Archive for June, 2011

Genomic Impact of Eukaryotic Transposable Elements

June 24th, 2011

For details, see the conference website:

Shrinking Arabette: the Arabidopsis lyrata Genome

June 19th, 2011

I’m trying to get through my backlog of genome papers.

Today, I enjoyed reading Weigel’s group Nature Genetics paper on the Arabidopsis lyrata genome and its comparison with the A. thaliana genome.

Take-home lesson: ~90% of the two Arabidopsis genomes have remained syntenic, but more than 50% (~114 Mb) of the A. lyrata genome is missing from the A. thaliana genome. The lacking sequences were found in transposable elements (TEs) (~50%) and in intergenic regions (~25%). This massive shrinkage is mostly due to hundreds of thousands of smaller insertions and deletions, but as barely impacted the protein-coding gene repertoire. The gene content of A. thaliana is only 17% smaller than that of A. lyrata. The striking reduction of A. thaliana genome occurred in less than 10 millions years and likely resulted from a reduced TE activity and/or more efficient TE purge.

BTW, the 207-Mb A. lyrata genome was sequenced by JGI using Sanger sequencing (yes — one of the last one now that JGI has phase out its ABI machines).

Hu et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43, 476–481.

Photo: Arabidopsis lyrata. © Dr. Deborah Alongi Johnson from University of Sheffield

EMBO Metagenomics Workshop

June 19th, 2011

my Tree of the Month

June 19th, 2011

Trees encroach on any neighbor’s land.

Prospering in the Trastevere (Roma). © F Martin


HGT in Fungi

June 18th, 2011

In their recent Current Biology paper, Slot & Roskas’s suggested the horizontal gene transfer (HGT) of a 23- gene cluster from the Aspergillus lineage to Podospora. This 23-gene cluster includes genes that putatively encode the entire sterigmatocystin synthesis pathway, a toxic and mutagenic compound and a precursor of aflatoxins. In his interesting commentary of this paper, Thomas Richards discussed the known HGTs in fungi as summarized in the figure below.

“Genome Evolution: Horizontal Movements in the Fungi. Fungi possess robust cell walls and do not engulf prey cells by phagotrophy. As a consequence they are thought to be relatively immune from the invasion of foreign genes. Nonetheless, a growing body of evidence suggests gene transfer has amended the metabolic networks of many fungal species.”

Figure. Fungal-derived horizontal gene transfer into the Ascomycota.


Slot, J.C., and Rokas, A. (2011). Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol. 21, 134–139.

Richards, Thomas A.  Genome evolution: horizontal movements in the fungi. Curr. Biol. 21: R166-R167.



Earth Microbiome

June 18th, 2011

Slide presentations of the 1st International Earth Microbiome Project Conference held at the BGI Shenzhen are available at GigaSciences, BGI -

26NPS Bioenergy Trees … follow up

June 17th, 2011

26 New Phytologist Symposium ‘Bioenergy Trees’

Following the Bioenergy Trees NPS meeting last month at Nancy, we have a number of updates now on the website (, including: Photos from the Symposium, Podcast interviews with the Poster Prize Winners and copies of the winning posters, Podcast interviews with lead organiser Francis Martin and Poster Prize Judge, Steve Strauss, Feature article written by New Phyt’s intern Karina Vanadzina, giving an overview of 2nd generation biofuels and the contribution of the Symposium to this research.

Don’t forget to follow us on Twitter (@NewPhyt) for updates about this and other New Phyt symposia and for information about the journal.

Our colleague, Berthold Heinz, is now inviting you to the forthcoming meeting that is being held in Vienna, Austria and which will be relevant for many of you working on bioenergy trees.

The Future Role of Bio-energy from Tree Biomass in Europe – 6-11 November 2011 – Europahaus, Vienna/Austria

Meeting Website:

Photo: Populus trichocarpa ‘Fritzi Pauley’ © F Martin

10th VAAM Symposium “Molecular Biology of Fungi”

June 9th, 2011

Dear friends and colleagues,

We are pleased to invite you to attend the 10th VAAM Symposium
“Molecular Biology of Fungi” on September 11 -14, 2011 in Marburg. The
Symposium will be held at the Aula of the Old University, Philipps
University Marburg.

Especially junior group-leaders, post-docs and experienced PhD students
are invited to apply for a talk.

For more information or to register please go to our website

Early Registration and Abstract Submission will end on July, 31st.

In case you don’t require further notifications and circulars, please
reply to this e-mail with “Do not send announcements” in the Subject line.

Attached please find a form how to prepare your abstract.

We hope to see you in beautiful Marburg for what is sure to be an
exciting and productive symposium.

Prof. Dr. Michael Bölker, Prof. Dr. Regine Kahmann, Dr. Björn Sandrock
and Birgit Niedziella