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Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production

Siraprapa Brooks, Jack A. Weaver, Anthikan Klomchit, Shumukh Alharthi, Thanyarat Onlamun, Rithika Nurani, Thienthu Khanh Vong, Fabrizio Alberti, Claudio Greco Orcid Logo

Frontiers in Chemical Biology, Volume: 3

Swansea University Authors: Shumukh Alharthi, Claudio Greco Orcid Logo

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DOI (Published version): 10.3389/fchbi.2024.1362147

Abstract

Endophytic fungi constitute a rich source of secondary metabolites that can be manipulated to produce desirable novel analogs for combating current agricultural challenges for crop production, especially controlling plant disease. The endophytic fungus Daldinia eschscholtzii MFLUCC 19-0629, was newl...

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Published in: Frontiers in Chemical Biology
ISSN: 2813-530X
Published: Frontiers Media SA 2024
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The endophytic fungus Daldinia eschscholtzii MFLUCC 19-0629, was newly isolated from tropical ancient plants, Oncosperma sp., and displays a broad-spectrum of antifungal and antibacterial activities against several plant pathogens including Ralstonia solanacearum, Fusarium oxysporum, Colletotrichum gloeosporioides, Colletotrichum acutatum, Stagonosporopsis cucurbitacearum, Corynespora cassiicola and Stemphylium spp. A high-quality genome sequence was obtained using Oxford nanopore technology, the accuracy and length of reads resulting in no need for Illumina or other sequencing techniques, for D. eschscholtzii MFLUCC 19-0629, resulting in a genome size of 37.56 Mb assembled over 11 contigs of significant size, likely to be at the chromosomal level. Bioinformatics analysis revealed that this strain is biosynthetically talented encoding 67 predicted biosynthetic gene clusters (BGCs). Only eight of the 67 BGCs matched or demonstrated high similarity to previously characterized BGCs linked to the production of known secondary metabolites. The high number of predicted unknown BGCs makes this strain a promising source of novel natural products. The discovery that D. eschscholtzii MFLUCC 19-0629 has a broad spectrum of antimicrobial activity against seven major plant pathogenic microorganisms relevant to crop production and its complete genome sequence carries immense importance in the advancement of novel microbial biocontrol agents (MBCAs). 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spelling v2 66224 2024-04-30 Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production 78d65007643ec30405caaf9df99c06e8 Shumukh Alharthi Shumukh Alharthi true false cacac6459bd7cf4a241f63661006036f 0000-0003-3067-0999 Claudio Greco Claudio Greco true false 2024-04-30 BGPS Endophytic fungi constitute a rich source of secondary metabolites that can be manipulated to produce desirable novel analogs for combating current agricultural challenges for crop production, especially controlling plant disease. The endophytic fungus Daldinia eschscholtzii MFLUCC 19-0629, was newly isolated from tropical ancient plants, Oncosperma sp., and displays a broad-spectrum of antifungal and antibacterial activities against several plant pathogens including Ralstonia solanacearum, Fusarium oxysporum, Colletotrichum gloeosporioides, Colletotrichum acutatum, Stagonosporopsis cucurbitacearum, Corynespora cassiicola and Stemphylium spp. A high-quality genome sequence was obtained using Oxford nanopore technology, the accuracy and length of reads resulting in no need for Illumina or other sequencing techniques, for D. eschscholtzii MFLUCC 19-0629, resulting in a genome size of 37.56 Mb assembled over 11 contigs of significant size, likely to be at the chromosomal level. Bioinformatics analysis revealed that this strain is biosynthetically talented encoding 67 predicted biosynthetic gene clusters (BGCs). Only eight of the 67 BGCs matched or demonstrated high similarity to previously characterized BGCs linked to the production of known secondary metabolites. The high number of predicted unknown BGCs makes this strain a promising source of novel natural products. The discovery that D. eschscholtzii MFLUCC 19-0629 has a broad spectrum of antimicrobial activity against seven major plant pathogenic microorganisms relevant to crop production and its complete genome sequence carries immense importance in the advancement of novel microbial biocontrol agents (MBCAs). This also unveils the prospect of uncovering new compounds that could be utilized for sustainable agriculture and pharmaceutical purposes. Journal Article Frontiers in Chemical Biology 3 Frontiers Media SA 2813-530X secondary metabolites, fungal endophytes, biosynthetic gene clusters, microbial biocontrol agents, Daldinia, genome 1 3 2024 2024-03-01 10.3389/fchbi.2024.1362147 COLLEGE NANME Biosciences Geography and Physics School COLLEGE CODE BGPS Swansea University Not Required The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. CG was supported by the BBSRC BB/V005723/2. SA’s PhD Scholarship was supported by Taif University. JW was supported by a scholarship from the Engineering and Physical Sciences Research Council and the Biotechnology and Biological Sciences Research Council (EP/L016494/1) through the Centre for Doctoral Training in Synthetic Biology (SynBioCDT). FA was supported by a UKRI Future Leaders Fellowship (MR/V022334/1). SB was supported by Mae Fah Luang University under the grant name “Reinventing University 2021” and Minister of Higher Education, Science, Research and Innovation under grant name “Talent Mobility 2023 (TM65005).” 2024-05-07T16:50:33.8167358 2024-04-30T17:15:42.6087303 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Siraprapa Brooks 1 Jack A. Weaver 2 Anthikan Klomchit 3 Shumukh Alharthi 4 Thanyarat Onlamun 5 Rithika Nurani 6 Thienthu Khanh Vong 7 Fabrizio Alberti 8 Claudio Greco 0000-0003-3067-0999 9 66224__30304__db4434472780403888503b84576abb22.pdf 66224.VoR.pdf 2024-05-07T16:48:57.7904223 Output 2381453 application/pdf Version of Record true © 2024 Brooks, Weaver, Klomchit, Alharthi, Onlamun, Nurani, Vong, Alberti and Greco. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). true eng https://creativecommons.org/licenses/by/4.0/
title Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
spellingShingle Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
Shumukh Alharthi
Claudio Greco
title_short Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
title_full Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
title_fullStr Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
title_full_unstemmed Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
title_sort Unveiling the potential of Daldinia eschscholtzii MFLUCC 19-0629 through bioactivity and bioinformatics studies for enhanced sustainable agriculture production
author_id_str_mv 78d65007643ec30405caaf9df99c06e8
cacac6459bd7cf4a241f63661006036f
author_id_fullname_str_mv 78d65007643ec30405caaf9df99c06e8_***_Shumukh Alharthi
cacac6459bd7cf4a241f63661006036f_***_Claudio Greco
author Shumukh Alharthi
Claudio Greco
author2 Siraprapa Brooks
Jack A. Weaver
Anthikan Klomchit
Shumukh Alharthi
Thanyarat Onlamun
Rithika Nurani
Thienthu Khanh Vong
Fabrizio Alberti
Claudio Greco
format Journal article
container_title Frontiers in Chemical Biology
container_volume 3
publishDate 2024
institution Swansea University
issn 2813-530X
doi_str_mv 10.3389/fchbi.2024.1362147
publisher Frontiers Media SA
college_str Faculty of Science and Engineering
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hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 1
active_str 0
description Endophytic fungi constitute a rich source of secondary metabolites that can be manipulated to produce desirable novel analogs for combating current agricultural challenges for crop production, especially controlling plant disease. The endophytic fungus Daldinia eschscholtzii MFLUCC 19-0629, was newly isolated from tropical ancient plants, Oncosperma sp., and displays a broad-spectrum of antifungal and antibacterial activities against several plant pathogens including Ralstonia solanacearum, Fusarium oxysporum, Colletotrichum gloeosporioides, Colletotrichum acutatum, Stagonosporopsis cucurbitacearum, Corynespora cassiicola and Stemphylium spp. A high-quality genome sequence was obtained using Oxford nanopore technology, the accuracy and length of reads resulting in no need for Illumina or other sequencing techniques, for D. eschscholtzii MFLUCC 19-0629, resulting in a genome size of 37.56 Mb assembled over 11 contigs of significant size, likely to be at the chromosomal level. Bioinformatics analysis revealed that this strain is biosynthetically talented encoding 67 predicted biosynthetic gene clusters (BGCs). Only eight of the 67 BGCs matched or demonstrated high similarity to previously characterized BGCs linked to the production of known secondary metabolites. The high number of predicted unknown BGCs makes this strain a promising source of novel natural products. The discovery that D. eschscholtzii MFLUCC 19-0629 has a broad spectrum of antimicrobial activity against seven major plant pathogenic microorganisms relevant to crop production and its complete genome sequence carries immense importance in the advancement of novel microbial biocontrol agents (MBCAs). This also unveils the prospect of uncovering new compounds that could be utilized for sustainable agriculture and pharmaceutical purposes.
published_date 2024-03-01T16:50:32Z
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