title: Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L.
abstract: Homeodomain-leucine zipper (HD-Zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. In this study, 55 predicted maize HD-Zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. Phylogenetic analysis of HD-Zip proteins from Zea mays, Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Physcomitrella patens showed that they group into four classes. We inferred that the copy numbers of classes I and III genes were relatively conserved in all five species. The 55 maize HD-Zip genes are distributed randomly on the ten chromosomes, with 15 segmental duplication and 4 tandem duplication events, suggesting that segmental duplications were the major contributors in the expansion of the maize HD-Zip gene family. Expression analysis of the 55 maize HD-Zip genes in different tissues and drought conditions revealed differences in the expression levels and patterns between the four classes. Promoter analysis revealed that a number of stress response-, hormone response-, light response-, and development-related cis-acting elements were present in their promoters. Our results provide novel insights into the molecular evolution and gene expression within the HD-Zip gene family in maize, and provide a solid foundation for future functional study of the HD-Zip genes in maize.
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China. mhd163com@163.com.
authors.forename: Hude
authors.initials: H
authors.lastname: Mao
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Yu
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China.
authors.forename: Zhanjie
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China.
authors.forename: Ran
authors.initials: R
authors.lastname: Han
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D058674:Chromosome Duplication; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D016350:Leucine Zippers; D005810:Multigene Family; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D014157:Transcription Factors
keywords: Expression; HD-Zip transcription factor; Maize; Molecular evolution; Promoter analysis