Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper
The Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence...
| Main Authors: | , , , , , |
|---|---|
| Format: | Artículo |
| Language: | Inglés |
| Published: |
Springer
2024
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/20.500.12955/2546 https://doi.org/10.1007/s10722-024-01941-4 |
| _version_ | 1855490476428230656 |
|---|---|
| author | Estrada, Richard Calderon Tantalean, José Franklin Saldaña Serrano, Carla Lizet Romero, Yolanda Vilcara, Edgardo Arbizu, Carlos Irvin |
| author_browse | Arbizu, Carlos Irvin Calderon Tantalean, José Franklin Estrada, Richard Romero, Yolanda Saldaña Serrano, Carla Lizet Vilcara, Edgardo |
| author_facet | Estrada, Richard Calderon Tantalean, José Franklin Saldaña Serrano, Carla Lizet Romero, Yolanda Vilcara, Edgardo Arbizu, Carlos Irvin |
| author_sort | Estrada, Richard |
| collection | Repositorio INIA |
| description | The Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence of this chili pepper was generated using the Illumina Hiseq 2500 sequencing technology. We sequenced the whole genome of the ACP using a paired-end 150 strategy, obtaining 330.46 GB of sequencing data. The genome size of the ACP was 2.98 Gb with a contig N50 of 237 Mb and 95.39% complete BUSCOs. Also, we identified 71.96% of repetitive DNA of the genome assembly, of which retroelements occupy 37.95% of the total genome. We downloaded genomes of the Solanoideae subfamily and conducted a comparative analysis of simple sequence repeats (SSRs) with our draft genome, and we identified lower number of SSRs in the ACP genome compared to other pepper species. This first ACP genome is expected to contribute to a better understanding of its genetics to adapt to the arid conditions of the Peruvian coastal ecosystem and evolution. |
| format | Artículo |
| id | INIA2546 |
| institution | Institucional Nacional de Innovación Agraria |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INIA25462024-07-19T22:31:59Z Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper Estrada, Richard Calderon Tantalean, José Franklin Saldaña Serrano, Carla Lizet Romero, Yolanda Vilcara, Edgardo Arbizu, Carlos Irvin Assembly Genomics Illumina sequencing NGS SSR data mining https://purl.org/pe-repo/ocde/ford#4.04.01 Genomics Genómica Sequence analysis Análisis de secuencias Microsatellites Microsatélite The Arnaucho chili pepper (ACP) is a traditional vegetable used in Peru because of its gastronomic properties. Due to its importance in the Peruvian diet and economy, this species is a resource that can be a candidate to plant breeding programs. In this study, the complete genome nucleotide sequence of this chili pepper was generated using the Illumina Hiseq 2500 sequencing technology. We sequenced the whole genome of the ACP using a paired-end 150 strategy, obtaining 330.46 GB of sequencing data. The genome size of the ACP was 2.98 Gb with a contig N50 of 237 Mb and 95.39% complete BUSCOs. Also, we identified 71.96% of repetitive DNA of the genome assembly, of which retroelements occupy 37.95% of the total genome. We downloaded genomes of the Solanoideae subfamily and conducted a comparative analysis of simple sequence repeats (SSRs) with our draft genome, and we identified lower number of SSRs in the ACP genome compared to other pepper species. This first ACP genome is expected to contribute to a better understanding of its genetics to adapt to the arid conditions of the Peruvian coastal ecosystem and evolution. 2024-07-19T22:31:57Z 2024-07-19T22:31:57Z 2024-03-25 info:eu-repo/semantics/article Estrada, R.; Calderon-Tantalean, J. F.; Saldaña, C. L.; Romero, Y.; Vilcara, E.& Arbizu, C. I. (2024). Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper. Genetic Resources and Crop Evolution. doi: 10.1007/s10722-024-01941-4 1573-5109 https://hdl.handle.net/20.500.12955/2546 https://doi.org/10.1007/s10722-024-01941-4 eng urn:issn:1573-5109 Genetic Resources and Crop Evolution info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ application/pdf application/pdf Springer NL Instituto Nacional de Innovación Agraria Repositorio Institucional - INIA |
| spellingShingle | Assembly Genomics Illumina sequencing NGS SSR data mining https://purl.org/pe-repo/ocde/ford#4.04.01 Genomics Genómica Sequence analysis Análisis de secuencias Microsatellites Microsatélite Estrada, Richard Calderon Tantalean, José Franklin Saldaña Serrano, Carla Lizet Romero, Yolanda Vilcara, Edgardo Arbizu, Carlos Irvin Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper |
| title | Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper |
| title_full | Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper |
| title_fullStr | Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper |
| title_full_unstemmed | Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper |
| title_short | Draft genome and SSR data mining of a Peruvian landrace of Capsicum chinense, the arnaucho chili pepper |
| title_sort | draft genome and ssr data mining of a peruvian landrace of capsicum chinense the arnaucho chili pepper |
| topic | Assembly Genomics Illumina sequencing NGS SSR data mining https://purl.org/pe-repo/ocde/ford#4.04.01 Genomics Genómica Sequence analysis Análisis de secuencias Microsatellites Microsatélite |
| url | https://hdl.handle.net/20.500.12955/2546 https://doi.org/10.1007/s10722-024-01941-4 |
| work_keys_str_mv | AT estradarichard draftgenomeandssrdataminingofaperuvianlandraceofcapsicumchinensethearnauchochilipepper AT calderontantaleanjosefranklin draftgenomeandssrdataminingofaperuvianlandraceofcapsicumchinensethearnauchochilipepper AT saldanaserranocarlalizet draftgenomeandssrdataminingofaperuvianlandraceofcapsicumchinensethearnauchochilipepper AT romeroyolanda draftgenomeandssrdataminingofaperuvianlandraceofcapsicumchinensethearnauchochilipepper AT vilcaraedgardo draftgenomeandssrdataminingofaperuvianlandraceofcapsicumchinensethearnauchochilipepper AT arbizucarlosirvin draftgenomeandssrdataminingofaperuvianlandraceofcapsicumchinensethearnauchochilipepper |