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Based on RNA-Seq technology,the transcriptome sequencing of the salt-tolerant sunflower variety P50 and salt-sensitive variety P29 under 120mmol/L NaCl stress were conducted and the dates were De novo assembled.106275 and 119350 unigenes were received in P50 and P29,and which mean length were 716bp and 685bp,respectively.After long-sequence clustering between both samples,110751 All-unigenes were obtained.The total length of sequences was 96970017nt,with a mean length of 876 nt.71610,52569,50827,46676,32215 and 52406 unigenes were severally matched to the NR,NT,Swiss-Prot,GO,KEGG and COG databases by blasting,and all of the annotated unigenes were 77536.71610 unigenes against NR databases were highly homologous to Vitis vinifera(15522,21.7%),Lycopersicon esculentum(10172,14.2%),Amygdalus persica(4964,6.9%),Ricimus communis(4582,6.4%),Populus trichocarpa(4252,5.9%),Fragaria vesca subsp.Vesca(3146,4.4%),Glycine max(2952,4.1%)and the other species(21698条,36.3%).Base on results of NR annotation,25 and 55 functional groups were severally obtained through COG and GO functional classification,many unigenes in sunflower transcriptome were found to correlate closely with signal transduction mechanisms,metabolic process,binding and catalytic activity.The unigenes were in128 pathways by KEGG analysis,including some of the salt-tolerance pathways.All-unigene sequences were aligned to protein databases in the priority order of NR,Swiss-Prot,KEGG and COG by blastx(evalue<0.00001),71260 coding sequences(CDS)were extracted from all-unigene sequences and translated into peptide sequences.For all-unigenes with no BLAST hits,9970 CDS were predicted using ESTScan and translated into peptide sequences.In order to identify genes with different expression levels of two samples,we calculated the expression levels of the unigenes by the RPKM(Reads Per kb per Million reads)method.The result showed that 21332 differently expressed genes were found with FDR≤0.001 and |log2Ratio|≥1,including 10306 up-regulated genes and 11206 down-regulated genes.To further increase our understanding of these DEGs,we performed GO enrichment analyses,and discovered oxidoreductase,GTPase activity,antioxidant activity,etc.were closely related to salt tolerance.The metabolic pathway enrichment analysis showed that the DGEs were associated with 40 metabolic pathways,such as starch and sucrose metabolism,fructose and mannose metabolism,glycerophospholipid metabolism,phenylalanine metabolism,nitrogen metabolism,transport and catabolism,phagosome and so on.Moreover,We found a number of family of transcription factors.The largest gene family was bHLH family,followed by AP2/ERF family,MYB family,WRKY family and C3H family,Which played an important role in the mechanism of salt tolerance in sunflower.