Cargando…

Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species

MicroRNAs (miRNAs) are regulators of the post-transcription stage of gene activity documented to play central roles in flower and fruit development in model plant species. However, little is known about their roles and differences in domesticated and wild Capsicum species. In this study, we used hig...

Descripción completa

Detalles Bibliográficos
Autores principales: Lopez-Ortiz, Carlos, Peña-Garcia, Yadira, Bhandari, Menuka, Abburi, Venkata Lakshmi, Natarajan, Purushothaman, Stommel, John, Nimmakayala, Padma, Reddy, Umesh K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8125703/
https://www.ncbi.nlm.nih.gov/pubmed/34064462
http://dx.doi.org/10.3390/ijms22094866
_version_ 1783693579798970368
author Lopez-Ortiz, Carlos
Peña-Garcia, Yadira
Bhandari, Menuka
Abburi, Venkata Lakshmi
Natarajan, Purushothaman
Stommel, John
Nimmakayala, Padma
Reddy, Umesh K.
author_facet Lopez-Ortiz, Carlos
Peña-Garcia, Yadira
Bhandari, Menuka
Abburi, Venkata Lakshmi
Natarajan, Purushothaman
Stommel, John
Nimmakayala, Padma
Reddy, Umesh K.
author_sort Lopez-Ortiz, Carlos
collection PubMed
description MicroRNAs (miRNAs) are regulators of the post-transcription stage of gene activity documented to play central roles in flower and fruit development in model plant species. However, little is known about their roles and differences in domesticated and wild Capsicum species. In this study, we used high-throughput sequencing to analyze the miRNA content at three developmental stages (flower, small fruit, and middle fruit) from two cultivated (C. baccatum and C. annuum) and two wild (C. chacoense and C. eximium) pepper species. This analysis revealed 22 known and 27 novel miRNAs differentially expressed across species and tissues. A number of stage- and species-specific miRNAs were identified, and Gene Ontology terms were assigned to 138 genes targeted by the miRNAs. Most Gene Ontology terms were for the categories “genetic information processing”, “signaling and cellular processes”, “amino acid metabolism”, and “carbohydrate metabolism”. Enriched KEGG analysis revealed the pathways amino acids, sugar and nucleotide metabolism, starch and sucrose metabolism, and fructose-mannose metabolism among the principal ones regulated by miRNAs during pepper fruit ripening. We predicted miRNA–target gene interactions regulating flowering time and fruit development, including miR156/157 with SPL genes, miR159 with GaMYB proteins, miR160 with ARF genes, miR172 with AP2-like transcription factors, and miR408 with CLAVATA1 gene across the different Capsicum species. In addition, novel miRNAs play an important role in regulating interactions potentially controlling plant pathogen defense and fruit quality via fructokinase, alpha-L-arabinofuranosidase, and aromatic and neutral amino acid transporter. Overall, the small RNA-sequencing results from this study represent valuable information that provides a solid foundation for uncovering the miRNA-mediated mechanisms of flower and fruit development between domesticated and wild Capsicum species.
format Online
Article
Text
id pubmed-8125703
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-81257032021-05-17 Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species Lopez-Ortiz, Carlos Peña-Garcia, Yadira Bhandari, Menuka Abburi, Venkata Lakshmi Natarajan, Purushothaman Stommel, John Nimmakayala, Padma Reddy, Umesh K. Int J Mol Sci Article MicroRNAs (miRNAs) are regulators of the post-transcription stage of gene activity documented to play central roles in flower and fruit development in model plant species. However, little is known about their roles and differences in domesticated and wild Capsicum species. In this study, we used high-throughput sequencing to analyze the miRNA content at three developmental stages (flower, small fruit, and middle fruit) from two cultivated (C. baccatum and C. annuum) and two wild (C. chacoense and C. eximium) pepper species. This analysis revealed 22 known and 27 novel miRNAs differentially expressed across species and tissues. A number of stage- and species-specific miRNAs were identified, and Gene Ontology terms were assigned to 138 genes targeted by the miRNAs. Most Gene Ontology terms were for the categories “genetic information processing”, “signaling and cellular processes”, “amino acid metabolism”, and “carbohydrate metabolism”. Enriched KEGG analysis revealed the pathways amino acids, sugar and nucleotide metabolism, starch and sucrose metabolism, and fructose-mannose metabolism among the principal ones regulated by miRNAs during pepper fruit ripening. We predicted miRNA–target gene interactions regulating flowering time and fruit development, including miR156/157 with SPL genes, miR159 with GaMYB proteins, miR160 with ARF genes, miR172 with AP2-like transcription factors, and miR408 with CLAVATA1 gene across the different Capsicum species. In addition, novel miRNAs play an important role in regulating interactions potentially controlling plant pathogen defense and fruit quality via fructokinase, alpha-L-arabinofuranosidase, and aromatic and neutral amino acid transporter. Overall, the small RNA-sequencing results from this study represent valuable information that provides a solid foundation for uncovering the miRNA-mediated mechanisms of flower and fruit development between domesticated and wild Capsicum species. MDPI 2021-05-04 /pmc/articles/PMC8125703/ /pubmed/34064462 http://dx.doi.org/10.3390/ijms22094866 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lopez-Ortiz, Carlos
Peña-Garcia, Yadira
Bhandari, Menuka
Abburi, Venkata Lakshmi
Natarajan, Purushothaman
Stommel, John
Nimmakayala, Padma
Reddy, Umesh K.
Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
title Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
title_full Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
title_fullStr Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
title_full_unstemmed Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
title_short Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
title_sort identification of mirnas and their targets involved in flower and fruit development across domesticated and wild capsicum species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8125703/
https://www.ncbi.nlm.nih.gov/pubmed/34064462
http://dx.doi.org/10.3390/ijms22094866
work_keys_str_mv AT lopezortizcarlos identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT penagarciayadira identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT bhandarimenuka identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT abburivenkatalakshmi identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT natarajanpurushothaman identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT stommeljohn identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT nimmakayalapadma identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies
AT reddyumeshk identificationofmirnasandtheirtargetsinvolvedinflowerandfruitdevelopmentacrossdomesticatedandwildcapsicumspecies