1
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Pogoda CS, Keepers KG, Reinert S, Talukder ZI, Smart BC, Attia Z, Corwin JA, Money KL, Collier-Zans ECE, Underwood W, Gulya TJ, Quandt CA, Kane NC, Hulke BS. Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance. Mol Ecol 2024; 33:e17218. [PMID: 38038696 DOI: 10.1111/mec.17218] [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: 08/05/2020] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co-vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human-altered environments.
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Affiliation(s)
- Cloe S Pogoda
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Kyle G Keepers
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Stephan Reinert
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Zahirul I Talukder
- USDA-ARS Sunflower and Plant Biology Research Unit, Edward T Schafer Agricultural Research Center, Fargo, North Dakota, USA
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Brian C Smart
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Ziv Attia
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Jason A Corwin
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Kennedy L Money
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Erin C E Collier-Zans
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - William Underwood
- USDA-ARS Sunflower and Plant Biology Research Unit, Edward T Schafer Agricultural Research Center, Fargo, North Dakota, USA
| | - Thomas J Gulya
- USDA-ARS Sunflower and Plant Biology Research Unit, Edward T Schafer Agricultural Research Center, Fargo, North Dakota, USA
| | - C Alisha Quandt
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | - Brent S Hulke
- USDA-ARS Sunflower and Plant Biology Research Unit, Edward T Schafer Agricultural Research Center, Fargo, North Dakota, USA
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2
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Fang J, Mamut R, Wang L, Anwar G. De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species. PLoS One 2023; 18:e0285818. [PMID: 37220163 DOI: 10.1371/journal.pone.0285818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/01/2023] [Indexed: 05/25/2023] Open
Abstract
In this study, the complete mitochondrial genome of Cladonia subulata (L.) FH Wigg was sequenced and assembled and then compared with those of other Cladonia species. The mitogenome of Cladonia subulata, the type species of Cladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 protein-coding genes, 2 rRNA genes, and 27 tRNA genes). The base composition had shown an obvious AT preference, and all 27 tRNA genes formed a typical clover structure. Comparison with other 7 Cladonia species indicated that the duplication/loss of tRNAs had occurred during evolution, and introns appeared to explain the variation in cox1 genes in Cladonia, the mitochondrial genome tends to be generally conservative and local dynamic changes. Repeat sequences were mainly located in gene intervals, which were mainly distributed among intergenic spacers and may cause rearrangement of the mitogenome. The phylogenetic results showed that Cladonia subulata and C. polycarpoides were assigned to the Cladonia Subclade. The results add to the available mitochondrial genome sequence information of Cladonia subulata, provide basic data for the systematic development, resource protection, and genetic diversity research in Cladonia subulata, and also provide theoretical support for further genomic research of lichens.
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Affiliation(s)
- Jinjin Fang
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Reyim Mamut
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Lidan Wang
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Gulmira Anwar
- College of Life Science and Technology, Xinjiang University, Urumqi, China
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3
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Hoffman JR, Karol KG, Ohmura Y, Pogoda CS, Keepers KG, McMullin RT, Lendemer JC. Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales. Mycologia 2023; 115:187-205. [PMID: 36736327 DOI: 10.1080/00275514.2022.2157665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the "true" reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.
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Affiliation(s)
- Jordan R Hoffman
- Department of Biology, The City University of New York Graduate Center, 365 5th Avenue, New York, New York 10016
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
| | - Kenneth G Karol
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
| | - Yoshihito Ohmura
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Japan
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309
| | - Richard T McMullin
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - James C Lendemer
- Institute of Systemic Botany, The New York Botanical Garden, Bronx, New York 10458-5126
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4
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Barstow AC, Prasifka JR, Attia Z, Kane NC, Hulke BS. Genetic mapping of a pollinator preference trait: Nectar volume in sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1056278. [PMID: 36600919 PMCID: PMC9806390 DOI: 10.3389/fpls.2022.1056278] [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: 09/28/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Although high pollinator visitation is crucial to ensure the yields of pollinator-dependent crops, the quantitative trait loci (QTL) controlling nectar volume in sunflower (Helianthus annuus L.), a pollinator preference trait, have yet to be identified. To address this, a recombinant inbred line mapping population, derived from lines with contrasting nectar volume, was used to identify loci responsible for the phenotype. As a result, linkage mapping and QTL analysis discovered major loci on chromosomes 2 and 16 that are associated with variation in nectar volume in sunflower. Increased nectar volume is also associated with increased sugars and total energy available per floret. The regions on chromosomes 2 and 16 associated with the nectar phenotype exhibit indications of chromosome structural variation, such that the phenotype is associated with rearrangements affecting regions containing hundreds of genes. Candidate genes underlying QTL on chromosomes 9 and 16 are homologous to genes with nectary function in Arabidopsis. These results have implications for sunflower breeding, to enhance pollination efficiency in sunflower, as well as current and future studies on sunflower evolution.
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Affiliation(s)
- Ashley C. Barstow
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Jarrad R. Prasifka
- Sunflower and Plant Biology Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, United States
| | - Ziv Attia
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, United States
| | - Nolan C. Kane
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, United States
| | - Brent S. Hulke
- Sunflower and Plant Biology Research Unit, Edward T. Schafer Agricultural Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service, Fargo, ND, United States
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5
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A comparative genomic analysis of lichen-forming fungi reveals new insights into fungal lifestyles. Sci Rep 2022; 12:10724. [PMID: 35750715 PMCID: PMC9232553 DOI: 10.1038/s41598-022-14340-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Lichen-forming fungi are mutualistic symbionts of green algae or cyanobacteria. We report the comparative analysis of six genomes of lichen-forming fungi in classes Eurotiomycetes and Lecanoromycetes to identify genomic information related to their symbiotic lifestyle. The lichen-forming fungi exhibited genome reduction via the loss of dispensable genes encoding plant-cell-wall-degrading enzymes, sugar transporters, and transcription factors. The loss of these genes reflects the symbiotic biology of lichens, such as the absence of pectin in the algal cell wall and obtaining specific sugars from photosynthetic partners. The lichens also gained many lineage- and species-specific genes, including those encoding small secreted proteins. These genes are primarily induced during the early stage of lichen symbiosis, indicating their significant roles in the establishment of lichen symbiosis.Our findings provide comprehensive genomic information for six lichen-forming fungi and novel insights into lichen biology and the evolution of symbiosis.
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6
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Bailey DW, Attia Z, Reinert S, S Hulke B, Kane NC. Effective strategies for isolating DNA from members of Asteraceae with high concentrations of secondary metabolites. Biotechniques 2022; 72:85-89. [PMID: 35124976 DOI: 10.2144/btn-2021-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Asteraceae are the largest plant family but among the least studied at the genome level. Our work investigated practical methods to reduce the influence of secondary metabolites - specifically, phenolic compounds - on the extraction of DNA from Silphium spp. This genus is in the Heliantheae tribe of Asteraceae that also includes sunflower (Helianthus annuus). Three methods were attempted in Silphium, with varying condition and age of the leaf sample. A modified cetyl trimethylammonium bromide (CTAB) method on young leaves resulted in the best DNA yield, with sufficient sample purity. No perceptible difference was observed between fresh and lyophilized samples for any extraction method or leaf age. These results provide an excellent basis for DNA extraction of difficult plant samples.
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Affiliation(s)
- Dustin W Bailey
- Ecology & Evolutionary Biology Department, University of Colorado, Boulder, CO 80309, USA
| | - Ziv Attia
- Ecology & Evolutionary Biology Department, University of Colorado, Boulder, CO 80309, USA
| | - Stephan Reinert
- Ecology & Evolutionary Biology Department, University of Colorado, Boulder, CO 80309, USA.,Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Brent S Hulke
- Sunflower and Plant Biology Research Unit, USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, USA
| | - Nolan C Kane
- Ecology & Evolutionary Biology Department, University of Colorado, Boulder, CO 80309, USA
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7
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Medina M, Baker DM, Baltrus DA, Bennett GM, Cardini U, Correa AMS, Degnan SM, Christa G, Kim E, Li J, Nash DR, Marzinelli E, Nishiguchi M, Prada C, Roth MS, Saha M, Smith CI, Theis KR, Zaneveld J. Grand Challenges in Coevolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.618251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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8
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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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9
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Wang L, Mamut R. Mitochondrial genome from the lichenized fungus Peltigera rufescens (Weiss) Humb, 1793 (Ascomycota: Peltigeraceae). Mitochondrial DNA B Resour 2021; 6:2186-2187. [PMID: 34263045 PMCID: PMC8259810 DOI: 10.1080/23802359.2021.1944374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Known colloquially as ‘dog-lichens’ or ‘pelt-lichens’, most species of Peltigera grow on soil and mosses. Some species contribute a significant amount of nitrogen to the environment and have been used as traditional medicines. We analyzed the complete mitochondrial genome of P. rufescens, which is a circular genome 65,199 bp in size and its CG content is 26.7%. It contains 15 protein-coding genes (PCGs), 27 transport RNAs (tRNAs), and 3 ribosomal RNAs (rRNAs). Also, the atp9 gene is present in the genome. We used the complete mitochondrial genome to construct a phylogenetic tree by the Bayesian method, which was consistent with the phylogenetic relationship published for P. membranacea which is closely related to P. rufescens.
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Affiliation(s)
- Lidan Wang
- College of Life Science and Technology, Xinjiang University, Urumchi, China
| | - Reyim Mamut
- College of Life Science and Technology, Xinjiang University, Urumchi, China
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10
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Keepers KG, Pogoda CS, Lendemer JC, Kane NC, Manzitto-Tripp EA. Author response to Tagirdzhanova et al. (2021): "Lichen fungi do not depend on alga for ATP production: A comment on Pogoda et al. (2018)". Mol Ecol 2021; 30:4160-4161. [PMID: 34251071 DOI: 10.1111/mec.16053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, New York City, New York, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Erin A Manzitto-Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Museum of Natural History, University of Colorado, Boulder, Colorado, USA
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11
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Tagirdzhanova G, McCutcheon JP, Spribille T. Lichen fungi do not depend on the alga for ATP production: A comment on Pogoda et al. (2018). Mol Ecol 2021; 30:4155-4159. [PMID: 34232528 DOI: 10.1111/mec.16010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 12/27/2022]
Abstract
Lichen fungi live in a symbiotic association with unicellular phototrophs and most have no known aposymbiotic stage. A recent study in Molecular Ecology postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit of ATP synthase, from a few mitochondrial genomes. Here, we show that while these fungi indeed have lost the mitochondrial ATP9, each retain a nuclear copy of this gene. Our analysis reaffirms that lichen fungi produce their own ATP.
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Affiliation(s)
- Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - John P McCutcheon
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB, T6G 2R3, Canada
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12
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13
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Pogoda CS, Reinert S, Talukder ZI, Attia Z, Collier-Zans ECE, Gulya TJ, Kane NC, Hulke BS. Genetic loci underlying quantitative resistance to necrotrophic pathogens Sclerotinia and Diaporthe (Phomopsis), and correlated resistance to both pathogens. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:249-259. [PMID: 33106896 DOI: 10.1007/s00122-020-03694-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
We provide results rooted in quantitative genetics, which combined with knowledge of candidate gene function, helps us to better understand the resistance to two major necrotrophic pathogens of sunflower. Necrotrophic pathogens can avoid or even benefit from plant defenses used against biotrophic pathogens, and thus represent a distinct challenge to plant populations in natural and agricultural systems. Sclerotinia and Phomopsis/Diaporthe are detrimental pathogens for many dicotyledonous plants, including many economically important plants. With no well-established methods to prevent infection in susceptible plants, host-plant resistance is currently the most effective strategy. Despite knowledge of a moderate, positive correlation in resistance to the two diseases in sunflower, detailed analysis of the genetics, in the same populations, has not been conducted. We present results of genome-wide analysis of resistance to both pathogens in a diversity panel of 218 domesticated sunflower genotypes of worldwide origin. We identified 14 Sclerotinia head rot and 7 Phomopsis stem canker unique QTLs, plus 1 co-located QTL for both traits, and observed extensive patterns of linkage disequilibrium between sites for both traits. Most QTLs contained one credible candidate gene, and gene families were common for the two disease resistance traits. These results suggest there has been strong, simultaneous selection for resistance to these two diseases and that a generalized mechanism for defense against these necrotrophic pathogens exists.
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Affiliation(s)
- Cloe S Pogoda
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Stephan Reinert
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Zahirul I Talukder
- Department of Plant Sciences, North Dakota State University, 166 Loftsgard Hall, Fargo, ND, 58108-6050, USA
| | - Ziv Attia
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Erin C E Collier-Zans
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Thomas J Gulya
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Brent S Hulke
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA.
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14
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
- Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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15
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Oosthuizen JR, Naidoo RK, Rossouw D, Bauer FF. Evolution of mutualistic behaviour between Chlorella sorokiniana and Saccharomyces cerevisiae within a synthetic environment. J Ind Microbiol Biotechnol 2020; 47:357-372. [PMID: 32385605 DOI: 10.1007/s10295-020-02280-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023]
Abstract
Yeast and microalgae are microorganisms with widely diverging physiological and biotechnological properties. Accordingly, their fields of applications diverge: yeasts are primarily applied in processes related to fermentation, while microalgae are used for the production of high-value metabolites and green technologies such as carbon capture. Heterotrophic-autotrophic systems and synthetic ecology approaches have been proposed as tools to achieve stable combinations of such evolutionarily unrelated species. We describe an entirely novel synthetic ecology-based approach to evolve co-operative behaviour between winery wastewater isolates of the yeast Saccharomyces cerevisiae and microalga Chlorella sorokiniana. The data show that biomass production and mutualistic growth improved when co-evolved yeast and microalgae strains were paired together. Combinations of co-evolved strains displayed a range of phenotypes, including differences in amino acid profiles. Taken together, the results demonstrate that biotic selection pressures can lead to improved mutualistic growth phenotypes over relatively short time periods.
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Affiliation(s)
- J R Oosthuizen
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
| | - R K Naidoo
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
| | - D Rossouw
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
| | - F F Bauer
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa.
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16
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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: 25] [Impact Index Per Article: 6.3] [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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Keepers KG, Pogoda CS, White KH, Anderson Stewart CR, Hoffman JR, Ruiz AM, McCain CM, Lendemer JC, Kane NC, Tripp EA. Whole Genome Shotgun Sequencing Detects Greater Lichen Fungal Diversity Than Amplicon-Based Methods in Environmental Samples. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00484] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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18
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Chen C, Li Q, Fu R, Wang J, Xiong C, Fan Z, Hu R, Zhang H, Lu D. Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics. Sci Rep 2019; 9:17447. [PMID: 31768013 PMCID: PMC6877775 DOI: 10.1038/s41598-019-53941-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Scytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.
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Affiliation(s)
- Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, 610066, Sichuan, P.R. China
| | - Qiang Li
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, P.R. China
| | - Rongtao Fu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Jian Wang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhonghan Fan
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Rongping Hu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Hong Zhang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Daihua Lu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China.
- Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, P.R. China.
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19
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Lendemer JC, Keepers KG, Tripp EA, Pogoda CS, McCain CM, Kane NC. A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens. AMERICAN JOURNAL OF BOTANY 2019; 106:1090-1095. [PMID: 31397894 DOI: 10.1002/ajb2.1339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.
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Affiliation(s)
- James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Christy M McCain
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
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20
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Pogoda CS, Keepers KG, Nadiadi AY, Bailey DW, Lendemer JC, Tripp EA, Kane NC. Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria. Ecol Evol 2019; 9:4245-4263. [PMID: 31016002 PMCID: PMC6467859 DOI: 10.1002/ece3.5056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/12/2019] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.
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Affiliation(s)
- Cloe S. Pogoda
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - Kyle G. Keepers
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - Arif Y. Nadiadi
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - Dustin W. Bailey
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
| | - James C. Lendemer
- Institute of Systematic BotanyThe New York Botanical GardenBronxNew York
| | - Erin A. Tripp
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
- Museum of Natural HistoryUniversity of ColoradoBoulderColorado
| | - Nolan C. Kane
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColorado
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21
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Kistenich S, Halvorsen R, Schrøder-Nielsen A, Thorbek L, Timdal E, Bendiksby M. DNA Sequencing Historical Lichen Specimens. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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22
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Brigham LM, Allende LM, Shipley BR, Boyd KC, Higgins TJ, Kelly N, Anderson Stewart CR, Keepers KG, Pogoda CS, Lendemer JC, Tripp EA, Kane NC. Genomic insights into the mitochondria of 11 eastern North American species of Cladonia. Mitochondrial DNA B Resour 2018; 3:508-512. [PMID: 33490518 PMCID: PMC7801001 DOI: 10.1080/23802359.2018.1463827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 11/15/2022] Open
Abstract
Cladonia is among the most species-rich genera of lichens globally. Species in this lineage, commonly referred to as reindeer lichens, are ecologically important in numerous regions worldwide. In some locations, species of Cladonia can comprise the dominant groundcover, and are a major food source for caribou and other mammals. Additionally, many species are known to produce substances with antimicrobial properties or other characteristics with potentially important medical applications. This exceptional morphological and ecological variation contrasts sharply with the limited molecular divergence often observed among species. As a new resource to facilitate ongoing and future studies of these important species, we analyse here the sequences of 11 Cladonia mitochondrial genomes, including new mitochondrial genome assemblies and annotations representing nine species: C. apodocarpa, C. caroliniana, C. furcata, C. leporina, C. petrophila, C. peziziformis, C. robbinsii, C. stipitata, and C. subtenuis. These 11 genomes varied in size, intron content, and complement of tRNAs. Genes annotated within these mitochondrial genomes include 15 protein-coding genes, the large and small ribosomal subunits (mtLSU and mtSSU), and 23-26 tRNAs. All Cladonia mitochondrial genomes contained atp9, an important energy transport gene that has been lost evolutionarily in some lichen mycobiont mitochondria. Using a concatenated alignment of five mitochondrial genes (nad2, nad4, cox1, cox2, and cox3), a Bayesian phylogeny of relationships among species was inferred and was consistent with previously published phylogenetic relationships, highlighting the utility of these regions in reconstructing phylogenetic history.
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Affiliation(s)
- Laurel M. Brigham
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Luis M. Allende
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Benjamin R. Shipley
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Kayla C. Boyd
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Tanya J. Higgins
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Nicholas Kelly
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | | | - Kyle G. Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cloe S. Pogoda
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - James C. Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, New York, NY, USA
| | - Erin A. Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Museum of Natural History, University of Colorado, Boulder, CO, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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23
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Funk ER, Adams AN, Spotten SM, Van Hove RA, Whittington KT, Keepers KG, Pogoda CS, Lendemer JC, Tripp EA, Kane NC. The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:305-308. [PMID: 33474154 PMCID: PMC7800062 DOI: 10.1080/23802359.2018.1445485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Known colloquially as 'Old Man's Beard', Usnea is a genus of lichenized Ascomycete fungi characterized by having a fruticose growth form and cartilaginous central axis. The complete mitochondrial genomes of Usnea halei, U. mutabilis, U. subfusca, U. subgracilis, and U. subscabrosa were sequenced using Illumina data and then assembled de novo. These mitogenomes ranged in size from 52,486 bp (U. subfusca) to 94,464 bp (U. subgracilis). All were characterized by having high levels of intronic and intergenic variation, such as ORFs that encode proteins with homology to two homing endonuclease types, LAGLIDADG and GIY-YIG. Genes annotated within these mitogenomes include 14 protein-coding genes, the large and small ribosomal subunits (LSU and SSU), and 23-26 tRNAs. Notably, the atp9 gene was absent from each genome. Genomic synteny was highly conserved across the five species. Five conserved mitochondrial genes (nad2, nad4, cox1, cox2, and cox3) were used to infer a best estimate maximum likelihood phylogeny among these five Usnea and other relatives, which yielded relationships consistent with prior published phylogenies.
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Affiliation(s)
- Erik R Funk
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Alexander N Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Sarah M Spotten
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Roxanne A Van Hove
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Kristina T Whittington
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cloe S Pogoda
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, USA
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Museum of Natural History, University of Colorado, Boulder, CO, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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