title: Genome-wide analysis and identification of stress-responsive genes of the NAM-ATAF1,2-CUC2 transcription factor family in apple.
abstract: NAC (NAM, ATAF1,2, and CUC2) proteins constitute one of the largest families of plant-specific transcription factors. To date, little is known about the NAC genes in the apple (Malus domestica). In this study, a total of 180 NAC genes were identified in the apple genome and were phylogenetically clustered into six groups (I-VI) with the NAC genes from Arabidopsis and rice. The predicted apple NAC genes were distributed across all of 17 chromosomes at various densities. Additionally, the gene structure and motif compositions of the apple NAC genes were analyzed. Moreover, the expression of 29 selected apple NAC genes was analyzed in different tissues and under different abiotic stress conditions. All of the selected genes, with the exception of four genes, were expressed in at least one of the tissues tested, which indicates that the NAC genes are involved in various aspects of the physiological and developmental processes of the apple. Encouragingly, 17 of the selected genes were found to respond to one or more of the abiotic stress treatments, and these 17 genes included not only the expected 7 genes that were clustered with the well-known stress-related marker genes in group IV but also 10 genes located in other subgroups, none of which contains members that have been reported to be stress-related. To the best of our knowledge, this report describes the first genome-wide analysis of the apple NAC gene family, and the results should provide valuable information for understanding the classification and putative functions of this family.
authors.affiliation: College of Agriculture, Ludong University, Yantai, Shandong 264025, PR China; MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, PR China.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Su
authors.forename: Shizhong
authors.initials: S
authors.lastname: Zhang
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Yuan
authors.forename: Changtian
authors.initials: C
authors.lastname: Chen
authors.forename: Xiao-Fei
authors.initials: XF
authors.lastname: Wang
authors.forename: Yu-Jin
authors.initials: YJ
authors.lastname: Hao
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D027845:Malus / Q000235:genetics / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors
keywords: Apple GFDB database; Apple Gene Function and Gene Family Database; BLAST; GDR; GSDS; GWD; Gene Structure Display Server; Gene family; Genome Database for Rosaceae; Genome-wide analysis; HMM; Hidden Markov Model; MEGA; MEME; MUSCEL; Malus domestica; Molecular Evolutionary Genetics Analysis; Multiple Em for Motif Elicitation; Multiple Sequence Comparison by Log-Expectation; NAC transcription factor; NAC, NAM, ATAF and CUC; NCBI; NJ; National Center for Biotechnology Information; Pfam; Protein family; SMART; Stress-responsive genes; TF; TRR; a Simple Modular Architecture Research Tool; genome-wide duplication; isoelectric points; pIs; the Basic Local Alignment Search Tool; the neighbor-joining; transcription factor; transcriptional regulation region