Archive for November, 2010

100 Rhizobium Genomes

November 28th, 2010


A joint venture has been established between the Centre for Rhizobium Studies (CRS) led by Dr Wayne Reeve at Murdoch University (Australia) and the Joint Genome Institute (JGI, USA) led by the Head of the Microbial Program Dr Nikos Kyrpides to completely decipher the genetic code for 100 geographically distinct root nodule rhizobial strains.’

Wayne Reeve will coordinate the activities of this GEBA-RNB (Genome Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria) project consisting of an international consortium of 32 scientists from 15 different countries.

The First Snow-Fall

November 28th, 2010

Snowy Oak

The First Snow-Fall

THE snow had begun in the gloaming,

And busily all the night,

Had been heaping field and highway

With a silence deep and white.

Every pine and fir and hemlock

Wore ermine too dear for an earl,

And the poorest twig on the elm-tree

Was ridged inch deep with pearl.

by James Russel Lowell (1819-1891)

Photo: Snowy Oak Tree in Bois de Faulx — from Première Neige. © F Martin

Listening: Zoë Keating (Into the Trees & One Cello x 16: Natoma)

Net Blotch in the ABySS

November 28th, 2010

ntnb_webpicPyrenophora teres f. teres (Dothideomycetes, Pleosporales) is a necrotrophic fungal pathogen and the cause of one of barley’s most important leaf diseases, the net-type of net blotch. Ellwood et al. report in Genome Biology the genome assembly and analysis for this species, the third necrotrophic fungus to be sequenced. The sequencing is based solely on short paired-end Solexa sequencing. The assembly of the 833 Mbp of sequences was carried out using ABySS and then, validated by comparison to BAC sequences and ESTs. This yielded a N50 of 408 scaffolds and an L50 of 26 kbp. The majority of initial contigs (140,326 of 147,010) were 200 bp or less and resulted from repetitive regions. The assembled draft genome was complemented by cytogenetic karyotyping and a genome-wide genetic map.

The total assembly was 41.95 Mbp and contains 11,799 predicted gene models >50 AA. The majority of the predicted genes (93.5%) were conserved within other species. Of notice is the occurrence of expanded gene families of specialised multi-functional enzymes known as non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) that produce secondary metabolites. These enzymes are likely involved in the synthesis of non-host selective low molecular weight compounds that cause chlorosis on barley leaves. As expected, P. teres f. teres contains a large number of genes (1031) coding for secreted proteins.

This genome assembly demonstrates that the short paired-end Solexa reads can be used to effectively capture higher complexity gene containing regions of fungi. This approach however failed in assembling the significant part of the genome coding for repeated sequences.

Ellwood et al. (2010) A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biology 11: R109.

Photo: Net-type of Net Blotch on Barley leaves. © WA Dpt of Agriculture and Food.

Microbiology: The new germ theory

November 25th, 2010

germIn Nature News:

What can microbiologists who study human bowels learn from those who study the bowels of Earth?

“The microbiota are bringing utensils to the dining-room table that the human host doesn’t have.”

More Fungal & Oomycete Genomes

November 25th, 2010

pp894-3The stream of papers on microbial eukaryote genomes remains steady:

Ellwood et al. (2010) A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biology 11: R109.

Lévesque et al. (2010) Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 11: R73

Sellam et al. (2010) Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. Genome Biology 11: R71

… and more to mine at the JGI:

Septoria musiva (sexual stage: Mycosphaerella populorum) causing leaf spots and cankers on poplars (Populus spp. and hybrids).

Dothistroma septosporum (sexual stage: Mycosphaerella pini) is a foliar pathogen of many pine species throughout the world, causing serious economic losses.

Photo: Net blotch (Pyrenophora teres) on barley. ©

Fighting Over Chocolate: Cacao Genome Released

November 22nd, 2010

Cocoa_smallI love chocolate!!! Cocoa powder and chocolate are produced from the beans (seeds) of the cacao tree (Theobroma cacao). I’m thus glad that its genome has now released by two competing international consortia.

A consortium lead by  Mars, the US Department of Agriculture (USDA), IBM and a number of universities, has released the genome of the cultivar Matina 1-6. The sequence is available on the Cacao Genome Database. This Mars’ release of the cacao tree genome comes before that of chocolate competitor Hershey, which had also been working to sequence this genome with the International Cocoa Genome Sequencing Consortium (ICGS), including French CIRAD labs, Genoscope and Pennsylvania State University. A pre-release is available on the Nature Precedings site. The ICGS sequenced the genome of the Belizean Criollo genotype (B97-61/B2).

Cocoa production has been plagued by serious losses due to pests and diseases. The release of the cacao genome sequence will provide scientists with access to the latest genomic tools, enabling more efficient research and accelerating the breeding process. This will likely release the release of improved cacao cultivars. The sequenced genotype, Matina 1-6, is representative of the genetic background most commonly found in the cacao producing countries. While the 420 Mb- sequence provided is a preliminary release, it already covers 92% of the genome (in 1782 supercontigs), with approximately 35,000 genes.

The cocoa tree joins other widely consumed crops, such as wheat, corn and rice, that have already had their genome sequenced.

Photo: Cocoa beans (©

I Want To Know Everything About Effectors

November 21st, 2010

NP effectors

Aphid Effectors

November 21st, 2010

Myzus persicae (10)I liked  ‘A Functional Genomics Approach Identifies Candidate Effectors from the Aphid Species Myzus persicae (Green Peach Aphid)‘ by Jorunn Bos et al.

Author Summary

“Aphids are insects that can induce feeding damage, achieve high population densities, and most importantly, transmit economically important plant diseases worldwide. To develop durable approaches to control aphids, it is critical to understand how aphids interact with plants at the molecular level. Aphid feeding induces plant defenses, which can be suppressed by aphid saliva. Thus, aphids can alter plant cellular processes to promote infestation of plants. Suppression of plant defenses is common in plant pathogens and involves secretion of effector proteins that modulate host cell processes. Evidence suggests that aphids, like plant pathogens, deliver effectors inside their host cells to promote infestation. However, the identity of these effectors and their functions remain elusive. Here, we report a novel approach based on a combination of bioinformatics and functional assays to identify candidate effectors from the aphid species Myzus persicae. Using this approach, we identified three candidate effectors that affect plant defense responses and/or aphid reproductive performance. Further characterization of these candidates promises to reveal new insights into the plant cellular processes targeted by aphids.”

Photo: The Green Peach Aphid (Myzus persicae) ©

Scientists: Publicizing your research gets you cited more often

November 21st, 2010

nytFrom Science of Blogging:

“There is no shortage of benefits for scientists – young and well-tenured – to publicize their research beyond peer-reviewed publications and conference presentations. And yet, few scientists look beyond the pages of their discipline’s journal to showcase their work.

While all researchers should strive to translate their work for mass consumption, the scientist’s day is a long one, and often this task is overshadowed by more pressing issues of academia; grants, lectures, publications, conferences, student’s dissertations, etc.

Part of the problem is that many researchers fail to recognize the more tangible benefits of exposing their research to a greater audience.

Take for example the findings of a 2003 study by Vincent Kiernan in the Chronicle of Higher Education which clearly shows a strong relationship between the media exposure of a given study and the resulting rate of citation of that work in the scientific literature in the ensuing years.

First, the author of the study found that studies that were covered by at least one media outlet were cited an average of 116 times in the following 4 years compared to 90 citations for those studies that failed to make any media splash (p < 0.001).” Read more

Pig Truffle Hunting

November 21st, 2010

melano_cross-sectionA few months ago, Claude Murat and I have given an interview to a crew from Reuters TV on the genome of the Perigord Truffle. A sample of this broadcast is now on You Tube, ‘Genetic code for truffles cracked‘ As expected, my comments on the truffle genome and DNA fingerprinting are framed by the usual  ‘folksy’ stuffs: pig truffle hunting and ‘omelette aux truffes’. I had had a hearty laugh when I saw those truffle hunters with their pig — they are a cliché from the 50’s — so ‘typical’ of the french peasants seen in the worst B-movies. Be sure that we do not pet pigs in the lab backyard for hunting truffles needed for our population genomics studies.

Reuters TV video:

Photo: Tuber melanosporum cross-section. © F Le Tacon

Prepare for the long Winter ahead …

November 11th, 2010


Champenoux State Forest, Bois Saint-Jean. Photo © F Martin

Fungal Forest Soil Communities Surveyed by COX1

November 11th, 2010

beech woodThe diversity of soil fungal species is mainly assessed by sequencing nuclear ribosomal gene regions (e.g. 454 seq’ing of rDNA ITS) amplified from soil-extracted DNA.

In their study of the soil fungal communities from the Breuil-Chenue State Forest in the Morvan range, France, Roland Marmeisse’s group showed that segments of the fungal cytochrome oxidase COX1 gene can be efficiently amplified from reverse-transcribed environmental RNA. The newly designed PCR primers amplified sequences from the most abundant soil fungal taxonomic groups, namely the Agaricomycetidae and the Pezizomycotina. The authors suggest that the analysis of COX1 sequences amplified from soil RNA and the analysis of ITS from environmental DNA surveyed different parts of the fungal community. COX1 cDNAs likely reflect the fraction of the community that is metabolically active at the time of sampling, whereas the rDNA ITS sequences may include resting fungal material, such as spores or dormant mycelial fragments.

The comparison of these metabolically-active fungal communities with those identified on the same forest sites by our massive 454 seq’ing of the rDNA ITS should be insightful.

Damon et al. (2010) Performance of the COX1 gene as a marker for the study of metabolically active Pezizomycotina and Agaricomycetes fungal communities from the analysis of soil RNA. FEMS Microbiology Ecology 74, published online: 26 OCT 2010

Photo: Beech woods © F Martin


November 7th, 2010


A new resource for metagenomics has recently been released, MeganDB. This web-based database of metagenomic data has been designed for the very popular and user’s friendly metagenome analysis tool MEGAN. All public metagenomes are pre-processed on their servers, so MEGAN can easily read them out. Analysis of your own data and especially the comparison of public datasets against your own samples is possible with MEGAN. As of today, 235 metagenomes have been uploaded and pre-processed in MeganDB. This server will provide you with recently created RMA files for MEGAN or the MEGAN webstart version, but also a series of tools that may help you to mine your datasets. If you need for instance a RMA file created from your own metagenomic sample, but you do not have enough CPU power or time to BLAST the sequences on your machine, then you can use MeganDB. A very useful service to the community.

MeganDB is software consisting of a set of different modules, developed at the participating universities by several authors:

  • Simon Domke, Department of Genome Oriented Bioinformatics, Technische Universität München  (metagenome export tools, MeganDB web portal and services, MEGAN client integration)
  • Thomas Rattei, Department of Computational Systems Biology, University of Vienna  (SIMAP, metagenome export, web services and portal)
  • Daniel Huson, Suparna Mitra, Nico Weber, Center for Bioinformatics, University of Tübingen  (MEGAN)

The Thinker

November 1st, 2010

La Marche from Simon Rouby on Vimeo.

The ‘Mankind Evolution': An amazing movie produced by Naïa.

Spruce Genome Project

November 1st, 2010

spruceNews from Sweden.

The Spruce genome project has taken off.

A spruce individual, originally collected in 1959 in eastern Jämtland, has been selected and after only one week of sequencing, more sequence data has been generated than during the whole human genome project.

Check the ‘Spruce genome project‘ web site for news.

Photo: Spruce wood in the Vosges © F Martin


November 1st, 2010


Registration for the 1st Plant Protease Conference in Hemavan, Sweden, from April 10 -14, 2011, is open.

The conference, organized by UPSC,  will deal with the biology, biochemistry and molecular biology of plant proteases collecting together the foremost scientists in the field. The approach of the conference is broad, but a special emphasis is paid on a few topic listed below.

  • Organellar proteases
  • Metacaspases
  • Subtilases
  • Proteases in senescence and cell death
  • Novel methods , such as proteomics and degradomics
  • Proteases in xylem tissues and cell wall formation