Thioredoxins (TRX) are small proteins (around 12 KDa) which are present in all organisms. In addition to these ‘classical’ thioredoxins, numerous proteins also exhibit thioredoxin like domains or multiple thioredoxin domains (P., 2001). Thioredoxin is a general name for small proteins and conserved WC(G/P)PC motif to catalyze thiol disulfide interchanges (Meyer, Buchanan, Vignols, & Reichheld, 2009). Trx proteins function in disulfide reductases to reduce H2 O2 to non-reactive H2O and to scavenge free radicals, This protects cells against oxidative stress and apoptosis (Wang et al., 2013). A large number of Trx proteins have been identified in plants(Meyer, Reichheld, & Vignols, 2005).There are six different types (m, f, x,…show more content… The results will provide strong evidence into the role and evolutionary history of Thioredoxin genes, and will help further investigation of the molecular and biological functions of Thioredoxin protein family in cotton.
Materials and methods
Identification of TRX proteins in cotton
The conserved TRX protein domain was downloaded from Hidden Markov Model (HMM) (PF00085). In order to identify the TRX proteins in cotton genome, the HHM profile of TRX protein was employed as query to perform a HMMER search (http://hmmer. janelia.org/)against the cotton sequence genome was downloaded from cotton genome project (http://www.cgp.genomics.org.cn),with E-value< 0.01. All redundant sequences were discarded from further analysis based on clustalW alignment results. Furthermore, SMART and PFAM database were used to verify the presence of the TRX protein domains.
Database searches and phylogenetic analysis
From cotton genome database, 150 protein amino acid sequences of GhTRX were aligned by Clustalx1.81 program and a phylogenetic tree was constructed using the MEGA6 program with the neighbor joining (NJ) method and internal branch support was estimated with 1000 bootstrap replicates(Tamura, Stecher, Peterson, Filipski, & Kumar, 2013). Motifs were generated using MEME (http://meme.sdsc.edu/meme4_6_1/cgi-bin/meme.cgi/) and visualized with Logo (http://weblogo.berkeley.edu/logo.cgi/). MEME was run from the web server with the minimum and