Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species
Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study,...
| Autores principales: | , , , , , , , |
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| Formato: | info:eu-repo/semantics/article |
| Lenguaje: | Inglés |
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MDPI
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/20.500.12955/2275 https://doi.org/10.3390/data7090123 |
| _version_ | 1855028770501558272 |
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| author | Saldaña Serrano, Carla Lizet Chávez Galarza, Julio César De la Cruz, Germán Jhoncon, Jorge H. Guerrero Abad, Juan Carlos Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin |
| author_browse | Arbizu Berrocal, Carlos Irvin Chávez Galarza, Julio César De la Cruz, Germán Guerrero Abad, Juan Carlos Jhoncon, Jorge H. Maicelo Quintana, Jorge Luis Saldaña Serrano, Carla Lizet Vásquez Pérez, Héctor Vladimir |
| author_facet | Saldaña Serrano, Carla Lizet Chávez Galarza, Julio César De la Cruz, Germán Jhoncon, Jorge H. Guerrero Abad, Juan Carlos Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin |
| author_sort | Saldaña Serrano, Carla Lizet |
| collection | Repositorio INIA |
| description | Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum was 155,681 bp in length and included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 87 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Similar to previous studies, our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect that this first sweet cucumber chloroplast genome will provide potential molecular markers and genomic resources to shed light on the genetic diversity and population studies of S. muricatum, which will allow us to identify varieties and ecotypes. Finally, the features and the structural differentiation will provide us with information about the genes of interest, generating tools for the most precise selection of the best individuals of sweet cucumber, in less time and with fewer resources. |
| format | info:eu-repo/semantics/article |
| id | INIA2275 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | INIA22752023-08-31T17:34:36Z Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species Saldaña Serrano, Carla Lizet Chávez Galarza, Julio César De la Cruz, Germán Jhoncon, Jorge H. Guerrero Abad, Juan Carlos Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin Chloroplast Genome Sweet cucumber Solanaceae Next-generation sequencing https://purl.org/pe-repo/ocde/ford#4.04.01 Chloroplasts Cloroplasto Genomes Genomas Solanum muricatum Solanaceae High-throughput sequencing Secuenciación de alto rendimiento Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum was 155,681 bp in length and included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 87 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Similar to previous studies, our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect that this first sweet cucumber chloroplast genome will provide potential molecular markers and genomic resources to shed light on the genetic diversity and population studies of S. muricatum, which will allow us to identify varieties and ecotypes. Finally, the features and the structural differentiation will provide us with information about the genes of interest, generating tools for the most precise selection of the best individuals of sweet cucumber, in less time and with fewer resources. 2023-08-31T17:34:34Z 2023-08-31T17:34:34Z 2022-09-01 info:eu-repo/semantics/article Saldaña, C. L., Chávez-Galarza, J. C., De la Cruz, G., Jhoncon, J. H., Guerrero-Abad, J. C., Vásquez, H. V., Maicelo, J. L., & Arbizu, C. I. (2022). Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species. Data, 7(9), 123. doi: 10.3390/data7090123 2306-5729 https://hdl.handle.net/20.500.12955/2275 https://doi.org/10.3390/data7090123 eng urn:isnn:2306-5729 Data info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf MDPI CH Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Chloroplast Genome Sweet cucumber Solanaceae Next-generation sequencing https://purl.org/pe-repo/ocde/ford#4.04.01 Chloroplasts Cloroplasto Genomes Genomas Solanum muricatum Solanaceae High-throughput sequencing Secuenciación de alto rendimiento Saldaña Serrano, Carla Lizet Chávez Galarza, Julio César De la Cruz, Germán Jhoncon, Jorge H. Guerrero Abad, Juan Carlos Vásquez Pérez, Héctor Vladimir Maicelo Quintana, Jorge Luis Arbizu Berrocal, Carlos Irvin Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species |
| title | Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species |
| title_full | Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species |
| title_fullStr | Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species |
| title_full_unstemmed | Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species |
| title_short | Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species |
| title_sort | revealing the complete chloroplast genome of an andean horticultural crop sweet cucumber solanum muricatum and its comparison with other solanaceae species |
| topic | Chloroplast Genome Sweet cucumber Solanaceae Next-generation sequencing https://purl.org/pe-repo/ocde/ford#4.04.01 Chloroplasts Cloroplasto Genomes Genomas Solanum muricatum Solanaceae High-throughput sequencing Secuenciación de alto rendimiento |
| url | https://hdl.handle.net/20.500.12955/2275 https://doi.org/10.3390/data7090123 |
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