Analysis On Transcriptome Of Cultivated And Wild Tomato Based On RNA-Seq Technology

Tomato is an indispensable vegetable in our daily life because of its short growth cycle,nutrient rich and vitamins rich.At the same time,tomato has a distant relationship with model organisms,such as Arabidopsis thaliana,maize and so on.Therefore,tomato is also regarded as model organism to research for fruit ripening.In addition,with the increasing demand for tomato,cultivating excellent tomato varieties and increasing the yield have become an increasing concern for researchers.At present,the research on tomato mainly focused on: the difference about salt tolerance,drought resistance,low temperature resistance and fruit nutrition between cultivated and wild tomato.Based on the previous studies on the expression traits of tomato,this study is mainly concentrated on the transcriptome of domesticated and wild tomato.The whole transcriptome of tomato is analyzed by RNA sequencing technique.The main contents are as follows:Firstly,we perform quality control for tomato transcriptional data,and compute the quality score of each base.Then we get 388666 transcripts after assembling,and analyze the distribution of transcripts' length.In addition to,the transcript's expression is different in every tissues.And the transcripts with high expression are mainly concentrated on floral,fruit,root and vegetative.Secondly,we mainly analyze the differentially expressed genes between domesticated and wild tomato.And we predict 126 up-regulated differentially expressed genes and 87 down-regulated differentially expressed genes.Then,we analyze the biological function and biological pathway of differentially expressed genes by GO functional annotation and pathway analysis.And the differentially expressed genes are mainly enriched in light-harvesting complex,plasma lemma complexity,starch and sucrose metabolism,linoleic acid metabolism,biosynthetic amino acids and so on.In addition to,we analyze the function of differentially expressed genes in different tissues.Finally,we predict 554 differentially expressed long non-coding RNAs and 426 mRNAs,and make a statistical analysis.In addition,we construct a co-expression network of long non-coding RNAs and mRNAs,and select mRNAs associated with long non-coding RNAs as target genes,and annotate target genes of long non-coding RNAs.The function of target genes is enriched in biological stimuli response,peptidase inhibitor activity,which can speculate the regulation function of long non-coding RNAs.Meanwhile,we also predict new transcripts of tomato,and each transcript contains one exon and one CDS at least.But,the function will be known in further study.