1
|
Szarka D, Gauthier NA, Rahnama M, Schardl CL. Seeing double on Cannabis: Haploids and heteroploids of Bipolaris gigantea on hemp and other dicots. Mycologia 2023; 115:614-629. [PMID: 37463242 DOI: 10.1080/00275514.2023.2224699] [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: 01/05/2023] [Accepted: 06/09/2023] [Indexed: 07/20/2023]
Abstract
Bipolaris gigantea (= Drechslera gigantea) causes Bipolaris leaf spot (BLS), a devastating and widespread disease on industrial hemp (Cannabis sativa). An investigation of relationships of isolates from hemp and other plants indicated variation in ploidy that has not previously been reported for Bipolaris. Isolates were obtained from BLS lesions on hemp and nearby weeds in 11 Kentucky counties and were similar to each other in morphology and growth characteristics. In total, 23 isolates were analyzed by multilocus phylogenetics, of which seven were also chosen for whole genome shotgun sequencing. Genes for RNA polymerase II subunit 2 (RPB2), translation elongation factor 1-α (TEF1), and mating type (MAT1) indicated that 13 of the isolates were haploid with only a single allele each of RPB2 and TEF1 and either the MAT1-1 or MAT1-2 idiomorph, whereas 10 were apparently "heteroploid" with two alleles each of RPB2 and TEF1 and both MAT1 idiomorphs. Haploids all had identical RPB2 alleles except for a 1-bp difference in two isolates, identical TEF1 alleles, and (if present) identical MAT1-2 alleles. Those alleles were also present in each heteroploid along with either of two related but distinct alleles for each gene. In contrast, haploids and heteroploids shared allelic variation of MAT1-1. In total, four haploid and two heteroploid genotypes were identified. Genome sequence data assembled to 30-32 Mb for each of four haploid isolates, but 10-31 Mb larger sizes for each of three heteroploids depending on sequencing platform and assembly program. The haploids and heteroploids caused similar disease on hemp.
Collapse
Affiliation(s)
- Desiree Szarka
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - Nicole A Gauthier
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - Mostafa Rahnama
- Department of Biology, Tennessee Tech University, Cookeville, Tennessee 38505
| | | |
Collapse
|
2
|
|
3
|
The Impact of Alkaloid-Producing Epichloë Endophyte on Forage Ryegrass Breeding: A New Zealand Perspective. Toxins (Basel) 2021; 13:toxins13020158. [PMID: 33670470 PMCID: PMC7922046 DOI: 10.3390/toxins13020158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/28/2021] [Accepted: 02/06/2021] [Indexed: 12/02/2022] Open
Abstract
For 30 years, forage ryegrass breeding has known that the germplasm may contain a maternally inherited symbiotic Epichloë endophyte. These endophytes produce a suite of secondary alkaloid compounds, dependent upon strain. Many produce ergot and other alkaloids, which are associated with both insect deterrence and livestock health issues. The levels of alkaloids and other endophyte characteristics are influenced by strain, host germplasm, and environmental conditions. Some strains in the right host germplasm can confer an advantage over biotic and abiotic stressors, thus acting as a maternally inherited desirable ‘trait’. Through seed production, these mutualistic endophytes do not transmit into 100% of the crop seed and are less vigorous than the grass seed itself. This causes stability and longevity issues for seed production and storage should the ‘trait’ be desired in the germplasm. This makes understanding the precise nature of the relationship vitally important to the plant breeder. These Epichloë endophytes cannot be ‘bred’ in the conventional sense, as they are asexual. Instead, the breeder may modulate endophyte characteristics through selection of host germplasm, a sort of breeding by proxy. This article explores, from a forage seed company perspective, the issues that endophyte characteristics and breeding them by proxy have on ryegrass breeding, and outlines the methods used to assess the ‘trait’, and the application of these through the breeding, production, and deployment processes. Finally, this article investigates opportunities for enhancing the utilisation of alkaloid-producing endophytes within pastures, with a focus on balancing alkaloid levels to further enhance pest deterrence and improving livestock outcomes.
Collapse
|
4
|
Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun Biol 2021; 4:201. [PMID: 33589695 PMCID: PMC7884421 DOI: 10.1038/s42003-021-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.
Collapse
|
5
|
Cagnano G, Lenk I, Roulund N, Jensen CS, Cox MP, Asp T. Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue ( Schedonorus pratensis). Mycologia 2020; 112:474-490. [PMID: 32412888 DOI: 10.1080/00275514.2020.1746607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many efforts have been made to select and isolate naturally occurring animal-friendly Epichloë strains for later reinfection into elite cultivars. Often this process involves large-scale screening of Epichloë-infected wild grass populations where strains are characterized and alkaloids measured. Here, we describe for the first time the use of genotyping-by-sequencing (GBS) on a collection of 217 Epichloë-infected grasses (7 S. arundinaceum, 4 L. perenne, and 206 S. pratensis). This genotyping strategy is cheaper than complete genome sequencing, is suitable for a large number of individuals, and, when applied to endophyte-infected grasses, conveniently genotypes both organisms. In total, 6273 single nucleotide polymorphisms (SNPs) in the endophyte data set and 38 323 SNPs in the host data set were obtained. Our findings reveal a composite structure with three distinct endophyte clusters unrelated to the three main S. pratensis gene pools that have most likely spread from different glacial refugia in Eurasia. All three gene pools can establish symbiosis with E. uncinata. A comparison of the endophyte clusters with microsatellite-based fingerprinting of the same samples allows a quick test to discriminate between these clusters using two simple sequence repeats (SSRs). Concentrations of loline alkaloids and mycelial biomass are correlated and differ significantly among the plant and endophyte subpopulations; one endophyte strain has higher levels of lolines than others, and one specific host genotype is particularly suitable to host E. uncinata. These findings pave the way for targeted artificial inoculations of specific host-endophyte combinations to boost loline production in the symbiota and for genome association studies with the aim of isolating genes involved in the compatibility between meadow fescue and E. uncinata.
Collapse
Affiliation(s)
- G Cagnano
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - I Lenk
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - N Roulund
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - C S Jensen
- DLF Seeds A/S, Højerupvej 31, 4660 Store Heddinge , Denmark
| | - M P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University , Palmerston North 4442, New Zealand
| | - T Asp
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University , Aarhus, Denmark
| |
Collapse
|
6
|
Hume DE, Stewart AV, Simpson WR, Johnson RD. Epichloëfungal endophytes play a fundamental role in New Zealand grasslands. J R Soc N Z 2020. [DOI: 10.1080/03036758.2020.1726415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Alan V. Stewart
- PGG Wrightson Seeds Limited, Kimihia Research Centre, Lincoln, New Zealand
| | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | |
Collapse
|
7
|
Behling AH, Shepherd LD, Cox MP. The importance and prevalence of allopolyploidy in Aotearoa New Zealand. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1676797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Anna H. Behling
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Murray P. Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| |
Collapse
|
8
|
Brian JI, Davy SK, Wilkinson SP. Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 2019; 7:e7178. [PMID: 31289699 PMCID: PMC6598746 DOI: 10.7717/peerj.7178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
Collapse
Affiliation(s)
- Joshua I Brian
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| |
Collapse
|
9
|
Moon CD, Scott B, Schardl CL, Christensen MJ. The evolutionary origins of Epichloë endophytes from annual ryegrasses. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Christina D. Moon
- Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Barry Scott
- Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | | | - Michael J. Christensen
- AgResearch, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
| |
Collapse
|
10
|
Affiliation(s)
- Kerry O'Donnell
- Microbial Properties Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604-3999
| |
Collapse
|
11
|
Nielsen K, Yohalem DS. Origin of a polyploid Botrytis pathogen through interspecific hybridization between Botrytis aclada and B. byssoidea. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karsten Nielsen
- Department of Crop Protection, Danish Institute of Agricultural Sciences, Research Center Flakkebjerg, 4200 Slagelse, Denmark
| | - David S. Yohalem
- Department of Crop Protection, Danish Institute of Agricultural Sciences, Research Center Flakkebjerg, 4200 Slagelse, Denmark
| |
Collapse
|
12
|
Affiliation(s)
| | - Adrian Leuchtmann
- Geobotanisches Institut ETH, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| |
Collapse
|
13
|
Myllys L, Lohtander K, Tehler A. β-tubulin, ITS and group I intron sequences challenge the species pair concept in Physcia aipolia and P. caesia. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Leena Myllys
- Department of Biology, University of Turku, FIN-20014 Turku, Finland
| | | | - Anders Tehler
- Sektionen för kryptogambotanik, Naturhistoriska riksmuseet, Box 50007, S-104 05 Stockholm, Sweden
| |
Collapse
|
14
|
Soto-Barajas MC, Vázquez-de-Aldana BR, Álvarez A, Zabalgogeazcoa I. Sympatric Epichloë species and chemotypic profiles in natural populations of Lolium perenne. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
15
|
Hassing B, Winter D, Becker Y, Mesarich CH, Eaton CJ, Scott B. Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne. PLoS One 2019; 14:e0209463. [PMID: 30759164 PMCID: PMC6374014 DOI: 10.1371/journal.pone.0209463] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby maintaining a mutualistic symbiotic interaction. Recent studies have suggested that small secreted proteins, termed effectors, play a vital role in the suppression of host defence responses. To date only a few effectors with important roles in mutualistic interactions have been described. Here we make use of the fully assembled E. festucae genome and EffectorP to generate a suite of 141 effector candidates. These were analysed with respect to their genome location and expression profiles in planta and in several symbiosis-defective mutants. We found an association between effector candidates and a class of transposable elements known as MITEs, but no correlation with other dynamic features of the E. festucae genome, such as transposable element-rich regions. Three effector candidates and a small GPI-anchored protein were chosen for functional analysis based on their high expression in planta compared to in culture and their differential regulation in symbiosis defective E. festucae mutants. All three candidate effector proteins were shown to possess a functional signal peptide and two could be detected in the extracellular medium by western blotting. Localization of the effector candidates in planta suggests that they are not translocated into the plant cell, but rather, are localized in the apoplastic space or are attached to the cell wall. Deletion and overexpression of the effector candidates, as well as the putative GPI-anchored protein, did not affect the plant growth phenotype or restrict growth of E. festucae mutants in planta. These results indicate that these proteins are either not required for the interaction at the observed life stages or that there is redundancy between effectors expressed by E. festucae.
Collapse
Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Küehn-Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Carl H. Mesarich
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Carla J. Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| |
Collapse
|
16
|
Leuchtmann A, Schardl CL, Siegel MR. Sexual compatibility and taxonomy of a new species of Epichloë symbiotic with fine fescue grasses. Mycologia 2018. [DOI: 10.1080/00275514.1994.12026487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Adrian Leuchtmann
- Geobotanisches Institut ETH, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | | | - Malcolm R. Siegel
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| |
Collapse
|
17
|
White JF, Sharp LT, Martin TI, Glenn AE. Endophyte-host associations in grasses. XXI. Studies on the structure and development ofBalansia obtecta. Mycologia 2018. [DOI: 10.1080/00275514.1995.12026518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- James F. White
- Department of Biology, Auburn University at Montgomery, Montgomery, Alabama, 36117
| | - Lynn T. Sharp
- Department of Biology, Auburn University at Montgomery, Montgomery, Alabama, 36117
| | - Tyler I. Martin
- Department of Biology, Auburn University at Montgomery, Montgomery, Alabama, 36117
| | - Anthony E. Glenn
- Department of Biology, Auburn University at Montgomery, Montgomery, Alabama, 36117
| |
Collapse
|
18
|
Kuldau GA, Liu JS, White JF, Siegel MR, Schardl CL. Molecular systematics of Clavicipitaceae supporting monophyly of genusEpichloëand form genusEphelis. Mycologia 2018. [DOI: 10.1080/00275514.1997.12026802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Gretchen A. Kuldau
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - Jih-Shiou Liu
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - James F. White
- Department of Plant Pathology, Rutgers University, New Brunswick, New Jersey 08903
| | - Malcolm R. Siegel
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | | |
Collapse
|
19
|
O'Donnell K, Cigelnik E, Nirenberg HI. Molecular systematics and phylogeography of theGibberella fujikuroispecies complex. Mycologia 2018. [DOI: 10.1080/00275514.1998.12026933] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Kerry O'Donnell
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois 61604-3999
| | - Elizabeth Cigelnik
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois 61604-3999
| | - Helgard I. Nirenberg
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Mikrobiologie, Königin-Luise-Straβe 19, D-14119 Berlin, Germany
| |
Collapse
|
20
|
Campbell MA, Tapper BA, Simpson WR, Johnson RD, Mace W, Ram A, Lukito Y, Dupont PY, Johnson LJ, Scott DB, Ganley ARD, Cox MP. Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy. Mycologia 2018; 109:715-729. [PMID: 29370579 DOI: 10.1080/00275514.2017.1406174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Endophytes of the genus Epichloë (Clavicipitaceae, Ascomycota) frequently occur within cool-season grasses and form interactions with their hosts that range from mutualistic to antagonistic. Many Epichloë species have arisen via interspecific hybridization, resulting in species with two or three subgenomes that retain all or nearly all of their original parental genomes, a process termed allopolyploidization. Here, we characterize Epichloë hybrida, sp. nov., a mutualistic species that has increasingly become a model system for investigating allopolyploidy in fungi. The Epichloë species so far identified as the closest known relatives of the two progenitors of E. hybrida are E. festucae var. lolii and E. typhina. We confirm that the nuclear genome of E. hybrida contains two homeologs of most protein-coding genes from E. festucae and E. typhina, with genome-wide gene expression analysis indicating a slight bias in overall gene expression from the E. typhina subgenome. Mitochondrial DNA is detectable only from E. festucae, whereas ribosomal DNA is detectable only from E. typhina. Inheriting ribosomal DNA from just one parent might be expected to preferentially favor interactions with ribosomal proteins from the same parent, but we find that ribosomal protein genes from both parental subgenomes are nearly all expressed equally in E. hybrida. Finally, we provide a comprehensive set of resources for this model system that are intended to facilitate further study of fungal hybridization by other researchers.
Collapse
Affiliation(s)
- Matthew A Campbell
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Brian A Tapper
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Wayne R Simpson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Richard D Johnson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Wade Mace
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - Arvina Ram
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Yonathan Lukito
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Pierre-Yves Dupont
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Linda J Johnson
- b AgResearch Ltd., Grasslands Research Centre , Tennent Drive, Palmerston North 4442 , New Zealand
| | - D Barry Scott
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| | - Austen R D Ganley
- c School of Biological Sciences, University of Auckland , Private Bag 92019, Auckland 1142 , New Zealand
| | - Murray P Cox
- a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand
| |
Collapse
|
21
|
Clayton W, Eaton CJ, Dupont PY, Gillanders T, Cameron N, Saikia S, Scott B. Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events. PLoS One 2017; 12:e0183748. [PMID: 28886068 PMCID: PMC5590859 DOI: 10.1371/journal.pone.0183748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/10/2017] [Indexed: 11/24/2022] Open
Abstract
Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.
Collapse
Affiliation(s)
- William Clayton
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Carla Jane Eaton
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Pierre-Yves Dupont
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | | | | | - Sanjay Saikia
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- * E-mail:
| |
Collapse
|
22
|
Arnold SL, Panaccione DG. Biosynthesis of the Pharmaceutically Important Fungal Ergot Alkaloid Dihydrolysergic Acid Requires a Specialized Allele of cloA. Appl Environ Microbiol 2017; 83:e00805-17. [PMID: 28476772 PMCID: PMC5494617 DOI: 10.1128/aem.00805-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/03/2017] [Indexed: 11/20/2022] Open
Abstract
Ergot alkaloids are specialized fungal metabolites that are important as the bases of several pharmaceuticals. Many ergot alkaloids are derivatives of lysergic acid (LA) and have vasoconstrictive activity, whereas several dihydrolysergic acid (DHLA) derivatives are vasorelaxant. The pathway to LA is established, with the P450 monooxygenase CloA playing a key role in oxidizing its substrate agroclavine to LA. We analyzed the activities of products of cloA alleles from different fungi relative to DHLA biosynthesis by expressing them in a mutant of the fungus Neosartorya fumigata that accumulates festuclavine, the precursor to DHLA. Transformants expressing CloA from Epichloë typhina × Epichloë festucae, which oxidizes agroclavine to LA, failed to oxidize festuclavine to DHLA. In substrate feeding experiments, these same transformants oxidized exogenously supplied agroclavine to LA, indicating that a functional CloA was produced. A genomic clone of cloA from Claviceps africana, a sorghum ergot fungus that produces a DHLA derivative, was cloned and expressed in the festuclavine-accumulating mutant of N. fumigata, but several introns in this genomic clone were not processed properly. Expression of a synthetic intron-free version of C. africanacloA resulted in the accumulation of DHLA as assessed by fluorescence high-pressure liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS). In substrate feeding experiments, the C. africana CloA also accepted agroclavine as the substrate, oxidizing it to LA. The data indicate that a specialized allele of cloA is required for DHLA biosynthesis and that the pharmaceutically important compound DHLA can be produced in engineered N. fumigataIMPORTANCE Ergot alkaloids are fungal metabolites that have impacted humankind historically as poisons and more recently as pharmaceuticals used to treat dementia, migraines, and other disorders. Much is known about the biosynthesis of ergot alkaloids that are derived from lysergic acid (LA), but important questions remain about a parallel pathway to ergot alkaloids derived from dihydrolysergic acid (DHLA). DHLA-derived alkaloids have minor structural differences compared to LA-derived alkaloids but can have very different activities. To understand how DHLA is made, we analyzed activities of a key enzyme in the DHLA pathway and found that it differed from its counterpart in the LA pathway. Our data indicate a critical difference between the two pathways and provide a strategy for producing DHLA by modifying a model fungus. The ability to produce DHLA in a model fungus may facilitate synthesis of DHLA-derived pharmaceuticals.
Collapse
Affiliation(s)
- Stephanie L Arnold
- West Virginia University, Division of Plant and Soil Sciences, Genetics and Developmental Biology Program, Morgantown, West Virginia, USA
| | - Daniel G Panaccione
- West Virginia University, Division of Plant and Soil Sciences, Genetics and Developmental Biology Program, Morgantown, West Virginia, USA
| |
Collapse
|
23
|
Bucheli E, Leuchtmann A. EVIDENCE FOR GENETIC DIFFERENTIATION BETWEEN CHOKE-INDUCING AND ASYMPTOMATIC STRAINS OF THE EPICHLOË GRASS ENDOPHYTE FROM BRACHYPODIUM SYLVATICUM. Evolution 2017; 50:1879-1887. [PMID: 28565581 DOI: 10.1111/j.1558-5646.1996.tb03575.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/1995] [Accepted: 02/02/1996] [Indexed: 11/27/2022]
Abstract
Life cycle and breeding system variation in Epichloë grass endophytes (choke disease) is tightly linked to the degree of stroma formation. It is not known whether this variation results from differences in host resistance, fungal virulence, or environmental conditions. We found genetic differentiation between 173 asymptomatic (NS) and 93 stromata-forming (S) Epichloë strains isolated from one grass species, Brachypodium sylvaticum, based on 13 presumed allozyme loci, of which six were variable. The fungal strains originated from 10 sites in Switzerland, three sites of which were represented by both NS and S subpopulations. In total, 19 allozyme genotypes, that were nonrandomly distributed among S and NS were detected. Genetic variation measured as GST between S and NS strains isolated from the same site ranged from 0.73 to 0.98. Clonality, measured as linkage disequilibrium at one site, was significant in the NS subpopulation (P ≪ 0.001), but not in the S subpopulation (P = 0.21), implying asexual reproduction by NS strains as well as successful horizontal transmission of S strains. Since all seeds are usually infected vegetatively, horizontal transmission implies the occurrence of multiple host infections. Altogether, these results provide indirect evidence that NS and S strains do not belong to one panmictic population and that differentiation patterns of stroma formation found in nature are due to genetic differences among fungi in associations with their host plants. We discuss the direction of evolution of disease expression in this system. The distribution of genetic variability suggests that the asymptomatic strains were derived from stromata-forming populations.
Collapse
Affiliation(s)
- Erika Bucheli
- Geobotanisches Institut ETH, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Adrian Leuchtmann
- Geobotanisches Institut ETH, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| |
Collapse
|
24
|
Moon CD, Guillaumin JJ, Ravel C, Li C, Craven KD, Schardl CL. New Neotyphodium endophyte species from the grass tribes Stipeae and Meliceae. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Christina D. Moon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546-0312
| | | | - Catherine Ravel
- INRA, UMR 1095, 234 Avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Chunjie Li
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Gansu Grassland Ecological Research Institute, Key Laboratory of Grassland Argo-Ecosystem, Ministry of Agriculture, Lanzhou 730020, China
| | | | | |
Collapse
|
25
|
Chen YG, Ji YL, Yu HS, Wang ZW. A new Neotyphodium species from Festuca parvigluma Steud. grown in China. Mycologia 2017; 101:681-5. [DOI: 10.3852/08-181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Zhi-wei Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
26
|
Voisey CR, Christensen MT, Johnson LJ, Forester NT, Gagic M, Bryan GT, Simpson WR, Fleetwood DJ, Card SD, Koolaard JP, Maclean PH, Johnson RD. cAMP Signaling Regulates Synchronised Growth of Symbiotic Epichloë Fungi with the Host Grass Lolium perenne. FRONTIERS IN PLANT SCIENCE 2016; 7:1546. [PMID: 27833620 PMCID: PMC5082231 DOI: 10.3389/fpls.2016.01546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
The seed-transmitted fungal symbiont, Epichloë festucae, colonizes grasses by infecting host tissues as they form on the shoot apical meristem (SAM) of the seedling. How this fungus accommodates the complexities of plant development to successfully colonize the leaves and inflorescences is unclear. Since adenosine 3', 5'-cyclic monophosphate (cAMP)-dependent signaling is often essential for host colonization by fungal pathogens, we disrupted the cAMP cascade by insertional mutagenesis of the E. festucae adenylate cyclase gene (acyA). Consistent with deletions of this gene in other fungi, acyA mutants had a slow radial growth rate in culture, and hyphae were convoluted and hyper-branched suggesting that fungal apical dominance had been disrupted. Nitro blue tetrazolium (NBT) staining of hyphae showed that cAMP disruption mutants were impaired in their ability to synthesize superoxide, indicating that cAMP signaling regulates accumulation of reactive oxygen species (ROS). Despite significant defects in hyphal growth and ROS production, E. festucae ΔacyA mutants were infectious and capable of forming symbiotic associations with grasses. Plants infected with E. festucae ΔacyA were marginally less robust than the wild-type (WT), however hyphae were hyper-branched, and leaf tissues heavily colonized, indicating that the tight regulation of hyphal growth normally observed in maturing leaves requires functional cAMP signaling.
Collapse
Affiliation(s)
- Christine R. Voisey
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Michael T. Christensen
- Formally of Forage Improvement, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Linda J. Johnson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Natasha T. Forester
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Milan Gagic
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Gregory T. Bryan
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Wayne R. Simpson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Damien J. Fleetwood
- Biotelliga Ltd., Institute for Innovation in BiotechnologyAuckland, New Zealand
| | - Stuart D. Card
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - John P. Koolaard
- Bioinformatics and Statistics Team, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Paul H. Maclean
- Bioinformatics and Statistics Team, AgResearch Ltd., Lincoln Research CentreChristchurch, New Zealand
| | - Richard D. Johnson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| |
Collapse
|
27
|
Mulinti P, Florea S, Schardl CL, Panaccione DG. Modulation of Ergot Alkaloids in a Grass-Endophyte Symbiosis by Alteration of mRNA Concentrations of an Ergot Alkaloid Synthesis Gene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4982-4989. [PMID: 27248330 DOI: 10.1021/acs.jafc.6b01604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The profile of ergot alkaloids in perennial ryegrass (Lolium perenne) containing the endophytic fungus Epichloë typhina × festucae includes high concentrations of the early pathway metabolites ergotryptamine and chanoclavine-I in addition to the pathway end-product ergovaline. Because these alkaloids differ in activity, we investigated strategies to alter their relative concentrations. An RNAi-based approach reduced the concentration of mRNA from the gene easA, which encodes an enzyme required for a ring closure that separates ergotryptamine and chanoclavine-I from ergovaline. Lower easA mRNA concentrations correlated with lower concentrations of ergovaline and higher concentrations of ergotryptamine and chanoclavine-I. Overexpression of easA led to higher concentrations of ergovaline in leaf blades but not in pseudostems; concentrations of the early pathway metabolites were not altered in overexpression strains. The data indicate that altering the concentration of mRNA from a single gene can change alkaloid flux, but the magnitude of the change was limited and variable.
Collapse
Affiliation(s)
- Prashanthi Mulinti
- Genetics and Developmental Biology Program, Division of Plant and Soil Sciences, West Virginia University , Morgantown, West Virginia 26506-6108, United States
| | - Simona Florea
- Department of Plant Pathology, University of Kentucky , Lexington, Kentucky 40546-0312, United States
| | - Christopher L Schardl
- Department of Plant Pathology, University of Kentucky , Lexington, Kentucky 40546-0312, United States
| | - Daniel G Panaccione
- Genetics and Developmental Biology Program, Division of Plant and Soil Sciences, West Virginia University , Morgantown, West Virginia 26506-6108, United States
| |
Collapse
|
28
|
Song H, Nan Z. Origin, divergence, and phylogeny of asexual Epichloë endophyte in Elymus species from western China. PLoS One 2015; 10:e0127096. [PMID: 25970178 PMCID: PMC4430518 DOI: 10.1371/journal.pone.0127096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/10/2015] [Indexed: 11/29/2022] Open
Abstract
Asexual Epichloë species are likely derived directly from sexual Epichloë species that then lost their capacity for sexual reproduction or lost sexual reproduction because of interspecific hybridization between distinct lineages of sexual Epichloë and/or asexual Epichloë species. In this study we isolated asexual Epichloë endophytes from Elymus species in western China and sequenced intron-rich regions in the genes encoding β-tubulin (tubB) and translation elongation factor 1-α (tefA). Our results showed that there are no gene copies of tubB and tefA in any of the isolates. Phylogenetic analysis showed that sequences in this study formed a single clade with asexual Epichloë bromicola from Hordeum brevisubulatum, which implies asexual Epichloë endophytes that are symbionts in a western Chinese Elymus species likely share a common ancestor with asexual E. bromicola from European H. brevisubulatum. In addition, our results revealed that asexual E. bromicola isolates that are symbionts in a western Chinese Elymus species and sexual Epichloë species that are symbionts in a North American Elymus species have a different origin. Further analysis found that Epichloë species likely originated in Eurasia. In addition, the results support the hypothesis that migratory birds or humans might have aided the dispersal of these fungal endophytes to other continents.
Collapse
Affiliation(s)
- Hui Song
- Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, 730020, P. R. China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Zhibiao Nan
- Key Laboratory of Grassland Agro-Ecosystems, Lanzhou, 730020, P. R. China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P. R. China
| |
Collapse
|
29
|
Hettiarachchige IK, Ekanayake PN, Mann RC, Guthridge KM, Sawbridge TI, Spangenberg GC, Forster JW. Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass. BMC Evol Biol 2015; 15:72. [PMID: 25902799 PMCID: PMC4458015 DOI: 10.1186/s12862-015-0349-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/14/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Perennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been described. In addition to these two well-characterised taxa, a third distinct group of previously unclassified perennial ryegrass-associated endophytes was identified as belonging to a putative novel taxon (or taxa) (PNT) in a previous analysis based on simple sequence repeat (SSR) marker diversity. As well as genotypic differences, distinctive alkaloid production profiles were observed for members of the PNT group. RESULTS A detailed phylogenetic analysis of perennial ryegrass-associated endophytes using components of whole genome sequence data was performed using complete sequences of 7 nuclear protein-encoding genes. Three independently selected genes (encoding a DEAD/DEAH box helicase [Sbp4], a glycosyl hydrolase [family 92 protein] and a MEAB protein), none of which have been previously used for taxonomic studies of endophytes, were selected together with the frequently used 'house-keeping' genes tefA and tubB (encoding translation elongation factor 1-α and β-tubulin, respectively). In addition, an endophyte-specific gene (perA for peramine biosynthesis) and the fungal-specific MT genes for mating-type control were included. The results supported previous phylogenomic inferences for the known species, but revealed distinctive patterns of diversity for the previously unclassified endophyte strains, which were further proposed to belong to not one but two distinct novel taxa. Potential progenitor genomes for the asexual endophytes among contemporary teleomorphic (sexual Epichloë) species were also identified from the phylogenetic analysis. CONCLUSIONS Unique taxonomic status for the PNT was confirmed through comparison of multiple nuclear gene sequences, and also supported by evidence from chemotypic diversity. Analysis of MT gene idiomorphs further supported a predicted independent origin of two distinct perennial ryegrass-associated novel taxa, designated LpTG-3 and LpTG-4, from different members of a similar founder population related to contemporary E. festucae. The analysis also provided higher resolution to the known progenitor contributions of previously characterised perennial ryegrass-associated endophyte taxa.
Collapse
Affiliation(s)
- Inoka K Hettiarachchige
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, Victoria, 3086, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| | - Piyumi N Ekanayake
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- Molecular Plant Breeding Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| | - Ross C Mann
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| | - Kathryn M Guthridge
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- Molecular Plant Breeding Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| | - Timothy I Sawbridge
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- Molecular Plant Breeding Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| | - German C Spangenberg
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, Victoria, 3086, Australia.
- Molecular Plant Breeding Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| | - John W Forster
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, Victoria, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, Victoria, 3086, Australia.
- Molecular Plant Breeding Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Melbourne, Victoria, 3083, Australia.
| |
Collapse
|
30
|
Duchemin W, Dupont PY, Campbell MA, Ganley ARD, Cox MP. HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species. BMC Bioinformatics 2015; 16:8. [PMID: 25592117 PMCID: PMC4300824 DOI: 10.1186/s12859-014-0433-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/16/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how expression of parental gene copies (homeologs) responds following genome merger. High throughput RNA sequencing now makes this analysis technically feasible, but tools to determine homeolog expression are still in their infancy. RESULTS Here we present HyLiTE - a single-step analysis to obtain tables of homeolog expression in a hybrid or allopolyploid and its parent species directly from raw mRNA sequence files. By implementing on-the-fly detection of diagnostic parental polymorphisms, HyLiTE can perform SNP calling and read classification simultaneously, thus allowing HyLiTE to be run as parallelized code. HyLiTE accommodates any number of parent species, multiple data sources (including genomic DNA reads to improve SNP detection), and implements a statistical framework optimized for genes with low to moderate expression. CONCLUSIONS HyLiTE is a flexible and easy-to-use program designed for bench biologists to explore patterns of gene expression following genome merger. HyLiTE offers practical advantages over manual methods and existing programs, has been designed to accommodate a wide range of genome merger systems, can identify SNPs that arose following genome merger, and offers accurate performance on non-model organisms.
Collapse
Affiliation(s)
- Wandrille Duchemin
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. .,Present address: Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Lyon I, Villeurbanne, F-69622, France.
| | - Pierre-Yves Dupont
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Matthew A Campbell
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Austen R D Ganley
- Institute of Mathematical and Natural Sciences, Massey University, Auckland, New Zealand.
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| |
Collapse
|
31
|
Functional Significance of Anastomosis in Arbuscular Mycorrhizal Networks. ECOLOGICAL STUDIES 2015. [DOI: 10.1007/978-94-017-7395-9_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
32
|
Horizontal transmission, persistence and competition capabilities of Epichloë endophytes in Hordelymus europaeus grass hosts using dual endophyte inocula. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
33
|
Heterologous expression of lysergic acid and novel ergot alkaloids in Aspergillus fumigatus. Appl Environ Microbiol 2014; 80:6465-72. [PMID: 25107976 DOI: 10.1128/aem.02137-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Different lineages of fungi produce distinct classes of ergot alkaloids. Lysergic acid-derived ergot alkaloids produced by fungi in the Clavicipitaceae are particularly important in agriculture and medicine. The pathway to lysergic acid is partly elucidated, but the gene encoding the enzyme that oxidizes the intermediate agroclavine is unknown. We investigated two candidate agroclavine oxidase genes from the fungus Epichloë festucae var. lolii × Epichloë typhina isolate Lp1 (henceforth referred to as Epichloë sp. Lp1), which produces lysergic acid-derived ergot alkaloids. Candidate genes easH and cloA were expressed in a mutant strain of the mold Aspergillus fumigatus, which typically produces a subclass of ergot alkaloids not derived from agroclavine or lysergic acid. Candidate genes were coexpressed with the Epichloë sp. Lp1 allele of easA, which encodes an enzyme that catalyzed the synthesis of agroclavine from an A. fumigatus intermediate; the agroclavine then served as the substrate for the candidate agroclavine oxidases. Strains expressing easA and cloA from Epichloë sp. Lp1 produced lysergic acid from agroclavine, a process requiring a cumulative six-electron oxidation and a double-bond isomerization. Strains that accumulated excess agroclavine (as a result of Epichloë sp. Lp1 easA expression in the absence of cloA) metabolized it into two novel ergot alkaloids for which provisional structures were proposed on the basis of mass spectra and precursor feeding studies. Our data indicate that CloA catalyzes multiple reactions to produce lysergic acid from agroclavine and that combining genes from different ergot alkaloid pathways provides an effective strategy to engineer important pathway molecules and novel ergot alkaloids.
Collapse
|
34
|
Tadych M, Bergen MS, White JF. Epichloë spp. associated with grasses: new insights on life cycles, dissemination and evolution. Mycologia 2014; 106:181-201. [PMID: 24877257 DOI: 10.3852/106.2.181] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epichloë species with their asexual states are specialized fungi associated with cool-season grasses. they grow endophytically in tissues of aerial parts of host plants to form systemic and mostly asymptomatic associations. Their life cycles may involve vertical transmission through host seeds and/or horizontal transmission from one plant to other plants of the same species through fungal propagules. Vertical transmission has been well studied, but comparatively little research has been done on horizontal dissemination. The goal of this review is to provide new insights on modes of dissemination of systemic grass endophytes. The review addresses recent progress in research on (i) the process of growth of Epichloë endophytes in the host plant tissues, (ii) the types and development of reproductive structures of the endophyte, (iii) the role of the reproductive structures in endophyte dissemination and host plant infection processes and (iv) some ecological and evolutionary implications of their modes of dissemination. Research in the Epichloë grass endophytes has accelerated in the past 25 y and has demonstrated the enormous complexity in endophyte-grass symbioses. There still remain large gaps in our understanding of the role and functions of these fungi in agricultural systems and understanding the functions, ecology and evolution of these endophytes in natural grass populations.
Collapse
|
35
|
Leuchtmann A, Bacon CW, Schardl CL, White JF, Tadych M. Nomenclatural realignment of Neotyphodium species with genus Epicholë. Mycologia 2014; 106:202-15. [PMID: 24459125 DOI: 10.3852/13-251] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Nomenclatural rule changes in the International Code of Nomenclature for algae, fungi and plants, adopted at the 18th International Botanical Congress in Melbourne, Australia, in 2011, provide for a single name to be used for each fungal species. The anamorphs of Epichloë species have been classified in genus Neotyphodium, the form genus that also includes most asexual Epichloë descendants. A nomenclatural realignment of this monophyletic group into one genus would enhance a broader understanding of the relationships and common features of these grass endophytes. Based on the principle of priority of publication we propose to classify all members of this clade in the genus Epichloë. We have reexamined classification of several described Epichloë and Neotyphodium species and varieties and propose new combinations and states. In this treatment we have accepted 43 unique taxa in Epichloë, including distinct species, subspecies, and varieties. We exclude from Epichloë the two taxa Neotyphodium starrii, as nomen dubium, and Neotyphodium chilense, as an unrelated taxon.
Collapse
|
36
|
Cox MP, Dong T, Shen G, Dalvi Y, Scott DB, Ganley ARD. An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns. PLoS Genet 2014; 10:e1004180. [PMID: 24603805 PMCID: PMC3945203 DOI: 10.1371/journal.pgen.1004180] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/02/2014] [Indexed: 12/13/2022] Open
Abstract
Polyploidy, a state in which the chromosome complement has undergone an increase, is a major force in evolution. Understanding the consequences of polyploidy has received much attention, and allopolyploids, which result from the union of two different parental genomes, are of particular interest because they must overcome a suite of biological responses to this merger, known as “genome shock.” A key question is what happens to gene expression of the two gene copies following allopolyploidization, but until recently the tools to answer this question on a genome-wide basis were lacking. Here we utilize high throughput transcriptome sequencing to produce the first genome-wide picture of gene expression response to allopolyploidy in fungi. A novel pipeline for assigning sequence reads to the gene copies was used to quantify their expression in a fungal allopolyploid. We find that the transcriptional response to allopolyploidy is predominantly conservative: both copies of most genes are retained; over half the genes inherit parental gene expression patterns; and parental differential expression is often lost in the allopolyploid. Strikingly, the patterns of gene expression change are highly concordant with the genome-wide expression results of a cotton allopolyploid. The very different nature of these two allopolyploids implies a conserved, eukaryote-wide transcriptional response to genome merger. We provide evidence that the transcriptional responses we observe are mostly driven by intrinsic differences between the regulatory systems in the parent species, and from this propose a mechanistic model in which the cross-kingdom conservation in transcriptional response reflects conservation of the mutational processes underlying eukaryotic gene regulatory evolution. This work provides a platform to develop a universal understanding of gene expression response to allopolyploidy and suggests that allopolyploids are an exceptional system to investigate gene regulatory changes that have evolved in the parental species prior to allopolyploidization. Organisms are complex biological systems that must continue to function even as their genomes evolve. While evolution is usually gradual, the formation of new species by the hybridization of different parents—allopolyploidization—occurs nearly instantaneously. A key question is what happens to expression of the two parental gene copies following genome merger. To determine this, we focused on a fungal allopolyploid from a group that dominates many of the world's pastoral economies. To investigate the fate of gene expression in this system, we developed a novel pipeline to assign high throughput RNA sequence reads to the two parental gene copies, thus allowing quantification of expression. We found transcriptional responses to be predominantly conservative: most gene copies either inherit parental expression patterns, or if differentially expressed in the parents, that difference is lost in the hybrid. Moreover, we identified an extraordinary level of concordance in the fate of genome-wide allopolyploid gene expression with that seen in cotton. The very different nature of these two allopolyploids suggests that there is a set of universal rules for the transcriptional response to genome merger. We propose a mechanistic model whereby this conserved response reflects similarities in mutational processes that underlie gene regulatory evolution.
Collapse
Affiliation(s)
- Murray P. Cox
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail: (MPC); (ARDG)
| | - Ting Dong
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - GengGeng Shen
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Yogesh Dalvi
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - D. Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- * E-mail: (MPC); (ARDG)
| |
Collapse
|
37
|
Oberhofer M, Güsewell S, Leuchtmann A. Effects of natural hybrid and non-hybrid Epichloë endophytes on the response of Hordelymus europaeus to drought stress. THE NEW PHYTOLOGIST 2014; 201:242-253. [PMID: 24102453 DOI: 10.1111/nph.12496] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/02/2013] [Indexed: 06/02/2023]
Abstract
Interspecific hybrid endophytes of the genus Epichloë (Ascomycota, Clavicipitaceae) are prevalent in wild grass populations, possibly because of their larger gene variation, resulting in increased fitness benefits for host plants; however, the reasons are not yet known. We tested hypotheses regarding niche expansion mediated by hybrid endophytes, population-dependent interactions and local co-adaptation in the woodland grass Hordelymus europaeus, which naturally hosts both hybrid and non-hybrid endophyte taxa. Seedlings derived from seeds of four grass populations made endophyte free were re-inoculated with hybrid or non-hybrid endophyte strains, or left endophyte free. Plants were grown in the glasshouse with or without drought treatment. Endophyte infection increased plant biomass and tiller production by 10-15% in both treatments. Endophyte types had similar effects on growth, but opposite effects on reproduction: non-hybrid endophytes increased seed production, whereas hybrid endophytes reduced or prevented it completely. The results are consistent with the observation that non-hybrid endophytes in H. europaeus prevail at dry sites, but cannot explain the prevalence of hybrid endophytes. Thus, our results do not support the hypothesis of niche expansion of hybrid-infected plants. Moreover, plants inoculated with native relative to foreign endophytes yielded higher infections, but both showed similar growth and survival, suggesting weak co-adaptation.
Collapse
Affiliation(s)
- Martina Oberhofer
- Plant Ecological Genetics, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, CH-8092, Zürich, Switzerland
- Department of Biology, University of North Carolina Greensboro, 321 McIver Street, Greensboro, NC, 27412, USA
| | - Sabine Güsewell
- Plant Ecology, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, CH-8092, Zürich, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, CH-8092, Zürich, Switzerland
| |
Collapse
|
38
|
Ekanayake PN, Rabinovich M, Guthridge KM, Spangenberg GC, Forster JW, Sawbridge TI. Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement. BMC Evol Biol 2013; 13:270. [PMID: 24330497 PMCID: PMC4028799 DOI: 10.1186/1471-2148-13-270] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/06/2013] [Indexed: 04/09/2023] Open
Abstract
Background Tall fescue and meadow fescue are important as temperate pasture grasses, forming mutualistic associations with asexual Neotyphodium endophytes. The most frequently identified endophyte of Continental allohexaploid tall fescue is Neotyphodium coenophialum, while representatives of two other taxa (FaTG-2 and FaTG-3) have been described as colonising decaploid and Mediterranean hexaploid tall fescue, respectively. In addition, a recent study identified two other putatively novel endophyte taxa from Mediterranean hexaploid and decaploid tall fescue accessions, which were designated as uncharacterised Neotyphodium species (UNS) and FaTG-3-like respectively. In contrast, diploid meadow fescue mainly forms associations with the endophyte taxon Neotyphodium uncinatum, although a second endophyte taxon, termed N. siegelii, has also been described. Results Multiple copies of the translation elongation factor 1-a (tefA) and β-tubulin (tub2) ‘house-keeping’ genes, as well as the endophyte-specific perA gene, were identified for each fescue-derived endophyte taxon from whole genome sequence data. The assembled gene sequences were used to reconstruct evolutionary relationships between the heteroploid fescue-derived endophytes and putative ancestral sub-genomes derived from known sexual Epichloë species. In addition to the nuclear genome-derived genes, the complete mitochondrial genome (mt genome) sequence was obtained for each of the sequenced endophyte, and phylogenetic relationships between the mt genome protein coding gene complements were also reconstructed. Conclusions Complex and highly reticulated evolutionary relationships between Epichloë-Neotyphodium endophytes have been predicted on the basis of multiple nuclear genes and entire mitochondrial protein-coding gene complements, derived from independent assembly of whole genome sequence reads. The results are consistent with previous studies while also providing novel phylogenetic insights, particularly through inclusion of data from the endophyte lineage-specific gene, as well as affording evidence for the origin of cytoplasmic genomes. In particular, the results obtained from the present study imply the possible occurrence of at least two distinct E. typhina progenitors for heteropoid taxa, as well the ancestral contribution of an endophyte species distinct from (although related to) contemporary E. baconii to the extant hybrid species. Furthermore, the present study confirmed the distinct taxonomic status of the newly identified fescue endophyte taxa, FaTG-3-like and UNS, which are consequently proposed to be renamed FaTG4 and FaTG5, respectively.
Collapse
Affiliation(s)
| | | | | | | | - John W Forster
- Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3086, Australia.
| | | |
Collapse
|
39
|
|
40
|
Rasmussen S, Liu Q, Parsons AJ, Xue H, Sinclair B, Newman JA. Grass-endophyte interactions: a note on the role of monosaccharide transport in the Neotyphodium lolii-Lolium perenne symbiosis. THE NEW PHYTOLOGIST 2012; 196:7-12. [PMID: 22803786 DOI: 10.1111/j.1469-8137.2012.04250.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Susanne Rasmussen
- AgResearch, Grasslands Research Centre, PB 11008, Palmerston North, New Zealand
- (Author for correspondence: tel +64 6 351 8182; email )
| | - Qianhe Liu
- AgResearch, Grasslands Research Centre, PB 11008, Palmerston North, New Zealand
| | - Anthony J Parsons
- Institute of Natural Resources, Massey University, Palmerston North, New Zealand
| | - Hong Xue
- AgResearch, Grasslands Research Centre, PB 11008, Palmerston North, New Zealand
| | - Bruce Sinclair
- AgResearch, Grasslands Research Centre, PB 11008, Palmerston North, New Zealand
| | - Jonathan A Newman
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| |
Collapse
|
41
|
Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent. Fungal Genet Biol 2012; 49:882-95. [PMID: 22922546 DOI: 10.1016/j.fgb.2012.08.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/25/2012] [Accepted: 08/01/2012] [Indexed: 11/22/2022]
Abstract
The origin of the fungal wheat pathogen Phaeosphaeria nodorum remains unclear despite earlier intensive global population genetic and phylogeographical studies. We sequenced 1683 bp distributed across three loci in 355 globally distributed Phaeosphaeria isolates, including 74 collected in Iran near the center of origin of wheat. We identified nine phylogenetically distinct clades, including two previously unknown species tentatively named P1 and P2 collected in Iran. Coalescent analysis indicates that P1 and P2 are sister species of P. nodorum and the other Phaeosphaeria species identified in our analysis. Two species, P. nodorum and P. avenaria f. sp. tritici 1 (Pat1), comprised ~85% of the sampled isolates, making them the dominant wheat-infecting pathogens within the species complex. We designed a PCR-RFLP assay to distinguish P. nodorum from Pat1. Approximately 4% of P. nodorum and Pat1 isolates showed evidence of hybridization. Measures of private allelic richness at SSR and sequence loci suggest that the center of origin of P. nodorum coincides with its host in the Fertile Crescent. We hypothesize that the origin of this species complex is also in the Fertile Crescent, with four species out of nine found exclusively in the Iranian collections.
Collapse
|
42
|
di Menna ME, Finch SC, Popay AJ, Smith BL. A review of the Neotyphodium lolii / Lolium perenne symbiosis and its associated effects on animal and plant health, with particular emphasis on ryegrass staggers. N Z Vet J 2012; 60:315-28. [PMID: 22913513 DOI: 10.1080/00480169.2012.697429] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Ryegrass staggers is a seasonal mycotoxicosis of grazing livestock characterised by tremors, in coordination and a staggering gait almost unaccompanied by physical lesions. Deaths occur only as a consequence of accident or starvation. Outbreaks, in summer and autumn, occur only on pasture in which endophyte (Neotyphodium lolii)-infected perennial ryegrass (Lolium perenne) predominates and usually on which animals are grazed intensively. Animals recover when moved to a different type of grazing or after rain has promoted pasture growth. The disease was recognised for 80 years before its cause was discovered as a consequence of a grazing trial of sheep on three ryegrass cultivars which happened to have three different levels of endophyte infection. The endophyte was first formally described as Acremonium loliae, later corrected to Acremonium lolii, and was finally placed in the genus Neotyphodium. It produces a number of secondary metabolites of which lolitrem B is the principal one causing ryegrass staggers symptoms. Ergopeptides are also produced which cause heat stress and lack of productivity. N. lolii is symptomless in the plant, seed borne and grows intercellularly in the aerial parts, mainly in reproductive tillers and leaf sheaths but sparsely in leaf blades. It dies in stored seed and infection rates of different ryegrass cultivars have depended on seed storage times during their production. In addition, N. Lolii produces insect feeding deterrents, among them peramine, which protects infected plants from pest predation. Because of this, control of ryegrass staggers by elimination of endophyte-infected ryegrass is not feasible in areas in which insect predation is a serious pasture problem. However, N. lolii strains vary in the secondary metabolites they produce allowing the selection of strains that produce desirable metabolites. By inoculating such strains into uninfected ryegrass plants it is possible to produce cultivars which do not cause ryegrass staggers but resist insect predation. This review aims to provide a comprehensive summary of the current understanding of the N. lolii / L. perenne symbiosis, the toxins it is known to produce, their effects on animals and plants and the strategies used to control their ill effects while maximising their beneficial ones.
Collapse
Affiliation(s)
- M E di Menna
- AgResearch Limited, Ruakura Research Centre, Private Bag 3123, Hamilton, 3240, New Zealand.
| | | | | | | |
Collapse
|
43
|
Saari S, Faeth SH. Hybridization of Neotyphodium endophytes enhances competitive ability of the host grass. THE NEW PHYTOLOGIST 2012; 195:231-236. [PMID: 22489964 DOI: 10.1111/j.1469-8137.2012.04140.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Associations with microbial symbionts may lead to niche differentiation of their host. Vertically transmitted Neotyphodium endophytes of grasses often hybridize in nature. Infection by these hybrid symbionts may result in different host-plant phenotypes from those caused as a result of infection by nonhybrid symbionts. Observations of wild Arizona fescue (Festuca arizonica) populations show that hybrid Neotyphodium-infected (H+) grasses dominate in resource-poor environments, whereas nonhybrid endophyte-infected (NH+) grasses dominate in environments with more resources. We studied the hypothesis that hybridization of endophytes increases stress tolerance of the host. • To test whether hybridization of Neotyphodium affects performance and competitive abilities of the host depending on resources, we conducted a glasshouse experiment where competition, nutrients and watering were manipulated. • H+ plants had greater wet biomass than NH+ and endophyte-free plants, when grown in competition, but only in low-water and low-nutrient treatments. By contrast, NH+ plants did not perform better than H+ or endophyte-free plants regardless of the treatment combination. • Our results suggest that hybridization of symbiotic Neotyphodium endophytes may increase competitive potential of the host in stressful environments and that this hybridization may be underlying niche expansion of Arizona fescue in the environments with low resources.
Collapse
Affiliation(s)
- S Saari
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402, USA.
| | | |
Collapse
|
44
|
Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc Natl Acad Sci U S A 2012; 109:10954-9. [PMID: 22711811 DOI: 10.1073/pnas.1201403109] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a genome alignment of five individuals of the ascomycete fungus Zymoseptoria pseudotritici, a close relative of the wheat pathogen Z. tritici (synonym Mycosphaerella graminicola), we observed peculiar diversity patterns. Long regions up to 100 kb without variation alternate with similarly long regions of high variability. The variable segments in the genome alignment are organized into two main haplotype groups that have diverged ∼3% from each other. The genome patterns in Z. pseudotritici are consistent with a hybrid speciation event resulting from a cross between two divergent haploid individuals. The resulting hybrids formed the new species without backcrossing to the parents. We observe no variation in 54% of the genome in the five individuals and estimate a complete loss of variation for at least 30% of the genome in the entire species. A strong population bottleneck following the hybridization event caused this loss of variation. Variable segments in the Z. pseudotritici genome exhibit the two haplotypes contributed by the parental individuals. From our previously estimated recombination map of Z. tritici and the size distribution of variable chromosome blocks untouched by recombination we estimate that the hybridization occurred ∼380 sexual generations ago. We show that the amount of lost variation is explained by genetic drift during the bottleneck and by natural selection, as evidenced by the correlation of presence/absence of variation with gene density and recombination rate. The successful spread of this unique reproductively isolated pathogen highlights the strong potential of hybridization in the emergence of pathogen species with sexual reproduction.
Collapse
|
45
|
|
46
|
Taxonomic placement of Epichloë poae sp. nov. and horizontal dissemination to seedlings via conidia. FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0170-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
47
|
OBERHOFER MARTINA, LEUCHTMANN ADRIAN. Genetic diversity in epichloid endophytes ofHordelymus europaeussuggests repeated host jumps and interspecific hybridizations. Mol Ecol 2012; 21:2713-26. [DOI: 10.1111/j.1365-294x.2012.05459.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Scott B, Becker Y, Becker M, Cartwright G. Morphogenesis, Growth, and Development of the Grass Symbiont Epichlöe festucae. TOPICS IN CURRENT GENETICS 2012. [DOI: 10.1007/978-3-642-22916-9_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
49
|
Conspicuous epiphytic growth of an interspecific hybrid Neotyphodium sp. endophyte on distorted host inflorescences. Fungal Biol 2012; 116:42-8. [DOI: 10.1016/j.funbio.2011.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 09/28/2011] [Accepted: 09/29/2011] [Indexed: 11/22/2022]
|
50
|
van Zijll de Jong E, Guthridge KM, Spangenberg GC, Forster JW. Sequence Analysis of SSR-Flanking Regions Identifies Genome Affinities between Pasture Grass Fungal Endophyte Taxa. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:921312. [PMID: 21350638 PMCID: PMC3042632 DOI: 10.4061/2011/921312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 12/10/2010] [Indexed: 11/20/2022]
Abstract
Fungal species of the Neotyphodium and Epichloë genera are endophytes of pasture grasses showing complex differences of life-cycle and genetic architecture. Simple sequence repeat (SSR) markers have been developed from endophyte-derived expressed sequence tag (EST) collections. Although SSR array size polymorphisms are appropriate for phenetic analysis to distinguish between taxa, the capacity to resolve phylogenetic relationships is limited by both homoplasy and heteroploidy effects. In contrast, nonrepetitive sequence regions that flank SSRs have been effectively implemented in this study to demonstrate a common evolutionary origin of grass fungal endophytes. Consistent patterns of relationships between specific taxa were apparent across multiple target loci, confirming previous studies of genome evolution based on variation of individual genes. Evidence was obtained for the definition of endophyte taxa not only through genomic affinities but also by relative gene content. Results were compatible with the current view that some asexual Neotyphodium species arose following interspecific hybridisation between sexual Epichloë ancestors. Phylogenetic analysis of SSR-flanking regions, in combination with the results of previous studies with other EST-derived SSR markers, further permitted characterisation of Neotyphodium isolates that could not be assigned to known taxa on the basis of morphological characteristics.
Collapse
Affiliation(s)
- Eline van Zijll de Jong
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, VIC 3083, Australia
| | | | | | | |
Collapse
|