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Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics
The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar “Hahong” by DNA- and RNA-sequencing. We found the dominance of Monilini...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464454/ https://www.ncbi.nlm.nih.gov/pubmed/32824817 http://dx.doi.org/10.3390/plants9081052 |
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author | Jo, Yeonhwa Back, Chang-Gi Choi, Hoseong Cho, Won Kyong |
author_facet | Jo, Yeonhwa Back, Chang-Gi Choi, Hoseong Cho, Won Kyong |
author_sort | Jo, Yeonhwa |
collection | PubMed |
description | The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar “Hahong” by DNA- and RNA-sequencing. We found the dominance of Monilinia fructigena followed by Sclerotinia borealis, S. sclerotiorum, and Botrytis cinerea in the mummified peach fruits. Moreover, we found a high number of Proteobacteria, including Frateuria aurantia, Neoasaia chiangmaiensis, Robbsia andropogonis, and Ewingella Americana. Furthermore, we identified several viruses and viroids. Bacteriophages were identified by DNA- and RNA-sequencing, while viruses and viroids with RNA genomes were identified by only RNA-sequencing. Moreover, we identified a novel mycovirus referred to as Monilinia umbra-like virus 1 (MULV1) from M. fructigena. Our results revealed the co-inhabitance of fungi and bacteria in the mummified peach fruits, although dominant microorganisms were present. RNA-sequencing revealed that several fungal and bacterial genes were actively transcribed. Comparative analyses suggested that RNA-sequencing provides more detailed information on microbial communities; however, combining DNA- and RNA-sequencing results increased the diversity of microorganisms, suggesting the importance of databases and analysis tools for microbiome studies. Taken together, our study provides a comprehensive overview of microbial communities in mummified peach fruits by DNA shotgun sequencing and RNA-sequencing. |
format | Online Article Text |
id | pubmed-7464454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-74644542020-09-04 Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics Jo, Yeonhwa Back, Chang-Gi Choi, Hoseong Cho, Won Kyong Plants (Basel) Article The dried peach fruits clinging to peach trees or lying on the ground nearby are known as mummified peach fruits. Here, we examined the microbiome communities of three different mummified peach fruits from the nectarine cultivar “Hahong” by DNA- and RNA-sequencing. We found the dominance of Monilinia fructigena followed by Sclerotinia borealis, S. sclerotiorum, and Botrytis cinerea in the mummified peach fruits. Moreover, we found a high number of Proteobacteria, including Frateuria aurantia, Neoasaia chiangmaiensis, Robbsia andropogonis, and Ewingella Americana. Furthermore, we identified several viruses and viroids. Bacteriophages were identified by DNA- and RNA-sequencing, while viruses and viroids with RNA genomes were identified by only RNA-sequencing. Moreover, we identified a novel mycovirus referred to as Monilinia umbra-like virus 1 (MULV1) from M. fructigena. Our results revealed the co-inhabitance of fungi and bacteria in the mummified peach fruits, although dominant microorganisms were present. RNA-sequencing revealed that several fungal and bacterial genes were actively transcribed. Comparative analyses suggested that RNA-sequencing provides more detailed information on microbial communities; however, combining DNA- and RNA-sequencing results increased the diversity of microorganisms, suggesting the importance of databases and analysis tools for microbiome studies. Taken together, our study provides a comprehensive overview of microbial communities in mummified peach fruits by DNA shotgun sequencing and RNA-sequencing. MDPI 2020-08-18 /pmc/articles/PMC7464454/ /pubmed/32824817 http://dx.doi.org/10.3390/plants9081052 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Jo, Yeonhwa Back, Chang-Gi Choi, Hoseong Cho, Won Kyong Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics |
title | Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics |
title_full | Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics |
title_fullStr | Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics |
title_full_unstemmed | Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics |
title_short | Comparative Microbiome Study of Mummified Peach Fruits by Metagenomics and Metatranscriptomics |
title_sort | comparative microbiome study of mummified peach fruits by metagenomics and metatranscriptomics |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464454/ https://www.ncbi.nlm.nih.gov/pubmed/32824817 http://dx.doi.org/10.3390/plants9081052 |
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