Datasets of fungal diversity and pseudo-chromosomal genomes of mangrove rhizosphere soil in China.


Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
20 Aug 2024
Historique:
received: 26 01 2024
accepted: 06 08 2024
medline: 21 8 2024
pubmed: 21 8 2024
entrez: 20 8 2024
Statut: epublish

Résumé

With climate change and anthropic influence on the coastal ecosystems, mangrove ecosystems are disappearing at an alarming rate. Accordingly, it becomes important to track, study, record and store the mangrove microbial community considering their ecological importance and potential for biotechnological applications. Here, we provide information on mangrove fungal community composition and diversity in mangrove ecosystems with different plant species and from various locations differing in relation to anthropic influences. We describe twelve newly assembled genomes, including four chromosomal-level genomes of fungal isolates from the mangrove ecosystems coupled with functional annotations. We envisage that these data will be of value for future studies including comparative genome analysis and large-scale temporal and/or spatial research to elucidate the potential mechanisms by which mangrove fungal communities assemble and evolve. We further anticipate that the genomes represent valuable resources for bioprospecting related to industrial or clinical uses.

Identifiants

pubmed: 39164251
doi: 10.1038/s41597-024-03748-5
pii: 10.1038/s41597-024-03748-5
doi:

Types de publication

Dataset Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

901

Subventions

Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : U2106228
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32100047

Informations de copyright

© 2024. The Author(s).

Références

He, Z. et al. Evolution of coastal forests based on a full set of mangrove genomes. Nat Ecol Evol 6, 738–749, https://doi.org/10.1038/s41559-022-01744-9 (2022).
doi: 10.1038/s41559-022-01744-9 pubmed: 35484219
Jia, S. L., Chi, Z., Liu, G. L., Hu, Z. & Chi, Z. M. Fungi in mangrove ecosystems and their potential applications. Crit Rev Biotechnol 40, 852–864, https://doi.org/10.1080/07388551.2020.1789063 (2020).
doi: 10.1080/07388551.2020.1789063 pubmed: 32633147
Alias, S. A., Zainuddin, N. & Jones, E. B. G. Biodiversity of marine fungi in Malaysian mangroves. Botanica Marina 53, https://doi.org/10.1515/bot.2010.066 (2010).
Sridhar, K. R. Mangrove fungi in India. Current science 86, 1586–1587 (2006).
Thatoi, H., Behera, B. C. & Mishra, R. R. Ecological role and biotechnological potential of mangrove fungi: a review. Mycology 4, 54–71, https://doi.org/10.1080/21501203.2013.785448 (2013).
doi: 10.1080/21501203.2013.785448
Bohu, T. et al. The role of fungi in the biogeochemical cycling of supergene gold and satellite transition metals: A potential new exploration tool. Ore Geology Reviews 140, https://doi.org/10.1016/j.oregeorev.2021.104595 (2022).
Behera, A. D., Chatterjee, S. & Das, S. Enzymatic degradation and metabolic pathway of phenanthrene by manglicolous filamentous fungus Trichoderma sp. CNSC-2. Microbiological research 276, 127483, https://doi.org/10.1016/j.micres.2023.127483 (2023).
doi: 10.1016/j.micres.2023.127483 pubmed: 37666077
Deshmukh, R., Khardenavis, A. A. & Purohit, H. J. Diverse metabolic capacities of fungi for bioremediation. Indian J Microbiol 56, 247–264, https://doi.org/10.1007/s12088-016-0584-6 (2016).
doi: 10.1007/s12088-016-0584-6 pubmed: 27407289 pmcid: 4920763
Ancheeva, E., Daletos, G. & Proksch, P. Lead compounds from mangrove-associated microorganisms. Mar Drugs 16, https://doi.org/10.3390/md16090319 (2018).
Duke, N. C. et al. A world without mangroves? Science 317, 41–42, https://doi.org/10.1126/science.317.5834.41b (2007).
doi: 10.1126/science.317.5834.41b pubmed: 17615322
Yao, H. et al. Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem. Microbiome 7, 57, https://doi.org/10.1186/s40168-019-0671-0 (2019).
doi: 10.1186/s40168-019-0671-0 pubmed: 30967154 pmcid: 6456958
Zhuang, W. et al. Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale. NPJ Biofilms Microbiomes 6, 52, https://doi.org/10.1038/s41522-020-00164-6 (2020).
doi: 10.1038/s41522-020-00164-6 pubmed: 33184266 pmcid: 7665043
Devadatha, B. et al. Occurrence and geographical distribution of mangrove fungi. Fungal Diversity 106, 137–227, https://doi.org/10.1007/s13225-020-00468-0 (2021).
doi: 10.1007/s13225-020-00468-0
Zhang, Z. F., Pan, Y. P., Liu, Y. & Li, M. High-level diversity of basal fungal lineages and the control of fungal community assembly by stochastic processes in mangrove sediments. Applied and environmental microbiology 87, e0092821, https://doi.org/10.1128/AEM.00928-21 (2021).
doi: 10.1128/AEM.00928-21 pubmed: 34190611
Chen, S., Cai, R., Liu, Z., Cui, H. & She, Z. Secondary metabolites from mangrove-associated fungi: source, chemistry and bioactivities. Nat Prod Rep 39, 560–595, https://doi.org/10.1039/d1np00041a (2022).
doi: 10.1039/d1np00041a pubmed: 34623363
Cadamuro, R. D. et al. Bioactive compounds from mangrove endophytic fungus and their uses for microorganism control. J Fungi (Basel) 7, https://doi.org/10.3390/jof7060455 (2021).
Xu, Z.-Y. et al. Secondary metabolites produced by mangrove endophytic fungus Aspergillus fumigatus HQD24 with immunosuppressive activity. Biochemical Systematics and Ecology 93, https://doi.org/10.1016/j.bse.2020.104166 (2020).
Gozari, M., Alborz, M., El-Seedi, H. R. & Jassbi, A. R. Chemistry, biosynthesis and biological activity of terpenoids and meroterpenoids in bacteria and fungi isolated from different marine habitats. Eur J Med Chem 210, 112957, https://doi.org/10.1016/j.ejmech.2020.112957 (2021).
doi: 10.1016/j.ejmech.2020.112957 pubmed: 33160760
He, X. et al. Varitatin A, a Highly modified fatty acid amide from Penicillium variabile cultured with a DNA methyltransferase Inhibitor. J Nat Prod 78, 2841–2845, https://doi.org/10.1021/acs.jnatprod.5b00742 (2015).
doi: 10.1021/acs.jnatprod.5b00742 pubmed: 26561719
Voorhies, M. et al. Chromosome-level genome assembly of a human fungal pathogen reveals synteny among geographically distinct species. mBio 13, e0257421, https://doi.org/10.1128/mbio.02574-21 (2022).
doi: 10.1128/mbio.02574-21 pubmed: 35089059
Perez-Cobas, A. E., Gomez-Valero, L. & Buchrieser, C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 6, https://doi.org/10.1099/mgen.0.000409 (2020).
Li, M. et al. Application of culturomics in fungal isolation from mangrove sediments. Microbiome 11, 272, https://doi.org/10.1186/s40168-023-01708-6 (2023).
doi: 10.1186/s40168-023-01708-6 pubmed: 38082427 pmcid: 10712113
Pham, T. T., Dinh, K. V. & Nguyen, V. D. Biodiversity and enzyme activity of marine fungi with 28 new records from the tropical coastal ecosystems in Vietnam. Mycobiology 49, 559–581, https://doi.org/10.1080/12298093.2021.2008103 (2021).
doi: 10.1080/12298093.2021.2008103 pubmed: 35035248 pmcid: 8725946
Shi, C. et al. Draft genomes and comparative analysis of seven mangrove rhizosphere-associated fungi isolated from kandelia obovata and acanthus ilicifolius. Frontiers in Fungal Biology 2, https://doi.org/10.3389/ffunb.2021.626904 (2021).
Peng, L. et al. Chromosome-level comprehensive genome of mangrove sediment-derived fungus Penicillium variabile HXQ-H-1. J Fungi (Basel) 6, https://doi.org/10.3390/jof6010007 (2019).
Naranjo-Ortiz, M. A. & Gabaldon, T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 95, 1198–1232, https://doi.org/10.1111/brv.12605 (2020).
doi: 10.1111/brv.12605 pubmed: 32301582 pmcid: 7539958
Hartl, L., Zach, S. & Seidl-Seiboth, V. Fungal chitinases: diversity, mechanistic properties and biotechnological potential. Applied microbiology and biotechnology 93, 533–543, https://doi.org/10.1007/s00253-011-3723-3 (2012).
doi: 10.1007/s00253-011-3723-3 pubmed: 22134638
Liao, S. et al. Deciphering the microbial taxonomy and functionality of two diverse mangrove ecosystems and their potential abilities to produce bioactive compounds. mSystems 5, https://doi.org/10.1128/mSystems.00851-19 (2020).
Wang, Y. et al. Dynamics of rhizosphere microbial structure and function associated with the biennial bearing of moso bamboo. J Environ Manage 351, 119977, https://doi.org/10.1016/j.jenvman.2023.119977 (2024).
doi: 10.1016/j.jenvman.2023.119977 pubmed: 38160549
Jia, Y. et al. Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies. Environ Microbiome 17, 43, https://doi.org/10.1186/s40793-022-00436-y (2022).
doi: 10.1186/s40793-022-00436-y pubmed: 35978448 pmcid: 9387074
Liu, G., Li, T., Zhu, X., Zhang, X. & Wang, J. An independent evaluation in a CRC patient cohort of microbiome 16S rRNA sequence analysis methods: OTU clustering, DADA2, and Deblur. Front Microbiol 14, 1178744, https://doi.org/10.3389/fmicb.2023.1178744 (2023).
doi: 10.3389/fmicb.2023.1178744 pubmed: 37560524 pmcid: 10408458
Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90, https://doi.org/10.1186/s40168-018-0470-z (2018).
doi: 10.1186/s40168-018-0470-z pubmed: 29773078 pmcid: 5956843
Liu, Y. X. et al. EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research. iMeta 2, https://doi.org/10.1002/imt2.83 (2023).
Liu, H., Wu, S., Li, A. & Ruan, J. SMARTdenovo: a de novo assembler using long noisy reads. GigaByte 2021, gigabyte15, https://doi.org/10.46471/gigabyte.15 (2021).
doi: 10.46471/gigabyte.15 pubmed: 36824332 pmcid: 9632051
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27, 722–736, https://doi.org/10.1101/gr.215087.116 (2017).
doi: 10.1101/gr.215087.116 pubmed: 28298431 pmcid: 5411767
Wang, J. et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS one 9, e112963, https://doi.org/10.1371/journal.pone.0112963 (2014).
doi: 10.1371/journal.pone.0112963
Wang, O. et al. Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res 29, 798–808, https://doi.org/10.1101/gr.245126.118 (2019).
doi: 10.1101/gr.245126.118 pubmed: 30940689 pmcid: 6499310
Zhang, Z. et al. Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content. iScience 24, 102219, https://doi.org/10.1016/j.isci.2021.102219 (2021).
doi: 10.1016/j.isci.2021.102219 pubmed: 33748707 pmcid: 7961107
Qi, Y. et al. MetaTrass: A high‐quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads. iMeta, https://doi.org/10.1002/imt2.46 (2022).
Guo, L. et al. SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. BMC Bioinformatics 22, 158, https://doi.org/10.1186/s12859-021-04081-z (2021).
doi: 10.1186/s12859-021-04081-z pubmed: 33765921 pmcid: 7993450
Tang, H. et al. JCVI: A versatile toolkit for comparative genomics analysis. iMeta https://doi.org/10.1002/imt2.211 (2024).
doi: 10.1002/imt2.211 pubmed: 39135692 pmcid: 11316928
Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol 23, 258, https://doi.org/10.1186/s13059-022-02823-7 (2022).
doi: 10.1186/s13059-022-02823-7 pubmed: 36522651 pmcid: 9753292
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9, R7, https://doi.org/10.1186/gb-2008-9-1-r7 (2008).
doi: 10.1186/gb-2008-9-1-r7 pubmed: 18190707 pmcid: 2395244
Manni, M., Berkeley, M. R., Seppey, M., Simao, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular biology and evolution 38, 4647–4654, https://doi.org/10.1093/molbev/msab199 (2021).
doi: 10.1093/molbev/msab199 pubmed: 34320186 pmcid: 8476166
Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC bioinformatics 4, 41–41, https://doi.org/10.1186/1471-2105-4-41 (2003).
doi: 10.1186/1471-2105-4-41 pubmed: 12969510 pmcid: 222959
Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research 46, W95–W101, https://doi.org/10.1093/nar/gky418 (2018).
doi: 10.1093/nar/gky418 pubmed: 29771380 pmcid: 6031026
Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252, https://doi.org/10.1093/bioinformatics/btz859 (2020).
doi: 10.1093/bioinformatics/btz859 pubmed: 31742321
Medema, M. H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research 39, W339–W346, https://doi.org/10.1093/nar/gkr466 (2011).
doi: 10.1093/nar/gkr466 pubmed: 21672958 pmcid: 3125804
NCBI Sequence Read Archive. https://identifiers.org/ncbi/insdc.sra:SRP507817 (2024).
Chen, J. Mangrove fungal community. figshare https://doi.org/10.6084/m9.figshare.25060154 (2024).
NCBI Bioproject. https://identifiers.org/ncbi/bioproject:PRJNA1116794 (2024).
Chen, J. et al. Talaromyces variabilis strain HXQ-H-1, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBND000000000 (2024).
Chen, J. et al. Apiospora guizhouensis strain F035, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNE000000000 (2024).
Chen, J. et al. Talaromyces fuscoviridis strain F034, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNF000000000 (2024).
Chen, J. et al. Neoroussoella solani strain F033, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNG000000000 (2024).
Chen, J. et al. Penicillium brefeldianum strain F032, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNH000000000 (2024).
Chen, J. et al. Neoroussoella solani strain F031, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNI000000000 (2024).
Chen, J. et al. Penicillium raperi strain F027, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNJ000000000 (2024).
Chen, J. et al. Aspergillus tubingensis strain F023, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNK000000000 (2024).
Chen, J. et al. Trichoderma atroviride strain F020, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNL000000000 (2024).
Chen, J. et al. Penicillium brefeldianum strain F015, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNM000000000 (2024).
Chen, J. et al. Trichoderma lixii strain F014, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNN000000000 (2024).
Chen, J. et al. Westerdykella dispersa strain F012, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBEBNO000000000 (2024).
China National GeneBank Sequence Archive. https://db.cngb.org/search/project/CNP0000487/ (2023).
China National GeneBank Sequence Archive. https://db.cngb.org/search/project/CNP0000910/ (2024).
Chen, J. Mangrove fungal genomes. figshare https://doi.org/10.6084/m9.figshare.25053398 (2024).

Auteurs

Jianwei Chen (J)

BGI Research, Qingdao, 266555, China.
Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China.
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.

Ling Peng (L)

BGI Research, Qingdao, 266555, China.

Changhao Zhou (C)

BGI Research, Qingdao, 266555, China.
Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China.

Liangwei Li (L)

BGI Research, Qingdao, 266555, China.

Qijin Ge (Q)

BGI Research, Qingdao, 266555, China.

Chengcheng Shi (C)

BGI Research, Qingdao, 266555, China.

Wenjie Guo (W)

BGI Research, Qingdao, 266555, China.

Tianci Guo (T)

BGI Research, Qingdao, 266555, China.

Ling Jiang (L)

State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.

Zhidong Zhang (Z)

Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.

Guangyi Fan (G)

BGI Research, Qingdao, 266555, China.
Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China.
BGI Research, Shenzhen, 518083, China.

Wenwei Zhang (W)

BGI Research, Shenzhen, 518083, China.

Karsten Kristiansen (K)

Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China. kk@bio.ku.dk.
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark. kk@bio.ku.dk.
BGI Research, Shenzhen, 518083, China. kk@bio.ku.dk.

Yangyang Jia (Y)

BGI Research, Shenzhen, 518083, China. jiayangyang@genomics.cn.

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