Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloë festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource. They permit the interrogation of 3806 Neotyphodium genes (NchipTM microarray), and 4195 Neotyphodium and 920 Epichloë genes (EndoChipTM microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass–symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloë was performed

La simbiosis con endófitos del género Neotyphodium y su impacto en la interacción del pasto hospedante con otros hongos

En los pastizales naturales se encuentran muchas especies de gramíneas asociadas a endófitos asexuales del género Neotyphodium. La persistencia de la simbiosis en las comunidades ha sido asociada a los beneficios que el endófito le confiere al hospedante frente a situaciones de herbivoría y estrés abiótico. El objetivo general de esta tesis es evaluar el impacto de la presencia del endófito sobre el desarrollo de otros hongos que forman asociaciones patogénicas con el mismo pasto hospedante y estudiar de qué manera esta triple interacción se relaciona con el resto de la comunidad y el ambiente abiótico. Como sistema de estudio se utilizó a la gramínea anual Lolium multiflorum, su endófito Neotyphodium occultans y hongos con estrategias de vida contrastantes que colonizan distintos tejidos en distintos estadios del hospedante y generan cambios diversos en su demografía y ecología. La hipótesis general de esta tesis es que la presencia de endófitos altera tanto de manera directa como indirecta la interacción entre la planta hospedante y la comunidad de patógenos, y que estos cambios impactan sobre la permanencia de la simbiosis y su interacción con el resto de la comunidad vegetal. A través de un meta-análisis y experimentos manipulativos en laboratorio, invernáculo y a campo demostramos que el mutualismo reduce la infección por diversos hongos patógenos a través de mecanismos tanto fisiológicos como ecológicos, e impacta sobre otras especies de pastos. La conclusión general de esta tesis es que esta triple interacción está lejos de ser simple como fue planteado en sus inicios. Esta interacción es compleja e incluye a otros organismos de la comunidad, tanto como mediadores de la infección o como beneficiarios de los efectos de la simbiosis.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier

The effect of endophyte on the performance of irrigated perennial ryegrasses in subtropical Australia

The effect of fungal endophyte (Neotyphodium lolii) infection on the performance of perennial ryegrass (Lolium perenne) growing under irrigation in a subtropical environment was investigated. Seed of 4 cultivars, infected with standard (common toxic or wild-type) endophyte or the novel endophyte AR1, or free of endophyte (Nil), was sown in pure swards, which were fertilised with 50 kg N/ha.month. Seasonal and total yield, persistence, and rust susceptibility were assessed over 3 years, along with details of the presence of endophyte and alkaloids in plant shoots. Endophyte occurrence in tillers in both the standard and AR1 treatments was above 95% for Bronsyn and Impact throughout and rose to that level in Samson by the end of the second year. Meridian AR1 only reached 93% while, in the standard treatment, the endophyte had mostly died before sowing. Nil Zendophyte treatments carried an average of ?0.6% infection throughout. Infection of the standard endophyte was associated with increased dry matter (DM) yields in all 3 years compared with no endophyte. AR1 also significantly increased yields in the second and third years. Over the full 3 years, standard and AR1 increased yields by 18% and 11%, respectively. Infection with both endophytes was associated with increased yields in all 4 seasons, the effects increasing in intensity over time. There was 27% better persistence in standard infected plants compared with Nil at the end of the first year, increasing to 198% by the end of the experiment, while for AR1 the improvements were 20 and 134%, respectively. The effect of endophyte on crown rust (Puccinia coronata) infection was inconsistent, with endophyte increasing rust damage on one occasion and reducing it on another. Cultivar differences in rust infection were greater than endophyte effects. Plants infected with the AR1 endophyte had no detectable ergovaline or lolitrem B in leaf, pseudostem, or dead tissue. In standard infected plants, ergovaline and lolitrem B were highest in pseudostem and considerably lower in leaf. Dead tissue had very low or no detectable ergovaline but high lolitrem B concentrations. Peramine concentration was high and at similar levels in leaf and pseudostem, but not detectable in dead material. Concentration was similar in both AR1 and standard infected plants. Endophyte presence appeared to have a similar effect in the subtropics as has been demonstrated in temperate areas, in terms of improving yields and persistence and increasing tolerance of plants to stress factors.

La simbiosis entre pastos y hongos endofitos : su impronta aérea y subterránea en distintos contextos agroecológicos

Las plantas integran interacciones con múltiples especies mutualistas y antagonistas. Recientemente, se ha comenzado a considerar a los microorganismos simbiontes y en particular a hongos endofitos como moduladores de otras interacciones y, en consecuencia, de la estructura y el funcionamiento de las comunidades. El objetivo de esta tesis fue evaluar los efectos de la simbiosis entre pastos y hongos endofitos asexuales (Neotyphodium spp., Clavicipitaceae) sobre las comunidades del suelo y las relaciones de retroalimentación planta-suelo. Se postuló que la simbiosis Lolium multiflorum-N. occultans modifica la estructura de las comunidades aéreas a través de cambios en el suelo, y que estos efectos pueden variar con el contexto ecológico. Se realizaron ocho experimentos (en mesocosmos y a campo) en los que se manipuló la proporción de plantas con endofitos bajo distintas condiciones ambientales generadas por el pastoreo o la historia de uso. La presencia de la simbiosis redujo las tasas de descomposición y modificó la estructura de las redes tróficas del suelo, probablemente a través de la actividad radicular de la planta hospedante. La simbiosis generó respuestas de retroalimentación negativa sobre otras especies herbáceas, mejoró la capacidad invasora de L. multiflorum, aumentó la riqueza de especies vegetales y redujo la cobertura de pastos nativos y exóticos. Sin embargo, estos efectos sobre las comunidades aéreas y subterráneas fueron evidentes solo bajo ciertas condiciones dadas por el pastoreo y la historia de uso del suelo. Las interacciones múltiples que establecen las plantas y la historia del ambiente deberían ser consideradas en los modelos que describen los mecanismos que determinan la estructura y el funcionamiento de las comunidades. Esta tesis sostiene que la simbiosis pasto-endofito es más que un mutualismo defensivo ya que modula interacciones múltiples entre componentes aéreos y subterráneos e influye sobre la invasión y el ensamble de las comunidades

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.