Archive for August, 2009

Unexpected high fungal diversity in forest soils

August 28th, 2009

hetraieSoil fungi play a major role in ecological and biogeochemical processes in forest ecosystems. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). Within the framework of our metagenomics project aimed to assess the microbial diversity in temperate forests, we surveyed the fungal diversity in six different forest soils at the Breuil-Chenue long-term observatory using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). The paper reporting this study is now online on the New Phytologist Early View pages.

No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units (MOTU). Most MOTUs (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant MOTUs showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp.

This study, together with two other surveys exploring the diversity of fungal communities in  Quercus macrocarpa phyllosphere (Jumpponen & Jones, 2009) and the diversity of arbuscular mycorrhiza fungi in a boreonemoral forest (Öpik et al., 2009), validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will likely accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

Buée et al. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, doi: 10.1111/j.1469-8137.2009.03003.x

Jumpponen & Jones (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, doi: 10.1111/j.1469-8137.2009.02990.x

Öpik et al. (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist, doi: 10.1111/j.1469-8137.2009.02920.x

August 28th, 2009

hongosThe Xth International Fungal Biology Conference will be held in Ensenada, Baja California, Mexico on December 6 – 10, 2009. The International Fungal Biology Conferences are a prestigious series of conferences held at 3-4 year intervals at different locations around the world.

Several talks and symposia will be dedicated to genomics and postgenomics of fungi.

Please visit the website for details on the scientific programme, registration, hotel accommodations, transportation etc.

Unwrapping the genome of a protein µfactory

August 25th, 2009

PicpaThe methylotrophic yeast Pichia pastoris has become a highly successful system for the expression of heterologous genes. It is widely used for the production of recombinant proteins. Several factors have contributed to its rapid acceptance, the most important of which include (1) A promoter derived from the alcohol oxidase I (AOX1) gene of P. pastoris that is uniquely suited for the controlled expression of foreign genes, (2) The strong preference of P. pastoris for respiratory growth, a physiological feature that greatly facilitates its culturing at high cell densities relative to fermentative yeasts and (3) strains capable of human-type N-glycosylation are available increasing the utility of this ‘humanized’ yeast for biopharmaceutical production. In addition, P. pastoris is a widely used model organism for studying peroxisomal biogenesis and methanol assimilation.

In the June issue of Nature Biotechnology, Nico Callewaert’s group (from Ghent VIB) published the genome sequence of P. pastoris. To my knowledge, this  is the first fungal genome published that has been assembled exclusively from ‘454 GS-FLX’ reads. Using this approach, they highly oversampled the genome (897,000, 20 times coverage) and generated 70,500 paired-end sequence tags, to enable the assembly of all but seven contigs into nine ‘supercontigs’ (plus the mitochondrial genome). The genome is organized in four chromosomes with a total estimated size of 9.4 Mbp and 5,313 protein-coding genes. To facilitate the ‘customization’ of novel strains for protein production, in-depth gene curations of genes involved in protein secretion, protein glycosylation and protein degradation were performed. The wealth of information generated by these genome sequence and annotation will likely facilitate the design of highly productive biopharmaceutical strains.

De Schutter, K., Lin, Y.-C., Tiels, P., Van Hecke, A., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, L. (2009) Genome sequence of the recombinant protein production host Pichia pastoris, a methylotrophic yeast. Nature Biotechnology 27, 561 – 566.

August 24th, 2009

22nps_logo

The 22nd New Phytologist Symposium entitled ‘Effectors in plant–microbe interactions’ will be held at INRA Versailles Research Centre, Paris, France from 13 to 16 September 2009. For full details about the meeting, see The New Phytologist web site.

“Effectors are defined as molecules produced by bio-aggressors/pathogens/symbionts to manipulate their host plants, thereby facilitating infection (virulence or symbiotic factors, toxins, inhibitors) and/or triggering defense responses (avirulence factors, elicitors). This dual (and conflicting) activity of effectors has been broadly reported in many plant–microbial interactions. This research topic is actively investigated using a combination of approaches and benefits from the recent advances in plant and microbial functional genomics and genome-wide evolutionary analyses. The 22nd New Phytologist Symposium aims to bring together scientists working on plant–microbe interactions across a range of organisms (viruses, bacteria, fungi and nematodes) to identify and focus on these important questions.” from H. Slater.

Integrated Microbial Genomes

August 19th, 2009

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The Integrated Microbial Genomes (IMG) 2.9 has just been released: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

The Integrated Microbial Genomes (IMG) system ( Nucleic Acids Research, 2008, Vol. 36, Database issue ) is a data management, analysis and annotation platform for publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. As today, it contains 1535 bacterial genomes, but only 25 fungal genomes, including 4 basidiomycota.

IMG can be used for finding a genome or a gene, find functions and compare genomes. See the online tutorial at: http://img.jgi.doe.gov/w/doc/about_index.html

Community annotation: the right way to do it?

August 16th, 2009

modelsOne of the challenges of genome sequencing project is large-scale gene annotation. Community annotation is a collaborative effort to engage experts in the biology of a given species to improve the quality of the automated (algorithmic) genome annotation. The release of the Populus trichocarpa, Laccaria bicolor and Tuber melanosporum genome sequences and their automated annotation represent the critical first steps in harnessing the power of genomics research for our mycorrhiza community. The next challenges are to refine the genome annotation and to actively capture, improve, and associate with the genome the wealth of information that exists within the research community for functional and comparative analyses. The primary goals of the Laccaria and Tuber genome Consortia are:

  • To verify and improve the accuracy and consistency of the genome annotation
  • To refine current gene models and capture information about alternative splicing and untranslated regions
  • To integrate information from these fungi  biology with the genome sequences
  • To provide searchable databases with expert curation that can support functional analyses

It does work! Up to 60  users came in to annotate their favorite genes and we  eventually ended up with a comprehensive collection of annotations for about 15% of these sequenced genomes; most of the curated genes belonging to primary metabolism or core cellular activities.

Nikos Kirpides in its Nature Biotechnology paper (see below) is challenging this community assistance:

Why would anyone expect—or even worse, depend on—a community annotation effort? Imagine investing millions of dollars into state-of-the-art sequencing facilities, and then expecting volunteers from the community to stop by and run the sequencing machines. One might argue that this analogy is not valid because running a sequencing facility requires well-trained personnel, standardized protocols, clear procedures, quality controls and, most of all, tight coordination. Yet, the same professional standards are required for data curation, and it is precisely these aspects that are rarely achieved through a community contribution approach. Community annotation should be encouraged and facilitated, but the curation of biological data cannot depend solely on volunteer work. High standards and quality implies professionalism, and this, in turn, requires investing in dedicated professionals. Until this is done, data curation—and consequently the whole field of microbial genomics—will not move beyond the amateur stage.

The failure of several community based annotations has brought the often overlooked but crucial activity of genome curators into the limelight. In the current scientific culture, evaluation committees hardly recognized this community annotation activity. For true community involvement, this would need to change. At the same time, biocuration needs to be recognized as a valid and important scientific duty.

Plant-fungi jumping genes: both exceedingly rare and ancient

August 16th, 2009

Genetic information can sometimes be transferred between species, a process called horizontal gene transfer (HGT). While horizontal genetic transfer occurs most commonly in bacteria, it has been detected in animals as well. It is believed that most such transfer has occurred either via the engulfment of one organism by another, which generally is restricted to single-celled species, or during the course of host-parasite interactions.  The land plants and fungi are very distant relatives, but they  share several ecological associations, including mycorrhizal interactions, raising the possibility that plant-fungi HGT may be a hitherto unexplored factor in their collective evolutionary history.

As reported in a Plant Cell paper online, Richards et al. have identified suspected HGT events by comparing the genomes of six plant species, including Populus trichocarpa, with those of 150 prokaryotes, 46 fungal species (including Laccaria bicolor) and five green algae. Through stringent phylogenomic analyses, they found five fungus-to-plant and four plant-to-fungus transfers, including three cases in which transfer had been presaged by a jump from a prokaryote to a eukaryote. On the basis of these results, they suggest that plant-fungi HGTs are both exceedingly rare and ancient. The data reported in this study suggest that gene flow between plants and fungi must be considered to be an extremely unlikely event from commercially cultivated crop species. The authors conclude that “HGT may have provided advantageous gene functions that could have conceivably widened substrate use and habitat spread in both plant and fungal species“. Unfortunately, the HGT between L. bicolor and P. trichocarpa involved a protein with domains of unknown function (DUF239) providing no clues on the putative ecological role of this protein.

Richards TA et al. 5 (2009) Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi. Plant Cell 21, 10.1105/tpc.109.06580.

New fungal genome projects at JGI

August 15th, 2009
Amanita thiersii (© indianamushrooms)

Amanita thiersii (© indianamushrooms)

The Department of Energy’s Joint Genome Institute announced 71 new genomic sequencing projects  for its 2010 Community Sequencing Program. The recent transition to new sequencing technologies has almost quintupled the amount of sequencing allocated to the program; about half that data is expected to be produced on 454’s sequencing platform, and the other half on Illumina Genome Analyzers. The new projects selected for CSP 2010, listed here, comprise 15 eukaryote genomes, six eukaryotes to be resequenced using short-read sequencing technologies, two transcriptome sequencing projects, 20 microbes, 20 metagenomes of microbial communities, and eight bacterial isolates to be resequenced. Projects are chosen based on relevance to bioenergy, global carbon cycling, and biogeochemistry.

In addition to the basidiomycetes Pisolithus tinctorius and Pisolithus microcarpus and the Dekkera (Brettanomyces) bruxellensis genome sequences (see below), the JGI will sequence several additional fungi: homokaryons of the brown-rot Postia placenta, the lignin-degrading fungus Phlebiopsis gigantea, the fusiform rust fungus Cronartium quercuum f.sp. fusiforme, the cellulose degrading basidiomycete Amanita thiersii, the fungal pathogen Cochliobolus sativus and several Dothideomycetes plant pathogens.  The phytopathogenic oomycete Phytophthora cinnamomi will also be sequenced.

Sequencing a winemaker’s nemesis

August 15th, 2009

verre de vinSeen on the JGI News feed: ‘Wineries have tried a number of different chemical mixtures to ward off infection [by contaminating micro-organisms], but none have proven fully effective. JGI and collaborators believes the genome [sequence] will provide answers on how Brettanomyces (Dekkera bruxellensis)) survives the initial battle with Saccharomyces, how it spreads so fast and, ultimately, on how to stop it.’

Brettanomyces, a yeast species, contaminates wine and corrupts the entire fermentation process leading to flavors best described as sweaty horse, manure, and burnt plastic, ruining a wine completely. This genome project will hopefully take the barnyard smell out of your glass of wine.

Microbial genomics: meeting the challenges and fulfilling the dream

August 15th, 2009

Nature BiotechnologyIn the July issue of Nature Biotechnology, Nikos Kirpides from JGI published a challenging paper entitled “Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream” where he discussed the past and future of microbial genomics. More than two-thirds of the 4,800 currently reported genome projects are microbial and the number of genomes and pangenomes will tremendously increase in the years to come. Unfortunately, several underlying problems hinder additional growth of the field and, even more importantly, compromise the ability of biologists to use and interpret the available data. This includes: (i) Genome publication and data release policy violating a longstanding scientific precept, i.e. examine the actual data, (ii) bias in the selection of species for genome projects, (iii) poor funding for the maintenance of biological databases, (iv) the lack of dedicated professionals for gene catalog curation, and (v) the lack of standard in genomics. As strongly recommended by  Nikos Kirpides “a systematic and comprehensive exploration of the planet microbial world  cannot be achieved by the efforts of individual researchers but requires the establishment of effective national and international collaborations.”

Pisolithus genome sequencing on the road

August 10th, 2009

Piso_eucalyptOur proposal ‘Sequencing of the pan-global basidiomycetes Pisolithus tinctorius and Pisolithus microcarpus for increased knowledge of the ectomycorrhizal symbiosis’ to JGI’s Community Sequencing Program 2010 has been approved for WGS sequencing in this cycle. Pisolithus are puffball belonging to the Gasteroid group (Basidiomycota, Agaricomycotina; Agaricomycetes; Agaricomycetidae; Boletales; Sclerodermatineae; Pisolithaceae).

The Eucalyptus genome is near completion at the JGI. As part of the development of a broader community-based Eucalyptus genomics resource, and as a means of conducting informative comparative genomics among fungi, we have proposed the genome sequencing for Pisolithus microcarpus, a prominent eucalypt-specific ectomycorrhizal symbiont worldwide. We have also propose the sequencing of its close relative P. tinctorius forming symbiosis with pine species only and commercially used in U.S.A. for large scale mycorrhizal inoculation of pine plantations.

The objectives of this collaborative project between JGI and INRA is to: 1) build an assembled genome sequence (8X) database, 2) develop 200,000 ESTs and carry out protein shotgun sequencing for supporting the annotation of the two genomes, 3) annotate the P. microcarpus and P. tinctorius genomes, 4) investigate alteration in transcriptome upon ectomycorrhiza formation using custom NimbleGen exon arrays, 5) investigate the genomic polymorphism between eucalypt- and pine-associated Pisolithus using CGH arrays and/or Illumina sequencing, and 5) complete an initial comparative analysis between these Pisolithus and other sequenced fungi, such as Paxillus involutus, Serpula lacrymans and Rhizopogon salebrosus.

The availability of genome sequence from two related fungi that play such a critical role in tree growth and health will increase our understanding of the symbiosis host specificity.  This work will greatly complement efforts to understand and exploit eucalypt trees and will give researchers an unprecedented resource to aid in our understanding of the relationship between this tree and its favorite fungus.

Up to 240,000 ‘454’ ESTs of P. microcarpus (strain 441) has recently been sequenced by the Genoscope and assembled by our team. This resource will soon be available online at the INRA genome portal.

Sign-up now for Microbial Genomics & Metagenomics workshop

August 10th, 2009

The U.S. Department of Energy Joint Genome Institutejgi (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.

For more information, see:

http://www.jgi.doe.gov/meetings/mgm/index.html

Summer DOE JGI Newsletter

August 10th, 2009

jgiThe Summer 2009 edition of the DOE JGI newsletter, The Primer, has arrived.  Features include:

  • The Community Sequencing Program (CSP) 2010 Targets/Allocation
  • Moving Microbial Genomics Forward
  • On Sequencing, Finishing and Analysis in Santa Fe
  • Supporting Life in Great Salt Lake
  • Brown-rot for Biofuels
  • Sequencing with a Single Cell
  • Notes from the 4th Annual JGI User Meeting
  • Improving Crops and Biofuels Feedstocks
  • A Shortcut called ChIP-seq
  • Algae as a Climate Change Sensor

The edition can also be downloaded from: http://www.jgi.doe.gov/News/primer/primer090714.pdf

In the Heart of Truffle Country

August 10th, 2009
Perigord Black Truffle (© C Murat)

Perigord Black Truffle (© C Murat)

There are gnarled vines and patches of woodland, and fortified hill villages. We are in the heart of the White Truffle country in Alba (Piemonte). The smell of fresh produce is hanging in the air. There’s one pervasive scent that’s quite unlike any other – rich, earthy and pungently aromatic: the Tartufo Bianco (White Truffle) aroma.

The next Tuber Genome Workshop will take place on October 12-14, 2009 in Alba during the Truffle Festival. The meeting will begin on Monday at 14:00 am and will end on Wednesday at 12:00 pm. The aim of the workshop is (1) to establish the current status of the Tuber melanosporum genome project and (2) to bring together  collaborators for discussing the post-genomics activities of the consortium. The new Tuber magnatum genome sequencing project will be launched at this meeting.

The format of the workshop will be roughly equally split between informal presentations (summarizing the current findings), what we hope will be spirited discussion and brainstorming about how to take advantage of the Tuber genomic sequences to inform our understanding of symbiosis and fungal biology.

Tremella genome released

August 9th, 2009

Tremella mesentericaKnown as the golden jelly fungus, Tremella mesenterica is commonly found on rotting wood, especially gorse, as a parasite of wood decay fungi. It belongs to the Basidiomycota (Agaricomycotina, Tremellomycetes, Tremellales, Tremellaceae). Its genome has been sequenced and recently released by the JGI. The genome is ~28Mb and the JGI annotation group predicted 8,313 genes. This fungus is among the species studied for getting a better understanding of wood degradation mechanisms and how it differs in jelly fungi from the more distantly related Agaricomycotina, such Pleurotus ostreatus or Coprinopsis cinerea.

Rhizopus oryzae genome published

August 9th, 2009

rhizopusThe genome of the fungus Rhizopus oryzae has been published. R. oryzae is a widely dispersed mold fungus found in soil and decomposing organic material. It can cause fatal infections in people with suppressed immune systems. It belongs to the Mucoraceae in the order Mucorales. As a representative of the paraphyletic basal group of the fungal kingdom called Zygomycetes, R. oryzae is widely used as a model to study fungal evolution. This genome analysis provides the first insights into the genome structure and dynamics of a basal fungal lineage. Whole-genome duplication (WGD) plays an important role in evolution of R. oryzae genome. The post-WGD retention of entire protein complexes and gene family expansions likely enable the mold to rapidly use more complex carbohydrates for energy sources and quickly accommodate major environmental changes in soil or hosts.

The genomic sequence is available at the Broad Institute database: http://www.broadinstitute.org/annotation/genome/rhizopus_oryzae/MultiHome.html.

Ref. Li-Jun Ma et al. (2009) Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication. PLoS Genet 5(7): e1000549.