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Gomez-Gutierrrez SV, Sic-Hernandez WR, Haridas S, LaButti K, Eichenberger J, Kaur N, Lipzen A, Barry K, Goodwin SB, Gribskov M, Grigoriev IV. Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1418145. [PMID: 39309730 PMCID: PMC11412873 DOI: 10.3389/ffunb.2024.1418145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/13/2024] [Indexed: 09/25/2024]
Abstract
Over a billion years of fungal evolution has enabled representatives of this kingdom to populate almost all parts of planet Earth and to adapt to some of its most uninhabitable environments including extremes of temperature, salinity, pH, water, light, or other sources of radiation. Cryomyces antarcticus is an endolithic fungus that inhabits rock outcrops in Antarctica. It survives extremes of cold, humidity and solar radiation in one of the least habitable environments on Earth. This fungus is unusual because it produces heavily melanized, meristematic growth and is thought to be haploid and asexual. Due to its growth in the most extreme environment, it has been suggested as an organism that could survive on Mars. However, the mechanisms it uses to achieve its extremophilic nature are not known. Comparative genomics can provide clues to the processes underlying biological diversity, evolution, and adaptation. This effort has been greatly facilitated by the 1000 Fungal Genomes project and the JGI MycoCosm portal where sequenced genomes have been assembled into phylogenetic and ecological groups representing different projects, lifestyles, ecologies, and evolutionary histories. Comparative genomics within and between these groups provides insights into fungal adaptations, for example to extreme environmental conditions. Here, we analyze two Cryomyces genomes in the context of additional psychrophilic fungi, as well as non-psychrophilic fungi with diverse lifestyles selected from the MycoCosm database. This analysis identifies families of genes that are expanded and contracted in Cryomyces and other psychrophiles and may explain their extremophilic lifestyle. Higher GC contents of genes and of bases in the third positions of codons may help to stabilize DNA under extreme conditions. Numerous smaller contigs in C. antarcticus suggest the presence of an alternative haplotype that could indicate the sequenced isolate is diploid or dikaryotic. These analyses provide a first step to unraveling the secrets of the extreme lifestyle of C. antarcticus.
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Affiliation(s)
| | - Wily R. Sic-Hernandez
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Joanne Eichenberger
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Navneet Kaur
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephen B. Goodwin
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture (USDA) - Agricultural Research Service, West Lafayette, IN, United States
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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2
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Liu W, Shi X, Cai Y, Sun W, He P, Perez-Moreno J, Liu D, Yu F. Two near-chromosomal-level genomes of globally-distributed Macroascomycete based on single-molecule fluorescence and Hi-C methods. Sci Data 2024; 11:964. [PMID: 39231989 PMCID: PMC11375150 DOI: 10.1038/s41597-024-03794-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/16/2024] [Indexed: 09/06/2024] Open
Abstract
Discinaceae holds significant importance within the Pezizales, representing a prominent group of macroascomycetes distributed globally. However, there is a dearth of genomic studies focusing on this family, resulting in gaps in our understanding of its evolution, development, and ecology. Here we utilized state-of-the-art genome assembly methodologies, incorporating third-generation single-molecule fluorescence and Hi-C-assisted methods, to elucidate the genomic landscapes of Gyromitra esculenta and Paragyromitra xinjiangensis. The genome sizes of two species were determined to be 47.10 Mb and 48.20 Mb, with 23 and 22 scaffolds, respectively. 10,438 and 11,469 coding proteins were identified, with functional annotations encompassing over 96.47% and 94.40%, respectively. Assessment of completeness using BUSCO revealed that 98.71% and 98.89% of the conserved proteins were identified. The application of comparative genomic technology has helped in identifying traits associated with of heterothallic life cycle traits and elucidating unique patterns of chromosomal evolution. Additionally, we identified potential saprotrophic nutritional modes and systematic phylogenetic relationships between the two species. Therefore, this study provides crucial genomic insights into the evolution, nutritional type, and ecological roles of species within the Pezizales.
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Affiliation(s)
- Wei Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yingli Cai
- Institute of Agro-products Processing, Yunnan Academy of Agricultural Sciences, Kunming, 650221, China
| | - Wenhua Sun
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Peixin He
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Jesus Perez-Moreno
- Edafología, Campus Montecillo, Colegio de Postgraduados, Texcoco, 56230, Mexico
| | - Dong Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Adams JN, Escalona M, Marimuthu MPA, Fairbairn CW, Beraut E, Seligmann W, Nguyen O, Chumchim N, Stajich JE. The reference genome assembly of the bright cobblestone lichen, Acarospora socialis. J Hered 2023; 114:707-714. [PMID: 37740386 PMCID: PMC10650946 DOI: 10.1093/jhered/esad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/24/2023] Open
Abstract
Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.
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Affiliation(s)
- Julia N Adams
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, United States
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, United States
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4
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Wang Y, Li R, Wang D, Qian B, Bian Z, Wei J, Wei X, Xu JR. Regulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii. Nat Commun 2023; 14:6972. [PMID: 37914724 PMCID: PMC10620189 DOI: 10.1038/s41467-023-42675-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Lichens are of great ecological importance but mechanisms regulating lichen symbiosis are not clear. Umbilicaria muhlenbergii is a lichen-forming fungus amenable to molecular manipulations and dimorphic. Here, we established conditions conducive to symbiotic interactions and lichen differentiation and showed the importance of UMP1 MAP kinase in lichen development. In the initial biofilm-like symbiotic complexes, algal cells were interwoven with pseudohyphae covered with extracellular matrix. After longer incubation, fungal-algal complexes further differentiated into primitive lichen thalli with a melanized cortex-like and pseudoparenchyma-like tissues containing photoactive algal cells. Mutants deleted of UMP1 were blocked in pseudohyphal growth and development of biofilm-like complexes and primitive lichens. Invasion of dividing mother cells that contributes to algal layer organization in lichens was not observed in the ump1 mutant. Overall, these results showed regulatory roles of UMP1 in symbiotic interactions and lichen development and suitability of U. muhlenbergii as a model for studying lichen symbiosis.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Rong Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Diwen Wang
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ben Qian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuyun Bian
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jin-Rong Xu
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
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5
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Mlambo G, Padayachee T, Nelson DR, Syed K. Genome-Wide Analysis of the Cytochrome P450 Monooxygenases in the Lichenized Fungi of the Class Lecanoromycetes. Microorganisms 2023; 11:2590. [PMID: 37894248 PMCID: PMC10608907 DOI: 10.3390/microorganisms11102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Lichens are unique organisms that exhibit a permanent symbiosis between fungi and algae or fungi and photosynthetic bacteria. Lichens have been found to produce biotechnologically valuable secondary metabolites. A handful of studies showed that tailoring enzymes such as cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing these metabolites. Despite the critical role of P450s in the biosynthesis of secondary metabolites, the systematic analysis of P450s in lichens has yet to be reported. This study is aimed to address this research gap. A genome-wide analysis of P450s in five lichens from the fungal class Lecanoromycetes revealed the presence of 434 P450s that are grouped into 178 P450 families and 345 P450 subfamilies. The study indicated that none of the P450 families bloomed, and 15 P450 families were conserved in all five Lecanoromycetes. Lecanoromycetes have more P450s and higher P450 family diversity compared to Pezizomycetes. A total of 73 P450s were found to be part of secondary metabolite gene clusters, indicating their potential involvement in the biosynthesis of secondary metabolites. Annotation of P450s revealed that CYP682BG1 and CYP682BG2 from Cladonia grayi and Pseudevernia furfuracea (physodic acid chemotype) are involved in the synthesis of grayanic acid and physodic acid, CYP65FQ2 from Stereocaulon alpinum is involved in the synthesis of atranorin, and CYP6309A2 from Cladonia uncialis is involved in the synthesis of usnic acid. This study serves as a reference for future annotation of P450s in lichens.
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Affiliation(s)
- Gugulethu Mlambo
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Vulindlela, KwaDlangezwa 3886, South Africa; (G.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Vulindlela, KwaDlangezwa 3886, South Africa; (G.M.); (T.P.)
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Vulindlela, KwaDlangezwa 3886, South Africa; (G.M.); (T.P.)
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6
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Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
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Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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7
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Spribille T, Resl P, Stanton DE, Tagirdzhanova G. Evolutionary biology of lichen symbioses. THE NEW PHYTOLOGIST 2022; 234:1566-1582. [PMID: 35302240 DOI: 10.1111/nph.18048] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/21/2021] [Indexed: 05/28/2023]
Abstract
Lichens are the symbiotic outcomes of open, interspecies relationships, central to which are a fungus and a phototroph, typically an alga and/or cyanobacterium. The evolutionary processes that led to the global success of lichens are poorly understood. In this review, we explore the goods and services exchange between fungus and phototroph and how this propelled the success of both symbiont and symbiosis. Lichen fungal symbionts count among the only filamentous fungi that expose most of their mycelium to an aerial environment. Phototrophs export carbohydrates to the fungus, which converts them to specific polyols. Experimental evidence suggests that polyols are not only growth and respiratory substrates but also play a role in anhydrobiosis, the capacity to survive desiccation. We propose that this dual functionality is pivotal to the evolution of fungal symbionts, enabling persistence in environments otherwise hostile to fungi while simultaneously imposing costs on growth. Phototrophs, in turn, benefit from fungal protection from herbivory and light stress, while appearing to exert leverage over fungal sex and morphogenesis. Combined with the recently recognized habit of symbionts to occur in multiple symbioses, this creates the conditions for a multiplayer marketplace of rewards and penalties that could drive symbiont selection and lichen diversification.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Philipp Resl
- Institute of Biology, University of Graz, Universitätsplatz 3, Graz, 8010, Austria
| | - Daniel E Stanton
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
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8
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Petersen C, Sørensen T, Westphal KR, Fechete LI, Sondergaard TE, Sørensen JL, Nielsen KL. High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing. Microb Genom 2022; 8. [PMID: 35438621 PMCID: PMC9453082 DOI: 10.1099/mgen.0.000816] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
During the last two decades, whole-genome sequencing has revolutionized genetic research in all kingdoms, including fungi. More than 1000 fungal genomes have been submitted to sequence databases, mostly obtained through second generation short-read DNA sequencing. As a result, highly fragmented genome drafts have typically been obtained. However, with the emergence of third generation long-read DNA sequencing, the assembly challenge can be overcome and highly contiguous assemblies obtained. Such attractive results, however, are extremely dependent on the ability to extract highly purified high molecular weight (HMW) DNA. Extraction of such DNA is currently a significant challenge for all species with cell walls, not least fungi. In this study, four isolates of filamentous ascomycetes (Apiospora pterospermum, Aspergillus sp. (subgen. Cremei), Aspergillus westerdijkiae, and Penicillium aurantiogriseum) were used to develop extraction and purification methods that result in HMW DNA suitable for third generation sequencing. We have tested and propose two straightforward extraction methods based on treatment with either a commercial kit or traditional phenol-chloroform extraction both in combination with a single commercial purification method that result in high quality HMW DNA from filamentous ascomycetes. Our results demonstrated that using these DNA extraction methods and coverage, above 75 x of our haploid filamentous ascomycete fungal genomes result in complete and contiguous assemblies.
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Affiliation(s)
- Celine Petersen
- Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark, Aalborg University
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark, Aalborg University
| | - Klaus R Westphal
- Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark, Aalborg University
| | - Lavinia I Fechete
- Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark, Aalborg University
| | - Teis E Sondergaard
- Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark, Aalborg University
| | - Jens L Sørensen
- Department of Chemistry and Bioscience, Niels-Bohrs Vej 8, 6700 Esbjerg, Denmark, Aalborg University
| | - Kåre L Nielsen
- Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark, Aalborg University
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9
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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10
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Cornet L, Magain N, Baurain D, Lutzoni F. Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens. Mol Phylogenet Evol 2021; 162:107100. [PMID: 33592234 DOI: 10.1016/j.ympev.2021.107100] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic. In this study, we developed a synteny-based approach and searched for Collinear Orthologous Regions (COR), under the assumption that genes that are present in the same order and orientation across a wide monophyletic clade are less likely to have undergone HGT. We searched sixteen reference Nostocales genomes and identified 99 genes, part of 28 COR comprising three to eight genes each. We then developed a bioinformatic pipeline, designed to minimize inter-genome contamination and processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset to 90 genes representing 25 COR, which were used to infer phylogenetic relationships within Nostocales and among lichenized Cyanobacteria. This dataset was narrowed down further to 71 genes representing 22 COR by selecting only genes part of one (largest) operon per COR. We found a relatively high level of congruence among trees derived from the 90-gene dataset, but congruence was only slightly higher among genes within a COR compared to genes across COR. However, topological congruence was significantly higher among the 71 genes part of one operon per COR. Nostocales phylogenies resulting from concatenation and species tree approaches based on the 90- and 71-gene datasets were highly congruent, but the most highly supported result was obtained when using synteny, collinearity, and operon information (i.e., 71-gene dataset) as gene selection criteria, which outperformed larger datasets with more genes.
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Affiliation(s)
- Luc Cornet
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, NC, USA; Evolution and Conservation Biology, InBioS, University of Liège, Liège, Belgium
| | - Denis Baurain
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.
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11
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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12
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Grewe F, Ametrano C, Widhelm TJ, Leavitt S, Distefano I, Polyiam W, Pizarro D, Wedin M, Crespo A, Divakar PK, Lumbsch HT. Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota). IMA Fungus 2020; 11:27. [PMID: 33317627 PMCID: PMC7734834 DOI: 10.1186/s43008-020-00051-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/29/2020] [Indexed: 11/10/2022] Open
Abstract
Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
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Affiliation(s)
- Felix Grewe
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA.
| | - Claudio Ametrano
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Todd J Widhelm
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Steven Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Isabel Distefano
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Wetchasart Polyiam
- Lichen Research Unit, Biology Department, Faculty of Science, Ramkhamhaeng University, Ramkhamhaeng 24 Road, Bangkok, 10240, Thailand
| | - David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pradeep K Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - H Thorsten Lumbsch
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
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13
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
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14
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Nelsen MP, Lücking R, Boyce CK, Lumbsch HT, Ree RH. The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens. Proc Natl Acad Sci U S A 2020; 117:21495-21503. [PMID: 32796103 PMCID: PMC7474681 DOI: 10.1073/pnas.2001913117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.
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Affiliation(s)
- Matthew P Nelsen
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605;
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, 14195 Berlin, Germany
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University, Stanford, CA 94305
| | - H Thorsten Lumbsch
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
| | - Richard H Ree
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
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15
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Greshake Tzovaras B, Segers FHID, Bicker A, Dal Grande F, Otte J, Anvar SY, Hankeln T, Schmitt I, Ebersberger I. What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen. Genome Biol Evol 2020; 12:309-324. [PMID: 32163141 PMCID: PMC7186782 DOI: 10.1093/gbe/evaa049] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/29/2022] Open
Abstract
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
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Affiliation(s)
- Bastian Greshake Tzovaras
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- Lawrence Berkeley National Laboratory, Berkeley, California
- Center for Research & Interdisciplinarity, Université de Paris, France
| | - Francisca H I D Segers
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
| | - Anne Bicker
- Institute for Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Germany
| | - Francesco Dal Grande
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Seyed Yahya Anvar
- Department of Human Genetics, Leiden University Medical Center, The Netherlands
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University Mainz, Germany
| | - Imke Schmitt
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Molecular Evolutionary Biology Group, Institute of Ecology, Diversity, and Evolution, Goethe University Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Germany
- LOEWE Center for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
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16
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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17
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Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 2019; 20:605. [PMID: 31337355 PMCID: PMC6652019 DOI: 10.1186/s12864-019-5629-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.
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Affiliation(s)
| | - Olaf Müller
- Department of Biology, Duke University, Durham, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | | | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Guillaume Blanc
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften & Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
| | - Fred Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
| | - Suzanne Joneson
- Department of Biology, Duke University, Durham, USA
- College of General Studies, University of Wisconsin - Milwaukee at Waukesha, Waukesha, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | | | | | - Francis Martin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Susan P. May
- Department of Biology, Duke University, Durham, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, USA
| | - Tami R. McDonald
- Department of Biology, Duke University, Durham, USA
- Department of Biology, St. Catherine University, St. Paul, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, USA
| | - Vivian Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Morin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California - Santa Barbara, Santa Barbara, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, and DOE Institute for Genomics and Proteomics, University of California, Los Angeles, USA
| | - Nimrod Rubinstein
- National Evolutionary Synthesis Center, Durham, USA
- Calico Life Sciences LLC, South San Francisco, USA
| | | | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Fachbereich Biowissenschaften, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason C. Slot
- College of Food, Agricultural, and Environmental Sciences, Department of Plant Pathology, The Ohio State University, Columbus, USA
| | - Darren Soanes
- College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Claire Veneault-Fourrey
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
- Université de Lorraine, INRA, Interactions Arbres-Microorganismes, Faculté des Sciences et Technologies, Vandoeuvre les Nancy Cedex, France
| | - Basil B. Xavier
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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18
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Lutzoni F, Nowak MD, Alfaro ME, Reeb V, Miadlikowska J, Krug M, Arnold AE, Lewis LA, Swofford DL, Hibbett D, Hilu K, James TY, Quandt D, Magallón S. Contemporaneous radiations of fungi and plants linked to symbiosis. Nat Commun 2018; 9:5451. [PMID: 30575731 PMCID: PMC6303338 DOI: 10.1038/s41467-018-07849-9] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous. Plants and fungi interact widely and in diverse ways, from mutualism to parasitism and decomposition. Here, Lutzoni et al. analyse the timing of plant and fungal evolutionary radiations and identify four major periods in which plant-fungal interactions likely drove lineage diversification.
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Affiliation(s)
| | - Michael D Nowak
- Natural History Museum, University of Oslo, NO-0318, Oslo, Norway
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Valérie Reeb
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Michael Krug
- Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität, 53115, Bonn, Germany
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David L Swofford
- Department of Biology, Duke University, Durham, NC, 27708, USA.,Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - David Hibbett
- Department of Biology, Clark University, Worcester, MA, 01610, USA
| | - Khidir Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dietmar Quandt
- Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität, 53115, Bonn, Germany
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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19
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Allen JL, McKenzie SK, Sleith RS, Alter SE. First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. AMERICAN JOURNAL OF BOTANY 2018; 105:1556-1567. [PMID: 30157288 DOI: 10.1002/ajb2.1150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome-wide recombination. METHODS Whole-genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single-nucleotide polymorphisms for further analyses. KEY RESULTS We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating-type locus was found. Hindcast species distribution models and the distribution of genetic diversity support C. linearis having a larger range during the Last Glacial Maximum in the southern portion of its current extent. CONCLUSIONS Our findings contribute to the understanding of factors that shape genetic diversity in C. linearis and in fungi more broadly. Because all populations are highly genetically differentiated, the extirpation of any population would mean the loss of unique genetic diversity; therefore, our results support the continued conservation of this species.
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Affiliation(s)
- Jessica L Allen
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - Sean K McKenzie
- Rockefeller University, 1230 York Avenue, New York, New York, 10065, USA
| | - Robin S Sleith
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - S Elizabeth Alter
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
- Biology Department, York College, 94-20 Guy R Brewer Blvd., Jamaica, New York, 11451, USA
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Abstract
The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.
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Calcott MJ, Ackerley DF, Knight A, Keyzers RA, Owen JG. Secondary metabolism in the lichen symbiosis. Chem Soc Rev 2018; 47:1730-1760. [PMID: 29094129 DOI: 10.1039/c7cs00431a] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lichens, which are defined by a core symbiosis between a mycobiont (fungal partner) and a photobiont (photoautotrophic partner), are in fact complex assemblages of microorganisms that constitute a largely untapped source of bioactive secondary metabolites. Historically, compounds isolated from lichens have predominantly been those produced by the dominant fungal partner, and these continue to be of great interest for their unique chemistry and biotechnological potential. In recent years it has become apparent that many photobionts and lichen-associated bacteria also produce a range of potentially valuable molecules. There is evidence to suggest that the unique nature of the symbiosis has played a substantial role in shaping many aspects of lichen chemistry, for example driving bacteria to produce metabolites that do not bring them direct benefit but are useful to the lichen as a whole. This is most evident in studies of cyanobacterial photobionts, which produce compounds that differ from free living cyanobacteria and are unique to symbiotic organisms. The roles that these and other lichen-derived molecules may play in communication and maintaining the symbiosis are poorly understood at present. Nonetheless, advances in genomics, mass spectrometry and other analytical technologies are continuing to illuminate the wealth of biological and chemical diversity present within the lichen holobiome. Implementation of novel biodiscovery strategies such as metagenomic screening, coupled with synthetic biology approaches to reconstitute, re-engineer and heterologously express lichen-derived biosynthetic gene clusters in a cultivable host, offer a promising means for tapping into this hitherto inaccessible wealth of natural products.
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Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, New Zealand.
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22
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Pogoda CS, Keepers KG, Lendemer JC, Kane NC, Tripp EA. Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses. Mol Ecol 2018; 27:1155-1169. [DOI: 10.1111/mec.14519] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 12/21/2017] [Accepted: 01/19/2018] [Indexed: 01/28/2023]
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Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon. Mol Phylogenet Evol 2017; 117:10-29. [DOI: 10.1016/j.ympev.2017.08.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023]
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Meiser A, Otte J, Schmitt I, Grande FD. Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi. Sci Rep 2017; 7:14881. [PMID: 29097759 PMCID: PMC5668418 DOI: 10.1038/s41598-017-14576-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/12/2017] [Indexed: 01/07/2023] Open
Abstract
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
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Affiliation(s)
- Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany.
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60486, Frankfurt, Germany.
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Ekanayaka AH, Ariyawansa HA, Hyde KD, Jones EBG, Daranagama DA, Phillips AJL, Hongsanan S, Jayasiri SC, Zhao Q. DISCOMYCETES: the apothecial representatives of the phylum Ascomycota. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0389-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Abstract
ABSTRACT
Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.
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Greshake B, Zehr S, Dal Grande F, Meiser A, Schmitt I, Ebersberger I. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens. Mol Ecol Resour 2015; 16:511-23. [PMID: 26345272 DOI: 10.1111/1755-0998.12463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/28/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022]
Abstract
Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.
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Affiliation(s)
- Bastian Greshake
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Simonida Zehr
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325, Frankfurt, Germany
| | - Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325, Frankfurt, Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
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28
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Scazzocchio C. Fungal biology in the post-genomic era. Fungal Biol Biotechnol 2014; 1:7. [PMID: 28955449 PMCID: PMC5611559 DOI: 10.1186/s40694-014-0007-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/15/2014] [Indexed: 12/12/2022] Open
Abstract
In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick’s central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The “next generation” sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.
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Affiliation(s)
- Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK.,Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, Orsay, 91405 France
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29
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Miadlikowska J, Kauff F, Högnabba F, Oliver JC, Molnár K, Fraker E, Gaya E, Hafellner J, Hofstetter V, Gueidan C, Otálora MAG, Hodkinson B, Kukwa M, Lücking R, Björk C, Sipman HJM, Burgaz AR, Thell A, Passo A, Myllys L, Goward T, Fernández-Brime S, Hestmark G, Lendemer J, Lumbsch HT, Schmull M, Schoch CL, Sérusiaux E, Maddison DR, Arnold AE, Lutzoni F, Stenroos S. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. Mol Phylogenet Evol 2014; 79:132-68. [PMID: 24747130 PMCID: PMC4185256 DOI: 10.1016/j.ympev.2014.04.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 03/02/2014] [Accepted: 04/02/2014] [Indexed: 11/28/2022]
Abstract
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
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Affiliation(s)
| | - Frank Kauff
- FB Biologie, Molecular Phylogenetics, 13/276, TU Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Filip Högnabba
- Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland
| | - Jeffrey C Oliver
- Department of Ecology and Evolutionary Biology, Yale University, 358 ESC, 21 Sachem Street, New Haven, CT 06511, USA
| | - Katalin Molnár
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Emily Fraker
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Ester Gaya
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Josef Hafellner
- Institut für Botanik, Karl-Franzens-Universität, Holteigasse 6, A-8010 Graz, Austria
| | | | - Cécile Gueidan
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | | | | | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Robert Lücking
- Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Curtis Björk
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Harrie J M Sipman
- Botanischer Garten und Botanisches Museum Berlin-Dahlem, Königin-Luise-Strasse 6-8, D-14195 Berlin, Germany
| | - Ana Rosa Burgaz
- Departamento de Biologı́a Vegetal I, Facultad de CC. Biológicas, Universidad Complutense de Madrid, E-28040-Madrid, Spain
| | - Arne Thell
- Botanical Museum, Lund University, Box 117, SE-221 00 Lund, Sweden
| | - Alfredo Passo
- BioLiq Laboratorio de Bioindicadores y Liquenología, Centro Regional Universitario Bariloche, INIBIOMA, Universidad Nacional del Comahue, Bariloche, 8400RN, Argentina
| | - Leena Myllys
- Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland
| | - Trevor Goward
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Samantha Fernández-Brime
- Department of Plant Biology (Botany Unit), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Geir Hestmark
- CEES, Department of Biosciences, University of Oslo, PB 1066 Blindern, 0315 Oslo, Norway
| | - James Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA
| | - H Thorsten Lumbsch
- Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Michaela Schmull
- Harvard University Herbaria, Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA
| | - Emmanuël Sérusiaux
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium
| | - David R Maddison
- Center for Genome Research and Biocomputing, Oregon State University, 3021 Agriculture and Life Sciences Building, Corvallis, OR 97331-7303, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, The University of Arizona, 1140 E. South Campus Drive, Forbes 303, Tucson, AZ 85721, USA
| | - François Lutzoni
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Soili Stenroos
- Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland
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30
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Hom EFY, Murray AW. Plant-fungal ecology. Niche engineering demonstrates a latent capacity for fungal-algal mutualism. Science 2014; 345:94-8. [PMID: 24994654 PMCID: PMC4409001 DOI: 10.1126/science.1253320] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mutualistic symbioses shape the evolution of species and ecosystems and catalyze the emergence of biological complexity, yet how such symbioses first form is unclear. We show that an obligate mutualism between the yeast Saccharomyces cerevisiae and the alga Chlamydomonas reinhardtii--two model eukaryotes with very different life histories--can arise spontaneously in an environment requiring reciprocal carbon and nitrogen exchange. This capacity for mutualism is phylogenetically broad, extending to other Chlamydomonas and fungal species. Furthermore, we witnessed the spontaneous association of Chlamydomonas algal cells physically interacting with filamentous fungi. These observations demonstrate that under specific conditions, environmental change induces free-living species to become obligate mutualists and establishes a set of experimentally tractable, phylogenetically related, synthetic systems for studying the evolution of symbiosis.
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Affiliation(s)
- Erik F Y Hom
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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31
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Draft Genome Sequence of Umbilicaria muehlenbergii KoLRILF000956, a Lichen-Forming Fungus Amenable to Genetic Manipulation. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00357-14. [PMID: 24762942 PMCID: PMC3999499 DOI: 10.1128/genomea.00357-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Umbilicaria muehlenbergii strain KoLRILF000956 is amenable to Agrobacterium tumefaciens-mediated transformation (ATMT), making it the only known genetically tractable lichen-forming fungus to date. We report another advancement in lichen genetics, a draft genome assembly for U. muehlenbergii with a size of 34,812,353 bp and a GC content of 47.12%, consisting of seven scaffolds.
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Wang YY, Liu B, Zhang XY, Zhou QM, Zhang T, Li H, Yu YF, Zhang XL, Hao XY, Wang M, Wang L, Wei JC. Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota). BMC Genomics 2014; 15:34. [PMID: 24438332 PMCID: PMC3897900 DOI: 10.1186/1471-2164-15-34] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 01/14/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Lichen is a classic mutualistic organism and the lichenization is one of the fungal symbioses. The lichen-forming fungus Endocarpon pusillum is living in symbiosis with the green alga Diplosphaera chodatii Bialsuknia as a lichen in the arid regions. RESULTS 454 and Illumina technologies were used to sequence the genome of E. pusillum. A total of 9,285 genes were annotated in the 37.5 Mb genome of E. pusillum. Analyses of the genes provided direct molecular evidence for certain natural characteristics, such as homothallic reproduction and drought-tolerance. Comparative genomics analysis indicated that the expansion and contraction of some protein families in the E. pusillum genome reflect the specific relationship with its photosynthetic partner (D. chodatii). Co-culture experiments using the lichen-forming fungus E. pusillum and its algal partner allowed the functional identification of genes involved in the nitrogen and carbon transfer between both symbionts, and three lectins without signal peptide domains were found to be essential for the symbiotic recognition in the lichen; interestingly, the ratio of the biomass of both lichen-forming fungus and its photosynthetic partner and their contact time were found to be important for the interaction between these two symbionts. CONCLUSIONS The present study lays a genomic analysis of the lichen-forming fungus E. pusillum for demonstrating its general biological features and the traits of the interaction between this fungus and its photosynthetic partner D. chodatii, and will provide research basis for investigating the nature of its drought resistance and symbiosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Park SY, Jeong MH, Wang HY, Kim JA, Yu NH, Kim S, Cheong YH, Kang S, Lee YH, Hur JS. Agrobacterium tumefaciens-mediated transformation of the lichen fungus, Umbilicaria muehlenbergii. PLoS One 2013; 8:e83896. [PMID: 24386304 PMCID: PMC3875497 DOI: 10.1371/journal.pone.0083896] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/09/2013] [Indexed: 11/18/2022] Open
Abstract
Transformation-mediated mutagenesis in both targeted and random manners has been widely applied to decipher gene function in diverse fungi. However, a transformation system has not yet been established for lichen fungi, severely limiting our ability to study their biology and mechanism underpinning symbiosis via gene manipulation. Here, we report the first successful transformation of the lichen fungus, Umbilicaria muehlenbergii, via the use of Agrobacterium tumefaciens. We generated a total of 918 transformants employing a binary vector that carries the hygromycin B phosphotransferase gene as a selection marker and the enhanced green fluorescent protein gene for labeling transformants. Randomly selected transformants appeared mitotically stable, based on their maintenance of hygromycin B resistance after five generations of growth without selection. Genomic Southern blot showed that 88% of 784 transformants contained a single T-DNA insert in their genome. A number of putative mutants affected in colony color, size, and/or morphology were found among these transformants, supporting the utility of Agrobacterium tumefaciens-mediated transformation (ATMT) for random insertional mutagenesis of U. muehlenbergii. This ATMT approach potentially offers a systematic gene functional study with genome sequences of U. muehlenbergii that is currently underway.
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Affiliation(s)
- Sook-Young Park
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Korea
- Dept. of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Min-Hye Jeong
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Korea
- Dept. of Biology, Sunchon National University, Sunchon, Korea
| | - Hai-Ying Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jung A. Kim
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Korea
| | - Nan-Hee Yu
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Korea
- Dept. of Biology, Sunchon National University, Sunchon, Korea
| | - Sungbeom Kim
- Dept. of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Yong Hwa Cheong
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Korea
| | - Seogchan Kang
- Dept. of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yong-Hwan Lee
- Dept. of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
- * E-mail: (JSH); (Y-HL)
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Korea
- * E-mail: (JSH); (Y-HL)
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