Archive for December, 2010

Enchanted and Borderless White Dreamscapes

December 29th, 2010

Borderless landscapeA blizzard that barreled up the Northeast of France and neighboring countries on Thursday continued to swirl over the Lorraine region into Sunday morning, with barrages of wind-driven snow that disrupted highway travel over Christmas week-end. On Monday, we enjoyed a enchanted and borderless white dreamscapes.

Christmas Eve

December 29th, 2010

Xmas Eve

Voices: What’s Next in Science

December 28th, 2010


I liked the prognostications for science in 2011 from 10 leading figures in 10 widely scattered disciplines, from genomics to mathematics to earth science, in The New York Times’s Science pages.

Basidiomycete Genome Meeting

December 19th, 2010

FomitopsisIgor Grigoriev, David Hibbett and I are organizing a one-day workshop on March 21, 2011 at the JGI in Walnut Creek to cover comparative genome analysis of basidiomycetes. This jamboree will take place between the Fungal Genetics Conference in Asilomar (Mar 15-20) and the JGI User Meeting (Mar 22-24). The workshop will  include sessions on wood decayers, symbionts and soil fungal metagenomics.

The various sessions will include an update on current genome sequencing projects running at the JGI, including the Wood Decayers and Mycorrhizal Symbionts projects, and cross-all-basidio comparisons.

People willing to make a contribution can contact Igor, David or myself.

Photo: Early stages of Fomitopsis fruiting body development. Spruce forest near Pierre Percée in the Vosges range. © F Martin

Holiday Greetings

December 19th, 2010


I wish you a happy, healthy and prosperous New Year

Mangez des Pommes – the Apple Genome

December 12th, 2010

Golden DeliciousA few months ago, the draft of the genome sequence of Peach (Prunus persica) (cultivar ‘Lovell’) has been released by the International Peach Genome Initiative. In the October issue of Nature Genetics, Riccardo Velasco from the Istituto Agrario S. Michele all’Adige and the Apple Genome Consortium are describing a high-quality draft genome sequence of the diploid apple cultivar ‘Golden Delicious’ of the domesticated apple (Malus × domestica Borkh., family Rosaceae, tribe Pyreae). The genome has been sequenced by the whole-genome shotgun approach using both Sanger and 454 sequencing. The total contig length (603.9 Mb) covers about 81% of the apple genome.

Domesticated apple belongs to Rosaceae, the same family as rose plants. But apples and other members of a sub-tribe called Pyreae have far more chromosomes than the rest of the Rosaceae family: 17 compared with the seven to nine chromosomes found in other Rosaceae plants. A genome-wide duplication, that took place >50 Myears ago, shaped the apple genome and caused the transition from the nine ancestral chromosomes to 17 chromosomes in the Pyreae. The authors elegantly reconstructed the relationships among apple chromosomes based on the most recent and the older GWD. I liked Figure 1B which nicely describes this complex process.

When predicted gene spaces of apple and pear were compared, a value of 96.3% nucleotide identity was computed between these two species of the tribe Pyreae, whereas the estimate for nucleotide identity between the tribes Pyreae and Amygdaleae (apple and peach) was 90.6%. When grape (Vitis, Vitaceae) was compared with apple and pear, nucleotide identity was estimated at 85.31%.

Up to 57,000 protein-coding genes were predicted in this apple genome. The putative proteome is thus much larger than other sequenced plant genomes, e.g., Arabidopsis thaliana (27,228), poplar (45,654), grape (33,514), rice (40,577), sorghum (34,496) and maize (32,540). Multigene family analysis revealed that among the groups of genes that have been expanded is a sub-clade of genes coding for transcription factors in the MADS-box group — previously implicated in fruit and flower-related processes. Noteworthy is the expansion of gene families involved in sorbitol metabolism, a carbohydrate involved in photoassimilate translocation throughout the tree. This includes aldose 6-P reductase (A6PR), which is rate-limiting for sorbitol biosynthesis, sorbitol-dehydrogenase (SDH), which converts sorbitol to fructose in the fruit, and sorbitol transporter PcSOT2, which is specific to Rosaceae fruit.  Retrotransposons represent the most abundant transposable-elements, comprising 38% of the total genome and 89% of all transposable elements.

Apple is the major fruit crop of temperate regions worldwide and was already enjoyed in China 3,000 years ago. The consortium was able to trace the apple’s ancestry by sequencing 23 genes across the genus Malus, and confirmed that the domestic fruit’s wild ancestor Malus sieversii originally grew in the mountains of southern Kazakhstan in the Tian Shan region.

The available apple genome will undoubtly accelerate the breeding of this economically important perennial crop species.

Velasco et al. (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics 42, 833-839.

Gazelles, elephants, blue whales and dodos

December 5th, 2010

gazelle3From Pathogens: Genes and Genomes:

Gazelles, elephants, blue whales and dodos: next-generation sequencing at the zoo

‘The big news today is that Life Tech, of SOLiD fame intend to acquire Ion Torrent, subject to certain technical milestones being reached. The best blog coverage is at Omics Omics and Genetic Future.

This means Illumina, Life Tech and Roche, our sequencing Big Three have all now got into bed with “next-next-generation” technology platforms. Roche have previously signed up IBM’s nanopore technology and Illumina have entered into a marketing and distribution alliance with Oxford Nanopore.

What does this all mean?’ …. Read More

Photo: ©

Sighting the Past Symbiosis

December 4th, 2010

428px-Haeckel_Hepaticae“Early plant life attempting to colonize land from marine environments would have encountered a very hostile environment. Heat and high levels of atmospheric carbon dioxide and a substrate poor in bio-available nutrients, would have been huge stresses upon organisms adapted to aqueous environments. Some fungi colonizing land at the same time developed the ability to form symbiotic relationships with early plant protostele/roots.  As with their modern day representatives, fungi grew in the thin soil substrate as spreading colonies of filamentous hyphae prospecting for nutrients, minerals and water.  If fungal symbiosis worked then as it does today, it is assumed that early plants gained nutrients and water from their fungal partner for growth in return for photosynthetically derived carbon.

The most ancient evidence of such a symbiosis, with fungal hyphae resembling the Glomus genus, has been dated to 460 million years ago (Mya) from Ordovician rocks in Wisconsin and in the Rhynie Chert flora.  This fossil record continues through the Carboniferous period in the roots of gymnosperms through to the Triassic period in Antarctica fossil beds.  The presumed symbiotic structures, where the fungal hyphae and the plant roots form a common tissue, have been classified roots infected with arbuscular mycorrhizal (AM) fungi.  It is likely that this plant-fungal symbiosis would have been key in the establishment of plants on land.”*

One way to confirm this paleobotanical speculation is to study the interactions between AMF and actual lower plants. In the 2 November online issue of Nature Communications, Humphreys et al. published a study of mutualistic mycorrhiza-like symbiosis in the most ancient extant clade of land plants, the thalloid liverwort (Marchantiophyta). They showed that colonization of this lower plant with AMF significantly promotes photosynthetic carbon uptake, growth and asexual reproduction. The host plant fitness increased thanks to AMF-enhanced uptake of phosphorus and nitrogen from soil. A simulated CO2-rich atmosphere, similar to that of the Palaeozoic when land plants originated, significantly amplified the net benefits of the symbiosis and likely selection pressures for establishment of the symbiosis. This study is providing the needed functional evidence supporting AMF symbionts as drivers of plant terrestrialisation in early Palaeozoic land ecosystems.

Claire P. Humphreys, Peter J. Franks, Mark Rees, Martin I. Bidartondo, Jonathan R. Leake & David J. Beerling (2010) Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants. Nature Communications 1, 103 doi:10.1038/ncomms1105.

* from: Plett JM & Martin F. Molecular Interactions in Mycorrhizal Development. In Plant-fungal interactions (Southworth D, ed.), Wiley Blackwell, in press.

Image: Haeckel Hepaticae © Wikimedia Commons.

Blurred Boundaries

December 4th, 2010

PoplarLaccariaECMOur review paper on the genomes of ectomycorrhizal fungi is available online at the Trends in Genetics site.

Plett JM & Martin F. 2010. Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends in Genetics. doi:10.1016/j.tig.2010.10.005

Abstract. “Soils contain a multitude of fungi with vastly divergent lifestyles ranging from saprotrophic to mutualistic and pathogenic. The recent release of many fungal genomes has led to comparative studies that consider the extent to which these lifestyles are encoded in the genome. The genomes of the symbiotic fungi Laccaria bicolor and Tuber melanosporum are proving especially useful in characterizing the genetic foundation of mutualistic symbiosis. New insights gleaned from these genomes, as compared to their saprotrophic and pathogenic cousins, have helped to redefine and shape our understanding of the nature of the symbiotic lifestyle. Here we detail the current state of research into this complex relationship and discuss avenues for future exploration.”

Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA.