adh loci in the legumes occurred as an ancient event.

Conclusion: This is the first report revealing that some legume species have at least two Adh gene loci belonging to separate clades. Phylogenetic analyses suggest that these genes resulted from relatively ancient duplication events.

Figure 1

Alignment of the predicted amino acid sequences from selected Adh gene representatives. The lines indicate the groups that correspond to those in Figure 2.

Figure 2

The phylogenetic tree based on Adh gene sequences obtained by the maximum-likelihood method. The log-likelihood of the best ML tree is -3981.05. The numbers below the branches are the bootstrap values of 50% or more support. The Adh genes from legumes roughly fall into two monophyletic clades that we denoted as Clade I and Clade II.

Figure 3

Part of the simplest reconciled tree that has the lowest number of duplication and deletion events. The reconciled tree involves 24 gene duplications and 44 gene losses for a total cost of 68, and requires 40 deep coalescenses. The solid boxes indicate gene duplications that were inferred on the basis of mismatches between the gene tree and the species tree. The open boxes indicate those duplications that required multiple copies of Adh genes within the same species. The gray lines indicate the lineages that are presumed to be lost after the duplications or were not found in our analysis.