Archive for February, 2012

Cellulose Factories

February 25th, 2012

Bringing trees into the fuel line, the special New Phytologist issue on ‘Bioenergy trees’ is now available:

A flippable PDF that collates the featured papers together is also available for download at

Thanks to those of you who contributed.

Photo: Cross-sections of Arabidopsis stems, showing vascular bundles from Li et al. (2012).

The Monarch Butterfly Genome

February 21st, 2012

I know … this paper is not describing the genome of a plant or a fungus, but it is unraveling the 273 Mb genome of the superbe monarch butterfly — a migratory Lepideptora traveling long distance to reach its overwintering grounds in central America. Anyway, Danaus plexippus is interacting with plants and is thus welcome to fly over this blog.

The authors summarized their work as follows:

[We present the draft 273 Mb genome of the migratory monarch butterfly (Danaus plexippus) and a set of 16,866 protein-coding genes. Orthology properties suggest that the Lepidoptera are the fastest evolving insect order yet examined. Compared to the silkmoth Bombyx mori, the monarch genome shares prominent similarity in orthology content, microsynteny,and protein family sizes. The monarch genome reveals a vertebrate-like opsin whose existence in insects is widespread; a full repertoire of molecular components for the monarch circadian clockwork; all members of the juvenile hormone biosynthetic pathway whose regulation shows unexpected sexual dimorphism; additional molecular signatures of oriented flight behavior; microRNAs that are differentially expressed between summer and migratory butterflies; monarch-specific expansions of chemoreceptors potentially important for long-distance migration; and a variant of the sodium/potassium pump that underlies a valuable chemical defense mechanism. The monarch genome enhances our ability to better understand the genetic and molecular basis of long-distance migration.]

Read: Shuai Zhan, Christine Merlin, Jeffrey L. Boore and Steven M. Reppert (2011) The Monarch Butterfly Genome Yields Insights into Long-Distance Migration. Cell 147, 5, 1171-1185.

Figure. Life cycle of the monarch butterfly. Complete metamorphosis from egg to larva (five instars) to pupa (chrysalis) to adult. The male butterfly (upper right) has visible black spots on its hind wings that are missing in females (lower left, underwing view). The larvae feed on milkweed (plants of the genus Asclepias). Photograph of engraving from James Edward Smith, Natural History of the Rarer Lepidopterous Insects of Georgia; from the Observations of John Abbot, 1797.

See also: Monarch Butterfly Genome Begins to Open the Black Box



MOMY in Woods Hole

February 17th, 2012

Dear Mycology Investigator,

The Molecular Mycology summer course at the Marine Biological Laboratories in Woods Hole provides an opportunity for researchers to learn new concepts and techniques relating to the study fungal pathogenesis and the discovery of novel antifungal strategies. Many course graduates are now leading medical mycology research efforts around the world. We depend upon the members of the medical mycology community to encourage outstanding applicants. We hope that you can identify at least one prospective course participant who would benefit from the experience and encourage them to apply.

This dynamic course provides state-of-the-art training in molecular methods and assays for studying fungal pathogens and fungi-host interactions. In addition, it provides opportunities to interact with colleagues from academia and industry with different areas of expertise relevant to the study of fungal diseases. The upcoming Molecular Mycology course promises to be exceptional. See the course website to see the list of interactive visiting and resident faculty who will make up the course curriculum.

Laboratory exercises, demos, lectures, and informal panel discussions make up the curriculum. Laboratory exercises focus on Candida, Aspergillus, and Cryptococcus, and include genetic manipulation, discussion of new genetic tools, genetic screening strategies, cell culture and animal models, host response assays, antifungal susceptibility assays and live cell imaging of fungi. Additional topics include current research problems and strategies in medical mycology and topics relating to careers in fungal pathogenesis. Among the topics to be addressed in lectures include new animal models, immunology and fungal diseases, and fungi within microbial communities.

The course is an intensive, two-week research training program, and its content is designed for advanced graduate students, post-docs, fellows, early independent investigators or PIs new to the field. The course runs from August 1-17, 2012.

**Students accepted to the course often receive GENEROUS scholarships towards tuition and travel. **

The course website and on-line application can be found at:

The application deadline is April 11, 2012.


Deb Hogan and Andy Alspaugh

MBL Molecular Mycology Course co-Directors

Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems

February 15th, 2012



Forests provide a wide range of services: wood products and biomass for bioenergy, as well as many ecosystem services, such as carbon sequestration, water and air quality, biodiversity preservation and amenities. The European forest area has been expanding over the last century and standing tree volume is increasing, but several models showed that the trend towards increased productivity might reverse after 2050. Today, forests face unprecedented changes, largely resulting from human activity. Forests will experience rapid changes in the near future, and characterising the ecological and evolutionary dynamics of their response to global change is an ongoing challenge. European forests are usually managed to provide multiple services, and are facing increasingly pressing demands from society to supply more products of higher quality to fuel and feed the ‘green’ economy of tomorrow, and to provide additional social and environmental services to satisfy populations. These sometimes conflicting injunctions are taking place within a context of weak timber markets, scarce public resources, and against a backdrop of unprecedented anthropogenic changes that question the very long-term sustainability of many forest ecosystems.


The Lab of Excellence (LABEX) for Advanced Research on the Biology of FoRest Ecosystems (ARBRE) was granted yesterday with € 7.5 million by the ‘Investissement d’Avenir‘ programme. The LABEX ARBRE  is a consortium of labs from INRA, Université de Lorraine, and AgroParisTech to address issues challenging forests through an interdisciplinary approach. ARBRE covers a broad spectrum of expertise, and has the potential to create a unique scientific consortium for experimental tree biology, functional ecology, wood sciences, economics, and for transferring knowledge to partners in forest management, wood transformation and other activities. One of the main strengths is the presence within ARBRE of research and training capacities that cover the whole forest-wood chain from production to transformation and economic valuation, which is a unique feature across Europe. Moreover, the contributions from the Office National des Forêts (ONF), Centre National de la Propriété Forestière (CNPF) and EFICENT-Observatory of European Forests (EFICENT-OEF) will facilitate knowledge transfer and help the emergence of novel research questions. ARBRE will support ~ 100 scientists.

The main research objectives of ARBRE are to further the understanding of biological, ecological and evolutionary processes that affect interactions between organisms in temperate forest ecosystems, and to develop new approaches to address key questions related to nutrient cycling, carbon storage and cycling, forest productivity, wood products, ecosystem services and sustainable forest management. We will implement a wide range of disciplines – from genomics to functional ecology and economics – to understand, monitor and predict community structures, dynamics and processes in forest ecosystems. ARBRE will also address significant questions in forest ecology and evolution through synthesis of existing data or development of novel theory, design novel wood products and make policy recommendations based on scientific data.


Relative to existing international research efforts in this field, ARBRE’s unique added value is its integrated approach aiming to: (i) develop a comprehensive molecular-level understanding of the forest soil microbiome, tree-microbe interactions, and tree development and functioning, to be achieved through the application of ‘-omics’ approaches and system biology; (ii) generate functional and mechanistic insights into the complex interactions between biogeochemical cycles, carbon sequestration and biodiversity in forests, including interspecific and intraspecific genetic variability. This will be achieved by using long-term observatories (LTO), dedicated field experiments including isotopes tracing and large database analysis; (iii) integrate biochemistry- and biophysics-based knowledge to understand wood formation and to produce timber with properties tailored for ‘green’ end-products; (iv) contribute to the broader development of social, economic, and regulatory policies related to forest sciences and innovation in France, focusing on biodiversity; (v) train highly qualified personnel for careers in France’s R&D-driven industries and institutions; (vi) disseminate scientific innovation rapidly to end users represented in the consortium [like Office National des Forêts (ONF), CNPF and others].

ARBRE will couple bottom-up (from the understanding of processes to forest functions) and top down approaches (from the production of goods and services back to processes) within a series of interconnected task forces or  workpackages (WPs). WP1 will integrate genomics know-how and toolkits to identify major genetic factors controlling soil microbiomes, root-microbe interactions, tree root development and functioning, focusing on stress responses. WP2 will investigate the processes taking place at the interfaces (soil/microbe/tree and tree/atmosphere) in disturbed forest ecosystems and will forecast the state and future evolution of temperate forests. WP3 will link wood properties of the forest resource to the ‘green’ end-products that can be tailored from wood fibers and their chemical components. WP4 will develop biodiversity indicators and a new set of economic instruments (such as payment instruments) for motivating forest managers based on those indicators.

ARBRE will also stimulate the development of educational programmes in tree and microbial biology, forest ecology and management, wood sciences and economic sciences. ARBRE will contribute to the development of a unique and coordinated training facility for engineering and research covering all fields relevant to the forest based sector, contributing to the development and recognition of Lorraine as one of the leading European Center for education in forest and wood sciences. ARBRE will open new positions for postdoctoral fellows and Ph.D. students in the coming months.




JGI Fungal Jamboree 2012

February 15th, 2012

Genome-wide analysis of poplar rust secreted proteins

February 8th, 2012

The obligate biotrophic rust fungus Melampsora larici-populina is the most devastating and widespread pathogen of poplars. Studies over recent years have identified various small secreted proteins (SSP) from plant biotrophic filamentous pathogens and have highlighted their role as effectors in host–pathogen interactions. The recent analysis of the M. larici-populina genome sequence (published in PNAS) has revealed the presence of >1,100 SSP-encoding genes in this rust fungus. In our MPMI paper, the expression and evolutionary dynamics of these SSP were investigated to characterize the arsenal of putative effectors that could be involved in the interaction between the rust fungus and its poplar host. Similarity with effectors previously described in Melampsora spp., richness in cysteines, and organization in large families are discussed. Positive selection analyses conducted over clusters of paralogous genes revealed fast-evolving candidate effectors. Transcript profiling of selected M. larici populina SSP showed a timely coordinated expression during leaf infection, and the accumulation of four candidate effectors in distinct rust infection structures was demonstrated by immunolocalization. This integrated and multifaceted approach will help in prioritizing candidate effector genes for functional studies.

Saunders et al. have recently published their analysis of M. larici-populina SSPs in PLoS One: Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi.

Photo: Melampsora larici-populina spores on poplar leaf (© INRA – B Petre). See also the MPMI cover page.


Biocomplexity of Plant-Fungal Interactions

February 7th, 2012

The book ‘Biocomplexity of Plant-Fungal Interactions‘ edited by Darlene Southworth (Southern Oregon University) has been published. The target audience is botanists who may not have considered the roles that close contacts with fungi play in the life of plants—at the level of the individual or the community. The chapters promote ideas that tell the reader the nature of the interactions and their significance. It includes chapters on endophytes, arbuscular and ectomycorrhizal symbioses, leaf-interacting fungi, ‘sex, diseases and deception’ and soil fungal networks. It looks great (I could be biased as Jonathan and I wrote a chapter on molecular interactions in mycorrhizal development).

You can buy the book on

Release of a draft genome sequence for Nicotiana benthamiana

February 7th, 2012

Nicotiana benthamiana is is a close relative of tobacco and species of Nicotiana indigenous to Australia. This herbaceous plant is a widely used model for investigating plant-microbe interactions and other research applications. It is particularly useful because it is related to tomato and potato and is amenable to virus-induced gene silencing (VIGS) which facilitates the efficient functional study of plant genes.

A. Collmer, G. Martin and P. Moffett’s groups at the Boyce Thompson Institute for Plant Research have released a draft sequence of the N. benthamiana genome which is accessible through the Sol Genomics Network BLAST tool and can be downloaded by ftp (see:

See BTI site for more details.

Photo: Nicotiana benthamiana © BTI

EMBO Plant-Microbe Interactions

February 6th, 2012

Register now

A New Phytologist feature dedicated to Bioenergy Trees

February 4th, 2012

The New Phytologist feature dedicated to Bioenergy Trees (an outcome of the 26th New Phytologist Symposium) is provisionally scheduled for vol 194, issue 1, which will be published online at the beginning of February. The cover page below will highlight the feature. The Symposium was great and the series of review and research papers are exciting.

L’Homme qui Peint des Arbres

February 4th, 2012

David Hockney, (July 9, 1937) is an English painter and famous pop-artist. I like his vivid paintings inspired by the East Yorkshire landscape with woodlands, forests and trees.

“… stand in the landscape you love, try and depict your feelings of space, and forget photographic vision, which is distancing us too much from the physical world.” (D Hockney, February 2007)

Visit his web site.

© David Hockney.