Bution of the 95?00 sequence similarity reached 18.4 of all-unigenes, while the 80?5 sequence similarity reached 60.2 . Species distribution (Fig. 2c) shows that 85 of the unigenes were homologous with Populus trichocarpa, minor similarities were followed with castor, grapes, peaches, P. trichocarpa ? populus, strawberries, soybeans and other. For unigenes that were not in the above-described databases, we predicted 471 nucleic acid sequences (sequence 5 3) and amino acid sequences by using ESTScan. In order to estimate the integrity and effectiveness of the transcriptome data annotation process, we searched for genes that involved COG functional classes. The COG database is a classification of an orthologous gene. Each COG protein is assumed to come from an ancestral protein. By comparing the new sequences and proteins in the COG database, the new sequence can predict and classify possible features. 14,748 unigenes of 53,362 all-unigenes found 25 functional categories in the COG database (Fig. 3). Versatile unigenes were classified intodifferent categories. The category for “General function prediction only” is the most representative class of a tree’s genes (4963 members). Subsequently, categories were followed as shown in Additional file 4: Figure S4.GO functional and KEGG pathway analysisFunctions of both salt treated and controlled S. linearistipularis genes were predicted by using GO functional annotations to explain how salt treatment affect gene function categories. Salix linearistipularis unigenes obtained from the GO functional annotation based on NR annotations; the Blast2GO NSC309132 manufacturer program was used to get GO annotation of unigenes. Based on sequence similarity, 36,839 unigenes were annotated to 55 function class (Additional file 5: Figure S5). There are 22 biological processes, 17 cellular components, and 16 molecular functions. 23,885 (44.76 ) unigenes were validly matched with the KEGG database, and categorized as 128 known metabolic or signaling pathways (Additional file 6: Figure S6). There were representative pathways as metabolic pathways (5177; 21.67 ), biosynthesis of secondary metabolites (2443; 10.23 ), plant-pathogen interaction (1568; 6.56 ), plant hormone signal transduction (1506; 6.31 ), spliceosome (859; 3.6 ), endocytosis (656; 2.75 ), and protein processing in endoplasmic reticulum (656; 2.75 ). These results demonstrated that salt treatment affected plant metabolic pathways.DEG between SLHtreated and SLHcontrolled S. linearistipularis groupsTo identify genes of S. linearistipularis with differential expressions under salt conditions, we compared the transcriptome profiles of salt stress treatment (SLH-treated) and control (SLH-control) S. linearistipularis groups. Changes in gene expression were calculated with a selected threshold: logRatio 0.584 2 (fold – change 1.5, and FDR 0.05). 3034 of a total of 53,362 unigenes were DEGs, 1397 up-regulated genes and 1637 down-regulated genes (Fig. 4). All genes were classified by the degree of DEG PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/25432023 into three categories:Nan et al. J of Biol Res-Thessaloniki (2016) 23:Page 5 ofFig. 2 The result of all-unigenes annotation according to NR. a e-value distribution, b similarity distribution, c species distribution0?.5-fold differences in expression levels of unigenes (1768 genes); 1.5?-fold differences in expression levels (2444 genes); more than 4-fold unigenes (590 genes).GO and KEGG pathway analysis of DEGsThe GO annotation of S. linearis.
