Advances in Omics of Chili Pepper

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 1104

Special Issue Editors


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Guest Editor
Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato 36824, Mexico
Interests: computational biology; transcriptomics; Capsicum; modeling of gene and metabolite expression; domestication

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Guest Editor
Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36924, México
Interests: Capsicum; chili pepper; tissue culture; biochemistry; molecular biology; secondary compounds; transcriptomics
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Special Issue Information

Dear Colleagues,

Chili peppers, belonging to the Capsicum genus, hold significant importance as vegetables valued for their culinary, medicinal, and ornamental purposes. Additionally, they serve as an exceptional model for studying gene regulation and plant secondary metabolism. With reference genomes for three species, tens of genome assemblies, thousands of gene expression studies, at least forty-five clinical trials, and a vast collection of other publicly available resources at the NCBI and other data repositories, this crop stands out as one of the most extensively and comprehensively documented species within the Solanaceae family.

This Special Issue of Plants aims to contribute to the comprehensive understanding of the molecular aspects of chili pepper biology. It will encompass advances in the understanding of their genomes and molecular phenotypes, including the expression of genes, metabolites, and proteins, as well as the mechanisms involved in regulating these traits. The primary focus is to present an up-to-date panorama of integrative omics advances related to this crop. Nevertheless, we will also consider relevant progress in specific molecular aspects of Capsicum.

Dr. Octavio Martínez
Prof. Dr. Neftalí Ochoa-Alejo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Capsicum
  • chili pepper
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics

Published Papers (1 paper)

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Research

17 pages, 393 KiB  
Article
Estimating Transcriptome Diversity and Specialization in Capsicum annuum L.
by Neftalí Ochoa-Alejo, M. Humberto Reyes-Valdés and Octavio Martínez
Plants 2024, 13(7), 983; https://doi.org/10.3390/plants13070983 - 29 Mar 2024
Viewed by 827
Abstract
Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation [...] Read more.
Chili pepper fruits of the genus Capsicum represent excellent experimental models to study the growth, development, and ripening processes in a non-climacteric species at the physiological, biochemical, and molecular levels. Fruit growth, development, and ripening involve a complex, harmonious, and finely controlled regulation of gene expression. The purpose of this study was to estimate the changes in transcriptome diversity and specialization, as well as gene specificities during fruit development in this crop, and to illustrate the advantages of estimating these parameters. To achieve these aims, we programmed and made publicly available an R package. In this study, we applied these methods to a set of 179 RNA-Seq libraries from a factorial experiment that includes 12 different genotypes at various stages of fruit development. We found that the diversity of the transcriptome decreases linearly from the flower to the mature fruit, while its specialization follows a complex and non-linear behavior during this process. Additionally, by defining sets of genes with different degrees of specialization and applying Gene Ontology enrichment analysis, we identified processes, functions, and components that play a central role in particular fruit development stages. In conclusion, the estimation of diversity, specialization, and specificity summarizes the global properties of the transcriptomes, providing insights that are difficult to achieve by other means. Full article
(This article belongs to the Special Issue Advances in Omics of Chili Pepper)
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