title: Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily of Gossypium raimondii.
abstract: BACKGROUND
  Aldehyde dehydrogenases (ALDHs) are members of the NAD(P)(+)-dependent protein superfamily which catalyzes aliphatic and aromatic aldehyde oxidation to non-toxic carboxylic acids. ALDH genes may offer promise for improving plant adaptation to environmental stress. Recently, elucidated genome sequences of Gossypium raimondii provide a foundation for systematic identification and analysis of ALDH genes. To date, this has been accomplished for many plant species except G. raimondii.
  
  
  RESULTS
  In this study, thirty unique ALDH sequences that code for 10 ALDH families were identified in the G. raimondii genome. Phylogenetic analysis revealed that ALDHs were split into six clades in G. raimondii, and ALDH proteins from the same families were clustered together. Phylogenetic relationships of ALDHs from 11 plant species suggest that ALDHs in G. raimondii shared the highest protein homology with ALDHs from poplar. Members within ALDH families possessed homologous exon-intron structures. Chromosomal distribution of ALDH did not occur evenly in the G. raimondii genome and many ALDH genes were involved in the syntenic region as documented by identification of physical locations among single chromosomes. In addition, syntenic analysis revealed that homologues of many G. raimondii ALDHs appeared in corresponding Arabidopsis and poplar syntenic blocks, indicating that these genes arose prior to G. raimondii, Arabidopsis and poplar speciation. Finally, based on gene expression analysis of microarray and RNA-seq, we can speculate that some G. raimondii ALDH genes might respond to drought or waterlogging stresses.
  
  
  CONCLUSIONS
  Genome-wide identification and analysis of the evolution and expression of ALDH genes in G. raimondii laid a foundation for studying this gene superfamily and offers new insights into the evolution history and speculated roles in Gossypium. These data can be used to inform functional genomic studies and molecular breeding in cotton.
authors: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, People's Republic of China. Electronic address: daohuahe@nwafu.edu.cn.
authors: Daohua
authors: D
authors: He
authors: College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
authors: Zhongping
authors: Z
authors: Lei
authors: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
authors: Hongyi
authors: H
authors: Xing
authors: College of Agronomy, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
authors: Baoshan
authors: B
authors: Tang
mesh_terms: D000444:Aldehyde Dehydrogenase / Q000235:genetics*; D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling; D023061:Gene Order; D017343:Genes, Plant; D018745:Genome, Plant; D003368:Gossypium / Q000145:classification / Q000201:enzymology* / Q000235:genetics / Q000502:physiology; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D013312:Stress, Physiological; D026801:Synteny
chemical_list: D010940:Plant Proteins; D000444:Aldehyde Dehydrogenase
keywords: ALDH; Cotton (Gossypium raimondii); Gene nomenclature; Genome; Plants