Dimensions: Phylogenetic and Functional Diversity of Tripartite Plant-Fungal-Bacterial Symbioses

维度：植物-真菌-细菌三方共生体的系统发育和功能多样性

• 批准号: 1737898
• 负责人: Gregory Bonito
• 金额: $ 175万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2023-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1737898&HistoricalAwards=false
• 关键词: Dimensions; Phylogenetic; Functional; Diversity; Tripartite

This project investigates the diversity, evolution and ecological functions within a diverse lineage of fungi, the Mucoromycota. These fungi are industrially important for lipid production and as biofertilizers in agricultural systems. They have co-evolved with plants through innovations of their growth within plant tissues, and are implicated in the successful invasion of land by plants. Many of the fungi in this group are plant growth promoters and carry within their cells bacterial endosymbionts belonging to lineages of bacteria that are known only from these fungi. Some of these bacteria produce potent toxins. This research investigates the role of these endobacteria on their fungal host's growth and metabolism, and the impact of endobacteria on fungal-plant interactions. It will produce a culture collection and database of these fungi available to other scientists. Reference DNA barcodes and genome sequences from these collections will be integrated into sequence-based classifiers as a resource for the broader community. A short-course on "Computational Thinking in Biodiversity and Evolutionary Research", and studies to determine how traditional agriculture and cultural practices impact Mucoromycota fungi in the soil are part of the project. Overall, this research will provide diverse and cross-disciplinary education, training, and outreach to postdocs, graduate and undergraduate students.The researchers will compare and analyze entire genomes to identify symbiosis traits that have co-evolved in plant-fungi-bacteria partners, and will assess the impact of bacterial endosymbionts on the function of their fungal host and its interaction with plants through metatranscriptomics. Changes in host plant phenotype, metabolome, transcriptome, and resilience to abiotic stress will be studied in experiments designed to test genetic traits in the host, fungi and bacteria. The phylogenetic dimension will integrate evolution and genomics to provide a robust phylogenomic framework and new computational tools for estimating co-evolutionary and horizontal gene transfer processes between Mucoromycota and their bacterial endosymbionts. The genetic dimension will apply genomic and metatranscriptomic studies of plant-fungal-bacterial symbionts, selected with guidance provided by the phylogenomics, to identify critical genes involved in symbiotic interactions. The functional component will dissect the role of candidate genes for plant host fitness in the context of different plant-fungal/bacterial partners and abiotic stressors. Together this integrated research will foster interdisciplinary collaborations to provide novel insights into the diversity, evolution and functioning of tripartite multi-kingdom symbiosis.

这个项目调查了真菌的多样性、进化和生态功能。这些真菌对油脂生产和农业系统中的生物肥料具有重要的工业意义。它们通过在植物组织内生长的创新与植物共同进化，并与植物成功入侵土地有关。这一类中的许多真菌都是植物生长促进剂，并在它们的细胞中携带细菌内共生体，这些细菌属于只从这些真菌中已知的细菌谱系。其中一些细菌会产生强烈的毒素。本研究探讨了这些内生细菌对真菌寄主生长和代谢的作用，以及内生细菌对真菌-植物相互作用的影响。它将产生这些真菌的培养集合和数据库，供其他科学家使用。这些收集的参考DNA条形码和基因组序列将被整合到基于序列的分类器中，作为更广泛社区的资源。关于“生物多样性和进化研究中的计算思维”的短期课程，以及确定传统农业和文化做法如何影响土壤中的毛霉菌的研究是该项目的一部分。总体而言，这项研究将为博士后、研究生和本科生提供多样化和跨学科的教育、培训和推广。研究人员将比较和分析整个基因组，以确定在植物-真菌-细菌伙伴中共同进化的共生特征，并将评估细菌内共生菌对其真菌宿主功能的影响，以及它通过转录组学与植物的相互作用。寄主植物的表型、代谢组、转录组和对非生物胁迫的恢复能力的变化将在旨在测试寄主、真菌和细菌的遗传特性的实验中进行研究。系统发育维度将整合进化和基因组学，以提供一个强大的系统基因组框架和新的计算工具，用于估计毛霉菌和它们的细菌内共生菌之间的共同进化和水平基因转移过程。遗传维度将应用在系统基因组学提供的指导下选择的植物-真菌-细菌共生体的基因组和后转录研究，以确定参与共生相互作用的关键基因。功能部分将剖析植物寄主适合性候选基因在不同植物-真菌/细菌配对和非生物逆境中的作用。这项综合研究将促进跨学科合作，为三方多王国共生的多样性、进化和功能提供新的见解。

项目成果

Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

• DOI: 10.3390/microorganisms11071830
• 发表时间: 2023-07-18
• 期刊: MICROORGANISMS
• 影响因子: 4.5
• 作者: Gryganskyi, Andrii P.;Golan, Jacob;Muszewska, Anna;Idnurm, Alexander;Dolatabadi, Somayeh;Mondo, Stephen J.;Kutovenko, Vira B.;Kutovenko, Volodymyr O.;Gajdeczka, Michael T.;Anishchenko, Iryna M.;Pawlowska, Julia;Tran, Ngoc Vinh;Ebersberger, Ingo;Voigt, Kerstin;Wang, Yan;Chang, Ying;Pawlowska, Teresa E.;Heitman, Joseph;Vilgalys, Rytas;Bonito, Gregory;Benny, Gerald L.;Smith, Matthew E.;Reynolds, Nicole;James, Timothy Y.;Grigoriev, Igor V.;Spatafora, Joseph W.;Stajich, Jason E.
• 通讯作者: Stajich, Jason E.

The impact of gene sequence alignment and gene tree estimation error on summary-based species network estimation

基因序列比对和基因树估计误差对基于摘要的物种网络估计的影响

• DOI: 10.1145/3535508.3545559
• 发表时间: 2022
• 期刊: and Health Informatics (BCB ’22
• 作者: Gao, Meijun;Wang, Wei;Liu, Kevin J.
• 通讯作者: Liu, Kevin J.

The Global Soil Mycobiome consortium dataset for boosting fungal diversity research

• DOI: 10.1007/s13225-021-00493-7
• 发表时间: 2021-11
• 期刊: Fungal Diversity
• 影响因子: 20.3
• 作者: L. Tedersoo;V. Mikryukov;Sten Anslan;M. Bahram;A. Khalid;A. Corrales;A. Agan;A. Vasco-Palacios;A. Saitta;A. Antonelli;A. Rinaldi;A. Verbeken;B. P. Sulistyo;Boris Tamgnoue;B. Furneaux;C. Ritter;C. Nyamukondiwa;C. Sharp;C. Marín;D. Dai;Daniyal Gohar;Dipon Sharmah;E. Biersma;E. Cameron;E. De Crop;Eveli Otsing;E. Davydov;F. Albornoz;F. Brearley;F. Buegger;G. Gates;Geoffrey L. Zahn;G. Bonito;Indrek Hiiesalu;Inga Hiiesalu;Irma Zettur;I. Barrio;J. Pärn;J. Heilmann‐Clausen;Jelena Ankuda;John Y. Kupagme;Joosep Sarapuu;J. Maciá‐Vicente;J. D. Fovo;J. Geml;J. Alatalo;J. Alvarez-Manjarrez;J. Monkai;K. Põldmaa;Kadri Runnel;K. Adamson;K. Bråthen;K. Pritsch;Kassim I. Tchan;K. Armolaitis;K. Hyde;K. Newsham;K. Panksep;L. A. Adebola;L. J. Lamit;M. Saba;M. E. da Silva Cáceres;M. Tuomi;M. Gryzenhout;M. Bauters;Miklós Bálint;N. Wijayawardene;Niloufar Hagh-Doust;N. Yorou;O. Kurina;P. Mortimer;Patrick Meidl;R. H. Nilsson;Rasmus Puusepp;R. Casique-Valdés;R. Drenkhan;R. Garibay-Orijel;R. Godoy;Saleh Alfarraj;S. Rahimlou;Sergei Põlme;S. Dudov;S. Mundra;T. Ahmed;Tarquin Netherway;T. Henkel;T. Roslin;V. Fedosov;V. Onipchenko;W. A. E. Yasanthika;Y. Lim;M. Piepenbring;D. Kļaviņa;U. Kõljalg;K. Abarenkov

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

• DOI: 10.1128/mbio.02027-20
• 发表时间: 2020-09-01
• 期刊: MBIO
• 影响因子: 6.4
• 作者: Myers, J. M.;Bonds, A. E.;James, T. Y.
• 通讯作者: James, T. Y.

A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae)

• DOI: 10.1074/jbc.ra118.006025
• 发表时间: 2019-01-25
• 期刊: JOURNAL OF BIOLOGICAL CHEMISTRY
• 影响因子: 4.8
• 作者: Johnson, Sean R.;Bhat, Wajid Waheed;Hamberger, Bjoern
• 通讯作者: Hamberger, Bjoern