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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...

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Autores principales: Jo, Yeonhwa, Back, Chang-Gi, Choi, Hoseong, Cho, Won Kyong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
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.
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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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