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1. Molecular determinants of outcomes in relapsed or refractory mantle cell lymphoma treated with ibrutinib or temsirolimus in the MCL3001 (RAY) trial

Author

Freeman, Ciara L., Pararajalingam, Prasath, Jin, Ling, Balasubramanian, Sriram, Jiang, Aixiang, Xu, Wendan, Grau, Michael, Zapukhlyak, Myroslav, Boyle, Merrill, Hodkinson, Brendan, Schaffer, Michael, Enny, Christopher, Deshpande, Sanjay, Sun, Steven, Vermeulen, Jessica, Morin, Ryan D., Scott, David W., and Lenz, Georg

Published
2022
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2. Notes, outline and divergence times of Basidiomycota

Author

He, Mao-Qiang, Zhao, Rui-Lin, Hyde, Kevin D., Begerow, Dominik, Kemler, Martin, Yurkov, Andrey, McKenzie, Eric H. C., Raspé, Olivier, Kakishima, Makoto, Sánchez-Ramírez, Santiago, Vellinga, Else C., Halling, Roy, Papp, Viktor, Zmitrovich, Ivan V., Buyck, Bart, Ertz, Damien, Wijayawardene, Nalin N., Cui, Bao-Kai, Schoutteten, Nathan, Liu, Xin-Zhan, Li, Tai-Hui, Yao, Yi-Jian, Zhu, Xin-Yu, Liu, An-Qi, Li, Guo-Jie, Zhang, Ming-Zhe, Ling, Zhi-Lin, Cao, Bin, Antonín, Vladimír, Boekhout, Teun, da Silva, Bianca Denise Barbosa, De Crop, Eske, Decock, Cony, Dima, Bálint, Dutta, Arun Kumar, Fell, Jack W., Geml, József, Ghobad-Nejhad, Masoomeh, Giachini, Admir J., Gibertoni, Tatiana B., Gorjón, Sergio P., Haelewaters, Danny, He, Shuang-Hui, Hodkinson, Brendan P., Horak, Egon, Hoshino, Tamotsu, Justo, Alfredo, Lim, Young Woon, Menolli, Jr., Nelson, Mešić, Armin, Moncalvo, Jean-Marc, Mueller, Gregory M., Nagy, László G., Nilsson, R. Henrik, Noordeloos, Machiel, Nuytinck, Jorinde, Orihara, Takamichi, Ratchadawan, Cheewangkoon, Rajchenberg, Mario, Silva-Filho, Alexandre G. S., Sulzbacher, Marcelo Aloisio, Tkalčec, Zdenko, Valenzuela, Ricardo, Verbeken, Annemieke, Vizzini, Alfredo, Wartchow, Felipe, Wei, Tie-Zheng, Weiß, Michael, Zhao, Chang-Lin, and Kirk, Paul M.

Published
2019
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3. Safety and activity of ibrutinib in combination with nivolumab in patients with relapsed non-Hodgkin lymphoma or chronic lymphocytic leukaemia: a phase 1/2a study

Author

Younes, Anas, Brody, Joshua, Carpio, Cecilia, Lopez-Guillermo, Armando, Ben-Yehuda, Dina, Ferhanoglu, Burhan, Nagler, Arnon, Ozcan, Muhit, Avivi, Irit, Bosch, Francesc, Caballero Barrigón, Maria Dolores, Hellmann, Andrzej, Kuss, Bryone, Ma, David D F, Demirkan, Fatih, Yağci, Münci, Horowitz, Netanel A, Marlton, Paula, Cordoba, Raul, Wrobel, Tomasz, Buglio, Daniela, Streit, Michael, Hodkinson, Brendan P, Schaffer, Michael, Alvarez, John, Ceulemans, Rob, Balasubramanian, Sriram, de Jong, Jan, Wang, Shean-Sheng, Fourneau, Nele, and Jurczak, Wojciech

Published
2019
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17. New Insights into Classification and Evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from Phylogenetic Analyses of Three Ribosomal RNA- and Two Protein-Coding Genes

Author

Miadlikowska, Jolanta, Kauff, Frank, Hofstetter, Valérie, Fraker, Emily, Grube, Martin, Hafellner, Josef, Reeb, Valérie, Hodkinson, Brendan P., Kukwa, Martin, Lücking, Robert, Hestmark, Geir, Otalora, Monica Garcia, Rauhut, Alexandra, Büdel, Burkhard, Scheidegger, Christoph, Timdal, Einar, Stenroos, Soili, Brodo, Irwin, Perlmutter, Gary B., Ertz, Damien, Diederich, Paul, Lendemer, James C., May, Philip, Schoch, Conrad L., Arnold, A. Elizabeth, Gueidan, Cécile, Tripp, Erin, Yahr, Rebecca, Robertson, Connie, and Lutzoni, François

Published
2006

19. Longitudinal expression profiling identifies a poor risk subset of patients with ABC-type diffuse large B-cell lymphoma

Author

Bewicke-Copley, Findlay, Korfi, Koorosh, Araf, Shamzah, Hodkinson, Brendan, Kumar, Emil, Cummin, Thomas, Ashton-Key, Margaret, Barrans, Sharon, van Hoppe, Suzan, Burton, Cathy, Elshiekh, Mohamed, Rule, Simon, Crosbie, Nicola, Clear, Andrew, Calaminici, Maria, Runge, Hendrik, Hills, Robert K., Scott, David W., Rimsza, Lisa M., Menon, Geetha, Sha, Chulin, Davies, John R., Nagano, Ai, Davies, Andrew, Painter, Daniel, Smith, Alexandra, Gribben, John, Naresh, Kikkeri N., Westhead, David R., Okosun, Jessica, Steele, Andrew, Hodson, Daniel J., Balasubramanian, Sriram, Johnson, Peter, Wang, Jun, and Fitzgibbon, Jude

Abstract

Despite the effectiveness of immuno-chemotherapy, 40% of patients with diffuse large B-cell lymphoma (DLBCL) experience relapse or refractory disease. Longitudinal studies have previously focused on the mutational landscape of relapse but fell short of providing a consistent relapse-specific genetic signature. In our study, we have focused attention on the changes in GEP accompanying DLBCL relapse using archival paired diagnostic/relapse specimens from 38 de novo patients with DLBCL. COO remained stable from diagnosis to relapse in 80% of patients, with only a single patient showing COO switching from activated B-cell–like (ABC) to germinal center B-cell–like (GCB). Analysis of the transcriptomic changes that occur following relapse suggest ABC and GCB relapses are mediated via different mechanisms. We developed a 30-gene discriminator for ABC–DLBCLs derived from relapse-associated genes that defined clinically distinct high- and low-risk subgroups in ABC–DLBCLs at diagnosis in datasets comprising both population-based and clinical trial cohorts. This signature also identified a population of <60-year–old patients with superior PFS and OS treated with ibrutinib–R-CHOP as part of the PHOENIX trial. Altogether this new signature adds to the existing toolkit of putative genetic predictors now available in DLBCL that can be readily assessed as part of prospective clinical trials.

Published
2023
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23. Phylogenetic diversity of two geographically overlapping lichens: isolation by distance, environment, or fragmentation?

Author

Moncada, Bibiana, primary, Mercado‐Díaz, Joel A., additional, Magain, Nicolas, additional, Hodkinson, Brendan P., additional, Smith, Clifford W., additional, Bungartz, Frank, additional, Pérez‐Pérez, Rosa‐Emilia, additional, Gumboski, Emerson, additional, Sérusiaux, Emmanuël, additional, Lumbsch, H. Thorsten, additional, and Lücking, Robert, additional

Published
2021
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24. Biomarkers of response to ibrutinib plus nivolumab in relapsed diffuse large B-cell lymphoma, follicular lymphoma, or Richter's transformation

Author

Hodkinson, Brendan P., primary, Schaffer, Michael, additional, Brody, Joshua D., additional, Jurczak, Wojciech, additional, Carpio, Cecilia, additional, Ben-Yehuda, Dina, additional, Avivi, Irit, additional, Forslund, Ann, additional, Özcan, Muhit, additional, Alvarez, John, additional, Ceulemans, Rob, additional, Fourneau, Nele, additional, Younes, Anas, additional, and Balasubramanian, Sriram, additional

Published
2021
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26. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hofstetter, Valérie, Robbertse, Barbara, Matheny, Brandon P., Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Sybren de Hoog, G., Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Gryzenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, Thorsten H., Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, OʼDonnell, Kerry, Sipman, Harrie, Rogers, Jack D., Shoemaker, Robert A., Sugiyama, Junta, Summerbell, Richard C., Untereiner, Wendy, Johnston, Peter R., Stenroos, Soili, Zuccaro, Alga, Dyer, Paul S., Crittenden, Peter D., Cole, Mariette S., Hansen, Karen, Trappe, James M., Yahr, Rebecca, Lutzoni, François, and Spatafora, Joseph W.

Published
2009
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27. Notes, outline and divergence times of Basidiomycota

Author

UCL - SST/ELI/ELIM - Applied Microbiology, He, Mao-Qiang, Zhao, Rui-Lin, Hyde, Kevin D., Begerow, Dominik, Kemler, Martin, Yurkov, Andrey, McKenzie, Eric H. C., Raspé, Olivier, Kakishima, Makoto, Sánchez-Ramírez, Santiago, Vellinga, Else C., Halling, Roy, Papp, Viktor, Zmitrovich, Ivan V., Buyck, Bart, Ertz, Damien, Wijayawardene, Nalin N., Cui, Bao-Kai, Schoutteten, Nathan, Liu, Xin-Zhan, Li, Tai-Hui, Yao, Yi-Jian, Zhu, Xin-Yu, Liu, An-Qi, Li, Guo-Jie, Zhang, Ming-Zhe, Ling, Zhi-Lin, Cao, Bin, Antonín, Vladimír, Boekhout, Teun, da Silva, Bianca Denise Barbosa, De Crop, Eske, Decock, Cony, Dima, Bálint, Dutta, Arun Kumar, Fell, Jack W., Geml, József, Ghobad-Nejhad, Masoomeh, Giachini, Admir J., Gibertoni, Tatiana B., Gorjón, Sergio P., Haelewaters, Danny, He, Shuang-Hui, Hodkinson, Brendan P., Horak, Egon, Hoshino, Tamotsu, Justo, Alfredo, Lim, Young Woon, Menolli, Nelson, Mešić, Armin, Moncalvo, Jean-Marc, Mueller, Gregory M., Nagy, László G., Nilsson, R. Henrik, Noordeloos, Machiel, Nuytinck, Jorinde, Orihara, Takamichi, Ratchadawan, Cheewangkoon, Rajchenberg, Mario, Silva-Filho, Alexandre G. S., Sulzbacher, Marcelo Aloisio, Tkalčec, Zdenko, Valenzuela, Ricardo, Verbeken, Annemieke, Vizzini, Alfredo, Wartchow, Felipe, Wei, Tie-Zheng, Weiß, Michael, Zhao, Chang-Lin, Kirk, Paul M., UCL - SST/ELI/ELIM - Applied Microbiology, He, Mao-Qiang, Zhao, Rui-Lin, Hyde, Kevin D., Begerow, Dominik, Kemler, Martin, Yurkov, Andrey, McKenzie, Eric H. C., Raspé, Olivier, Kakishima, Makoto, Sánchez-Ramírez, Santiago, Vellinga, Else C., Halling, Roy, Papp, Viktor, Zmitrovich, Ivan V., Buyck, Bart, Ertz, Damien, Wijayawardene, Nalin N., Cui, Bao-Kai, Schoutteten, Nathan, Liu, Xin-Zhan, Li, Tai-Hui, Yao, Yi-Jian, Zhu, Xin-Yu, Liu, An-Qi, Li, Guo-Jie, Zhang, Ming-Zhe, Ling, Zhi-Lin, Cao, Bin, Antonín, Vladimír, Boekhout, Teun, da Silva, Bianca Denise Barbosa, De Crop, Eske, Decock, Cony, Dima, Bálint, Dutta, Arun Kumar, Fell, Jack W., Geml, József, Ghobad-Nejhad, Masoomeh, Giachini, Admir J., Gibertoni, Tatiana B., Gorjón, Sergio P., Haelewaters, Danny, He, Shuang-Hui, Hodkinson, Brendan P., Horak, Egon, Hoshino, Tamotsu, Justo, Alfredo, Lim, Young Woon, Menolli, Nelson, Mešić, Armin, Moncalvo, Jean-Marc, Mueller, Gregory M., Nagy, László G., Nilsson, R. Henrik, Noordeloos, Machiel, Nuytinck, Jorinde, Orihara, Takamichi, Ratchadawan, Cheewangkoon, Rajchenberg, Mario, Silva-Filho, Alexandre G. S., Sulzbacher, Marcelo Aloisio, Tkalčec, Zdenko, Valenzuela, Ricardo, Verbeken, Annemieke, Vizzini, Alfredo, Wartchow, Felipe, Wei, Tie-Zheng, Weiß, Michael, Zhao, Chang-Lin, and Kirk, Paul M.

Abstract

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

Published
2019

28. PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination

Author

Stamatakis Alexandros, Hodkinson Brendan P, Lücking Robert, and Cartwright Reed A

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method. Results Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambiguous region coding (e.g., INAASE), with the advantage of a practically unlimited alignment size and increased analytical speed and the possibility of PICS-Ord scores to be analyzed together with DNA data in a partitioned maximum likelihood model. Conclusions Advantages of PICS-Ord over step matrix-based ambiguous region coding with INAASE include a practically unlimited number of OTUs and seamless integration of PICS-Ord codes into phylogenetic datasets, as well as the increased speed of phylogenetic analysis. Contrary to word- and frequency-based methods, PICS-Ord maintains the advantage of pairwise sequence alignment to derive distances, and the method is flexible with respect to the calculation of distance scores. In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. RAxML (version 7.2.6 or higher that was developed for this study) allows up to 32-state ordered or unordered characters. A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERED. Availability An implementation of the PICS-Ord algorithm is available from http://scit.us/projects/ngila/wiki/PICS-Ord. It requires both the statistical software, R http://www.r-project.org and the alignment software Ngila http://scit.us/projects/ngila.

Published
2011
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29. Immunogenomic Exploration of the Acute Myeloid Leukemia Microenvironment Identifies Determinants of T-Cell Fitness

Author

Brady, Lauren K., primary, Soong, David, additional, Lind, Evan F., additional, Kosaka, Yoko, additional, Lamble, Adam J., additional, Schaffer, Michael, additional, Hodkinson, Brendan P., additional, Lefave, Clare, additional, Laderas, Ted, additional, McWeeney, Shannon K., additional, Adams, Homer, additional, Abraham, Yann, additional, Safabakhsh, Pegah, additional, Tyner, Jeffrey W., additional, Druker, Brian J., additional, and Huang, Fei, additional

Published
2018
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30. Circulating tumor DNA for comprehensive noninvasive monitoring of lymphoma treated with ibrutinib plus nivolumab

Author

Bruscaggin, Alessio, di Bergamo, Lodovico Terzi, Spina, Valeria, Hodkinson, Brendan, Forestieri, Gabriela, Bonfiglio, Ferdinando, Condoluci, Adalgisa, Wu, Wei, Pirosa, Maria C., Faderl, Martin R., Koch, Ricardo, Schaffer, Michael, Alvarez, John D., Fourneau, Nele, Gerber, Bernhard, Stussi, Georg, Zucca, Emanuele, Balasubramanian, Sriram, and Rossi, Davide

Abstract

To advance the use of circulating tumor DNA (ctDNA) applications, their broad clinical validity must be tested in different treatment settings, including targeted therapies. Using the prespecified longitudinal systematic collection of plasma samples in the phase 1/2a LYM1002 trial (registered on www.clinicaltrials.gov as NCT02329847), we tested the clinical validity of ctDNA for baseline mutation profiling, residual tumor load quantification, and acquisition of resistance mutations in patients with lymphoma treated with ibrutinib+nivolumab. Inclusion criterion for this ancillary biological study was the availability of blood collected at baseline and cycle 3, day 1. Overall, 172 ctDNA samples from 67 patients were analyzed by the LyV4.0 ctDNA Cancer Personalized Profiling Deep Sequencing Assay. Among baseline variants in ctDNA, only TP53 mutations (detected in 25.4% of patients) were associated with shorter progression-free survival; clones harboring baseline TP53 mutations did not disappear during treatment. Molecular response, defined as a >2-log reduction in ctDNA levels after 2 cycles of therapy (28 days), was achieved in 28.6% of patients with relapsed diffuse large B-cell lymphoma who had ≥1 baseline variant and was associated with best response and improved progression-free survival. Clonal evolution occurred frequently during treatment, and 10.3% new mutations were identified after 2 treatment cycles in nonresponders. PLCG2 was the topmost among genes that acquired new mutations. No patients acquired the C481S BTK mutation implicated in resistance to ibrutinib in CLL. Collectively, our results provide the proof of concept that ctDNA is useful for noninvasive monitoring of lymphoma treated with targeted agents in the clinical trial setting.

Published
2021
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31. Commensal microbiota modulate gene expression in the skin

Author

Meisel, Jacquelyn S., primary, Sfyroera, Georgia, additional, Bartow-McKenney, Casey, additional, Gimblet, Ciara, additional, Bugayev, Julia, additional, Horwinski, Joseph, additional, Kim, Brian, additional, Brestoff, Jonathan R., additional, Tyldsley, Amanda S., additional, Zheng, Qi, additional, Hodkinson, Brendan P., additional, Artis, David, additional, and Grice, Elizabeth A., additional

Published
2018
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34. Temporal Stability in Chronic Wound Microbiota Is Associated With Poor Healing

Author

Loesche, Michael, primary, Gardner, Sue E., additional, Kalan, Lindsay, additional, Horwinski, Joseph, additional, Zheng, Qi, additional, Hodkinson, Brendan P., additional, Tyldsley, Amanda S., additional, Franciscus, Carrie L., additional, Hillis, Stephen L., additional, Mehta, Samir, additional, Margolis, David J., additional, and Grice, Elizabeth A., additional

Published
2017
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38. Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi

Author

Divakar, Pradeep K., Crespo, Ana, Wedin, Mats, Leavitt, Steven D., Kantvilas, Gintaras, Hawksworth, David, Myllys, Leena, McCune, Bruce, Randlane, Tiina, Bjerke, Jarle W., Ohmura, Yoshihito, Schmitt, Imke, Boluda, Carlos G., Alors, David, Roca-Valiente, Beatriz, Del-Prado, Ruth, Ruibal, Constantino, Buaruang, Kawinnat, Nunez-Zapata, Jano, Amo De Paz, Guillermo, Rico, Victor J., Molina, M. Carmen, Elix, John, Esslinger, Theodore L., Tronstad, Inger Kristin K., Lindgren, Hanna, Ertz, Damien, Gueidan, Cecile, Saag, Lauri, Mark, Kristiina, Singh, Garima, Dal Grande, Francesco, Parnmen, Sittiporn, Beck, Andreas, Benatti, Michel Navarro, Blanchon, Dan, Candan, Mehmet, Clerc, Philippe, Goward, Treveor, Grube, Martin, Hodkinson, Brendan P., Hur, Jae-Seoun, Kirika, Paul M., Lendemer, James C, Mattsson, Jan-Eric, Messuti, Maria Ines, Miadlikowska, Jolanta, Nelsen, Matthew, Ohlson, Jan I., Perez-Ortega, Sergio, Saag, Andres, Sipman, H. J. M., Sohrabi, Mohammad, Thell, Arne, Thor, Goran, Truong, Camille, Yahr, Rebecca, Upreti, Dalip K, Cubas, Paloma, Lumbsch, H Thorsten, Divakar, Pradeep K., Crespo, Ana, Wedin, Mats, Leavitt, Steven D., Kantvilas, Gintaras, Hawksworth, David, Myllys, Leena, McCune, Bruce, Randlane, Tiina, Bjerke, Jarle W., Ohmura, Yoshihito, Schmitt, Imke, Boluda, Carlos G., Alors, David, Roca-Valiente, Beatriz, Del-Prado, Ruth, Ruibal, Constantino, Buaruang, Kawinnat, Nunez-Zapata, Jano, Amo De Paz, Guillermo, Rico, Victor J., Molina, M. Carmen, Elix, John, Esslinger, Theodore L., Tronstad, Inger Kristin K., Lindgren, Hanna, Ertz, Damien, Gueidan, Cecile, Saag, Lauri, Mark, Kristiina, Singh, Garima, Dal Grande, Francesco, Parnmen, Sittiporn, Beck, Andreas, Benatti, Michel Navarro, Blanchon, Dan, Candan, Mehmet, Clerc, Philippe, Goward, Treveor, Grube, Martin, Hodkinson, Brendan P., Hur, Jae-Seoun, Kirika, Paul M., Lendemer, James C, Mattsson, Jan-Eric, Messuti, Maria Ines, Miadlikowska, Jolanta, Nelsen, Matthew, Ohlson, Jan I., Perez-Ortega, Sergio, Saag, Andres, Sipman, H. J. M., Sohrabi, Mohammad, Thell, Arne, Thor, Goran, Truong, Camille, Yahr, Rebecca, Upreti, Dalip K, Cubas, Paloma, and Lumbsch, H Thorsten

Abstract

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

Published
2015

39. A Phylogenetic, Ecological, and Functional Characterization of Non-Photoautotrophic Bacteria in the Lichen Microbiome

Author

Hodkinson, Brendan P. and Lutzoni, Francois M

Subjects
molecular cloning, 16S, Mothur, Bioinformatics, microbiota, 454 sequencing, ecology, Biology, Microbiology
Abstract

Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli and significant players in the ecology and physiology of lichens. Despite recent interest in this topic, the phylogeny, ecology, and function of these bacteria remain largely unknown. The experiments presented in this dissertation employ culture-free methods to examine the bacteria housed in these unique environments to ultimately inform an assessment of their status with regard to the lichen symbiosis. Microbiotic surveys of lichen thalli using new oligonucleotide-primers targeting the 16S SSU rRNA gene (developed as part of this study to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria) revealed the identity of diverse bacterial associates, including members of an undescribed lineage in the order Rhizobiales (Lichen-Associated Rhizobiales 1; `LAR1'). It is shown that the LAR1 bacterial lineage, uniquely associated with lichen thalli, is widespread among lichens formed by distantly related lichen-forming fungi and is found in lichens collected from the tropics to the arctic. Through extensive molecular cloning of the 16S rRNA gene and 454 16S amplicon sequencing, ecological trends were inferred based on mycobiont, photobiont, and geography. The implications for using lichens as microcosms to study larger principles of ecology and evolution are discussed. In addition to phylogenetic and ecological studies of lichen-associated bacterial communities, this dissertation provides a first assessment of the functions performed by these bacteria within the lichen microbiome in nature through 454 sequencing of two different lichen metatranscriptomes (one from a chlorolichen, Cladonia grayi, and one from a cyanolichen, Peltigera praetextata). Non-photobiont bacterial genes for nitrogen fixation were not detected in the Cladonia thallus (even though transcripts of cyanobacterial nitrogen fixation genes from two different pathways were detected in the cyanolichen thallus), implying that the role of nitrogen fixation in the maintenance of chlorolichens might have previously been overstated. Additionally, bacterial polyol dehydrogenases were found to be expressed in chlorolichen thalli (along with fungal polyol dehydrogenases and kinases from the mycobiont), suggesting the potential for bacteria to begin the process of breaking down the fixed carbon compounds secreted by the photobiont for easier metabolism by the mycobiont. This first look at the group of functional genes expressed at the level of transcription provides initial insights into the symbiotic network of interacting genes within the lichen microbiome.

Published
2011

41. Evolution of complex symbiotic relationships in a morphologically derived family of lichen‐forming fungi

Author

Divakar, Pradeep K., primary, Crespo, Ana, additional, Wedin, Mats, additional, Leavitt, Steven D., additional, Hawksworth, David L., additional, Myllys, Leena, additional, McCune, Bruce, additional, Randlane, Tiina, additional, Bjerke, Jarle W., additional, Ohmura, Yoshihito, additional, Schmitt, Imke, additional, Boluda, Carlos G., additional, Alors, David, additional, Roca‐Valiente, Beatriz, additional, Del‐Prado, Ruth, additional, Ruibal, Constantino, additional, Buaruang, Kawinnat, additional, Núñez‐Zapata, Jano, additional, Amo de Paz, Guillermo, additional, Rico, Víctor J., additional, Molina, M. Carmen, additional, Elix, John A., additional, Esslinger, Theodore L., additional, Tronstad, Inger Kristin K., additional, Lindgren, Hanna, additional, Ertz, Damien, additional, Gueidan, Cécile, additional, Saag, Lauri, additional, Mark, Kristiina, additional, Singh, Garima, additional, Dal Grande, Francesco, additional, Parnmen, Sittiporn, additional, Beck, Andreas, additional, Benatti, Michel Navarro, additional, Blanchon, Dan, additional, Candan, Mehmet, additional, Clerc, Philippe, additional, Goward, Trevor, additional, Grube, Martin, additional, Hodkinson, Brendan P., additional, Hur, Jae‐Seoun, additional, Kantvilas, Gintaras, additional, Kirika, Paul M., additional, Lendemer, James, additional, Mattsson, Jan‐Eric, additional, Messuti, María Inés, additional, Miadlikowska, Jolanta, additional, Nelsen, Matthew, additional, Ohlson, Jan I., additional, Pérez‐Ortega, Sergio, additional, Saag, Andres, additional, Sipman, Harrie J. M., additional, Sohrabi, Mohammad, additional, Thell, Arne, additional, Thor, Göran, additional, Truong, Camille, additional, Yahr, Rebecca, additional, Upreti, Dalip K., additional, Cubas, Paloma, additional, and Lumbsch, H. Thorsten, additional

Published
2015
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49. The ascomycota tree of life:a phylum-wide phylogeny clarifies the origin and evolutionof fundamental reproductive and ecological traits

Author

Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hoffstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja Amtoft, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Hoog, G. Sybren de, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Grysenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O’Donnell, Kerry, Sipman, Harrie, Rogers, Jack D., Shoemaker, Robert A., Sugiyama, Junta, Summerbell, Richard C., Untereiner, Wendy, Johnston, Peter R., Stenroos, Soili, Zuccaro, Alga, Dyer, Paul S., Crittenden, Peter D., Cole, Mariette S., Hansen, Karen, Trappe, James M., Yahr, Rebecca, Francois Lutzoni, Spatafora, Joseph W., Schoch, Conrad L., Sung, Gi-Ho, López-Giráldez, Francesc, Townsend, Jeffrey P., Miadlikowska, Jolanta, Hoffstetter, Valérie, Robbertse, Barbara, Matheny, P. Brandon, Kauff, Frank, Wang, Zheng, Gueidan, Cécile, Andrie, Rachael M., Trippe, Kristin, Ciufetti, Linda M., Wynns, Anja Amtoft, Fraker, Emily, Hodkinson, Brendan P., Bonito, Gregory, Groenewald, Johannes Z., Arzanlou, Mahdi, Hoog, G. Sybren de, Crous, Pedro W., Hewitt, David, Pfister, Donald H., Peterson, Kristin, Grysenhout, Marieka, Wingfield, Michael J., Aptroot, André, Suh, Sung-Oui, Blackwell, Meredith, Hillis, David M., Griffith, Gareth W., Castlebury, Lisa A., Rossman, Amy Y., Lumbsch, H. Thorsten, Lücking, Robert, Büdel, Burkhard, Rauhut, Alexandra, Diederich, Paul, Ertz, Damien, Geiser, David M., Hosaka, Kentaro, Inderbitzin, Patrik, Kohlmeyer, Jan, Volkmann-Kohlmeyer, Brigitte, Mostert, Lizel, O’Donnell, Kerry, Sipman, Harrie, Rogers, Jack D., Shoemaker, Robert A., Sugiyama, Junta, Summerbell, Richard C., Untereiner, Wendy, Johnston, Peter R., Stenroos, Soili, Zuccaro, Alga, Dyer, Paul S., Crittenden, Peter D., Cole, Mariette S., Hansen, Karen, Trappe, James M., Yahr, Rebecca, Francois Lutzoni, and Spatafora, Joseph W.

Published
2009

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