Abstract
The tree tomato (Solanum betaceum Cav.) is an underutilized fruit crop native to the Andean region and phylogenetically related to the tomato and potato. Tree tomato fruits have a high amount of nutrients and bioactive compounds. However, so far there are no studies at the genome or transcriptome level for this species. We performed a de novo assembly and transcriptome annotation for purple-fruited (A21) and an orange-fruited (A23) accessions. A total of 174,252 (A21) and 194,417 (A23) transcripts were assembled with an average length of 851 and 849 bp. A total of 34,636 (A21) and 36,224 (A23) transcripts showed a significant similarity to known proteins. Among the annotated unigenes, 22,096 (A21) and 23,095 (A23) were assigned to the Gene Ontology (GO) term and 14,035 (A21) and 14,540 (A23) were found to have Clusters of Orthologous Group (COG) term classifications. Furthermore, 22,096 (A21) and 23,095 (A23) transcripts were assigned to 155 and 161 (A23) KEGG pathways. The carotenoid biosynthetic process GO terms were significantly enriched in the purple-fruited accession A21. Finally, 68,647 intraspecific single-nucleotide variations (SNVs) and almost 2 million interspecific SNVs were identified. The results of this study provide a wealth of genomic data for the genetic improvement of the tree tomato.
Highlights
The tree tomato or tamarillo (Solanum betaceum Cav.) is a Solanaceae crop native to the Andean region [1,2]
The RNA sequencing of the two tree tomato accessions yielded 100,919,310 (14.68 Gb) and 113,802,281 (15.84 Gb) raw paired-end reads for A21 and A23, respectively (Table 1)
Regarding the SVNs found in the candidate genes involved in the carotenoids biosynthesis pathway, our results showed that the coding region of the prolycopene isomerase (CRTISO) gene exhibited the highest number of SNPs, which could be due to mutations in its coding sequence
Summary
The tree tomato or tamarillo (Solanum betaceum Cav.) is a Solanaceae crop native to the Andean region [1,2]. The tree tomato has caught the attention of growers and the industry due to its attractive, fleshy, edible fruits, which can be consumed either in salads or as a dessert fruit, or processed for making jams, yogurts, juices, or alcoholic beverages, among others [5]. It has developed from being a neglected crop, with a local interest in subsistence farms [6], into a promising fruit crop, having been introduced in several countries of Oceania, Southeast Asia, Europe and Africa [7].
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