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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Autores principales:	Juan Pacheco, Santiago Vilanova, Rubén Grillo-Risco, Francisco García-García, Jaime Prohens, Pietro Gramazio
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	de novo transcriptome assembly emerging crop functional annotation molecular markers RNA-Seq Solanaceae Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/102025be9d654b2dabc3514e77d3ec36
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spelling	oai:doaj.org-article:102025be9d654b2dabc3514e77d3ec362021-11-25T17:47:03ZDe novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color10.3390/horticulturae71104312311-7524https://doaj.org/article/102025be9d654b2dabc3514e77d3ec362021-10-01T00:00:00Zhttps://www.mdpi.com/2311-7524/7/11/431https://doaj.org/toc/2311-7524The 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.Juan PachecoSantiago VilanovaRubén Grillo-RiscoFrancisco García-GarcíaJaime ProhensPietro GramazioMDPI AGarticlede novo transcriptome assemblyemerging cropfunctional annotationmolecular markersRNA-SeqSolanaceaePlant cultureSB1-1110ENHorticulturae, Vol 7, Iss 431, p 431 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	de novo transcriptome assembly emerging crop functional annotation molecular markers RNA-Seq Solanaceae Plant culture SB1-1110
spellingShingle	de novo transcriptome assembly emerging crop functional annotation molecular markers RNA-Seq Solanaceae Plant culture SB1-1110 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
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.
format	article
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
title	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_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_sort	de novo transcriptome assembly and comprehensive annotation of two tree tomato cultivars (<i>solanum betaceum</i> cav.) with different fruit color
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/102025be9d654b2dabc3514e77d3ec36
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De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (<i>Solanum betaceum</i> Cav.) with Different Fruit Color

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