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Abstract
Although domesticated tomato is cultivated by wild tomato, there are a lot of differences between cultivated tomato and wild tomato, such as shape, physiological function and life history. Many studies show that wild tomato has better salt resistance and drought resistance. In addition to, domesticated tomato’s fruit is bigger and has more nutritious than wild tomato. The different features are closely related to differentially expressed genes. We identified 126 up-regulated differentially expressed genes and 87 down-regulated differentially expressed genes in cultivated tomato and wild tomato by RNA-Seq. These differentially expressed genes may be associated with salt resistance, drought resistance and fruit nutrition. These differentially expressed genes also further highlight the large-scale reconstruction between wild and cultivated species. In this paper, we mainly study GO enrichment analysis and pathway analysis of the differentially expressed genes. After GO and pathway enrichment analysis, a set of significantly enriched GO annotations and pathways were identified for the differentially expressed genes. What’s more, we also identified long non-coding RNAs and mRNAs in the two species and analyzed its essential features. In addition to, we construct a co-expression network of long non-coding RNAs and mRNAs, and annotate mRNAs associated with long non-coding RNAs as target genes, and speculate the regulation function of long non-coding RNAs. In total, our results reveal the effects of artificial and natural selection on tomato’s transcript, providing scientific basis for tomato’s research in the future.
Highlights
Tomato [1, 2] is one of the most scientifically investigated vegetables because of its high commercial importance [3]
The transcriptome of cultivated tomato was sequenced by Illumina high throughput sequencing and compared with the transcriptome of wild tomato, including differentially expressed genes and long non-coding RNAs
Our data reflects the differences between cultivated tomato and wild tomato and offers tomato’s basic transcriptional information in future tomato research
Summary
Tomato [1, 2] is one of the most scientifically investigated vegetables because of its high commercial importance [3]. The tomato is highly perishable, and post-harvesting losses reach 25 to 50%. There is a loss of 20–50% from harvesting to consumption [4,5,6]. The water content of tomato fruit is very high, and the water content is as high as 93–95% [7]. It is low in calories and rich in vitamins A, C and E and minerals, such as calcium, potassium, phosphorus.
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