IDEAS home Printed from https://ideas.repec.org/a/gam/jdataj/v7y2022i9p123-d903988.html
   My bibliography  Save this article

Revealing the Complete Chloroplast Genome of an Andean Horticultural Crop, Sweet Cucumber (Solanum muricatum) , and Its Comparison with Other Solanaceae Species

Author

Listed:
  • Carla L. Saldaña

    (Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru)

  • Julio C. Chávez-Galarza

    (Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
    Departamento Académico de Ciencias Básicas y Afines, Universidad Nacional de Barranca, Av. Toribio de Luzuriaga 376, Urbanización La Florida Mz J, Lima 15169, Peru)

  • Germán De la Cruz

    (Laboratorio de Genética y Biotecnología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional San Cristóbal de Huamanga, Portal Constitución 57, Ayacucho 05003, Peru)

  • Jorge H. Jhoncon

    (Centro de Investigación de Plantas Andinas y Nativas, Facultad de Ciencias, Universidad Nacional de Educación Enrique Guzmán y Valle, Av. Enrique Guzmán y Valle s/n, Lima 15472, Peru
    Unidad de Investigación, Wanxin Group EIRL. Av. La Marina 800, Lima 15084, Peru)

  • Juan C. Guerrero-Abad

    (Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru)

  • Héctor V. Vásquez

    (Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
    Facultad de Zootecnia, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Chachapoyas 01001, Peru)

  • Jorge L. Maicelo

    (Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
    Facultad de Zootecnia, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Chachapoyas 01001, Peru)

  • Carlos I. Arbizu

    (Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru)

Abstract

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.

Suggested Citation

  • Carla L. Saldaña & Julio C. Chávez-Galarza & Germán De la Cruz & Jorge H. Jhoncon & Juan C. Guerrero-Abad & Héctor V. Vásquez & Jorge L. Maicelo & Carlos I. Arbizu, 2022. "Revealing the Complete Chloroplast Genome of an Andean Horticultural Crop, Sweet Cucumber (Solanum muricatum) , and Its Comparison with Other Solanaceae Species," Data, MDPI, vol. 7(9), pages 1-14, September.
    • Handle: RePEc:gam:jdataj:v:7:y:2022:i:9:p:123-:d:903988
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2306-5729/7/9/123/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/2306-5729/7/9/123/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    1. Hiroshi Kuroda & Pal Maliga, 2003. "The plastid clpP1 protease gene is essential for plant development," Nature, Nature, vol. 425(6953), pages 86-89, September.
    2. Liyuan Wang & Huixian Xing & Yanchao Yuan & Xianlin Wang & Muhammad Saeed & Jincai Tao & Wei Feng & Guihua Zhang & Xianliang Song & Xuezhen Sun, 2018. "Genome-wide analysis of codon usage bias in four sequenced cotton species," PLOS ONE, Public Library of Science, vol. 13(3), pages 1-17, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.

      Corrections

      All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jdataj:v:7:y:2022:i:9:p:123-:d:903988. See general information about how to correct material in RePEc.

      If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

      If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

      If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

      For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

      Please note that corrections may take a couple of weeks to filter through the various RePEc services.

      IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.