Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs

• Published in: PloS one 2015-04, Vol.10 (4), p.e0124669-e0124669
• Main Authors: Tian, Feng-Xia, Zang, Jian-Lei, Wang, Tan, Xie, Yu-Li, Zhang, Jin, Hu, Jian-Jun
• Format: Article
• Language: English
• Subjects: Aldehyde dehydrogenase; Aldehyde Dehydrogenase - classification; Aldehyde Dehydrogenase - genetics; Aldehydes; ALDH gene; Analysis; Arabidopsis; Arabidopsis thaliana; Bacteria; Biosynthesis; Carboxylic acids; Chromosome Mapping; Chromosomes; Chromosomes, Plant; Cluster Analysis; Computational Biology; Data processing; Databases, Nucleic Acid; Dehydrogenases; Divergence; DNA microarrays; Enzymes; Evolution; Evolution, Molecular; Evolutionary biology; Gene Duplication; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene families; Genes; Genetics; Genome, Plant; Genomes; Genomics; Laboratories; Life sciences; Metabolism; Multigene Family; NAD; Oryza; Oxidation; Oxidoreductases; Phylogeny; Plant evolution; Plant species; Plants; Populus - classification; Populus - genetics; Populus trichocarpa; Proteins; Reproduction (copying); Stress, Physiological - genetics; Stresses; Trees
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0124669

Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.