title: Genome-wide Identification and analysis of the stress-resistance function of the TPS (Trehalose-6-Phosphate Synthase) gene family in cotton.
abstract: BACKGROUND
  Trehalose (a-D-glucopyranosyl a-D-glucopyranoside) is a nonreducing disaccharide and is widely distributed in bacteria, fungi, algae, plants and invertebrates. In the study, the identification of trehalose-6-phosphate synthase (TPS) genes stress-related in cotton, and the genetic structure analysis and molecular evolution analysis of TPSs were conducted with bioinformatics methods, which could lay a foundation for further research of TPS functions in cotton.
  
  
  RESULTS
  The genome information of Gossypium raimondii (group D), G. arboreum L. (group A), and G. hirsutum L. (group AD) was used in the study. Fifty-three TPSs were identified comprising 15 genes in group D, 14 in group A, and 24 in group AD. Bioinformatics methods were used to analyze the genetic structure and molecular evolution of TPSs. Real-time PCR analysis was performed to investigate the expression patterns of gene family members. All TPS family members in cotton can be divided into two subfamilies: Class I and Class II. The similarity of the TPS sequence is high within the same species and close within their family relatives. The genetic structures of two TPS subfamily members are different, with more introns and a more complicated gene structure in Class I. There is a TPS domain(Glyco transf_20) at the N-terminal in all TPS family members and a TPP domain(Trehalose_PPase) at the C-terminal in all except GrTPS6, GhTPS4, and GhTPS9. All Class II members contain a UDP-forming domain. The responses to environmental stresses showed that stresses could induce the expression of TPSs but the expression patterns vary with different stresses.
  
  
  CONCLUSIONS
  The distribution of TPSs varies with different species but is relatively uniform on chromosomes. Genetic structure varies with different gene members, and expression levels vary with different stresses and exhibit tissue specificity. The upregulated genes in upland cotton TM-1 is significantly more than that in G. raimondii and G. arboreum L. Shixiya 1.
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Min
authors.initials: M
authors.lastname: Mu
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Xu-Ke
authors.initials: XK
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Jun-Juan
authors.initials: JJ
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: De-Long
authors.initials: DL
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Zu-Jun
authors.initials: ZJ
authors.lastname: Yin
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
authors.forename: Wei-Li
authors.initials: WL
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China. yew158@163.com.
authors.forename: Wu-Wei
authors.initials: WW
authors.lastname: Ye
mesh_terms: D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005964:Glucosyltransferases / Q000235:genetics*; D003368:Gossypium / Q000201:enzymology / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins; D005964:Glucosyltransferases; C023180:trehalose-6-phosphate synthase
keywords: Gene family; Gossypium arboretum; Gossypium hirsutum L; Gossypium raimondii; Rehalose-6-phosphase synthase (TPS)