De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color
The tree tomato (<i>Solanum betaceum</i> 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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/7/11/431 |
| _version_ | 1827676491783077888 |
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| author | Juan Pacheco Santiago Vilanova Rubén Grillo-Risco Francisco García-García Jaime Prohens Pietro Gramazio |
| author_facet | Juan Pacheco Santiago Vilanova Rubén Grillo-Risco Francisco García-García Jaime Prohens Pietro Gramazio |
| author_sort | Juan Pacheco |
| collection | DOAJ |
| description | The tree tomato (<i>Solanum betaceum</i> 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. |
| first_indexed | 2024-03-10T05:27:15Z |
| format | Article |
| id | doaj.art-102025be9d654b2dabc3514e77d3ec36 |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-10T05:27:15Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj.art-102025be9d654b2dabc3514e77d3ec362023-11-22T23:33:35ZengMDPI AGHorticulturae2311-75242021-10-0171143110.3390/horticulturae7110431De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit ColorJuan Pacheco0Santiago Vilanova1Rubén Grillo-Risco2Francisco García-García3Jaime Prohens4Pietro Gramazio5Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, SpainInstituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, SpainPrincipe Felipe Research Center (CIPF), Bioinformatics and Biostatistics Unit, Eduardo Primo Yúfera 3, 46012 Valencia, SpainPrincipe Felipe Research Center (CIPF), Bioinformatics and Biostatistics Unit, Eduardo Primo Yúfera 3, 46012 Valencia, SpainInstituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, SpainInstituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, SpainThe tree tomato (<i>Solanum betaceum</i> 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.https://www.mdpi.com/2311-7524/7/11/431de novo transcriptome assemblyemerging cropfunctional annotationmolecular markersRNA-SeqSolanaceae |
| spellingShingle | Juan Pacheco Santiago Vilanova Rubén Grillo-Risco Francisco García-García Jaime Prohens Pietro Gramazio De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color Horticulturae de novo transcriptome assembly emerging crop functional annotation molecular markers RNA-Seq Solanaceae |
| title | De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color |
| title_full | De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color |
| title_fullStr | De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color |
| title_full_unstemmed | De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color |
| title_short | De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color |
| title_sort | de novo transcriptome assembly and comprehensive annotation of two tree tomato cultivars i solanum betaceum i cav with different fruit color |
| topic | de novo transcriptome assembly emerging crop functional annotation molecular markers RNA-Seq Solanaceae |
| url | https://www.mdpi.com/2311-7524/7/11/431 |
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