Monthly Archives: December 2012

Drought-Induced Decline in Mediterranean Truffle Harvest

Some of my favorite foods are truffles, and perhaps the best tasting truffle – in my humble opinion – is the famous Périgord Black Truffle, also known as Tuber melanosporum, which is known as a prized delicacy capable of fetching a pretty penny.

me holding truffle

Tuber melanosporum is an important ectomycorrhizal fungus that can be cultivated with crop trees such as Hazelnut, and other truffles can be cultivated with other nut trees such as Pecan.  Despite a concerted effort to understand the biology of T. melanosporum, both through a genome sequence and other molecular tools to understand population biology – as well as government efforts to promote cultivation with nut trees – harvests of the Périgord Black Truffle have been declining since the 1970s.  There has been no agreement in what has been causing this decline from a community of researchers.

truffle climate change paper header

In a brief report entitled “Drought-Induced Decline in Mediterranean Truffle Harvest” in the journal Nature Climate Change, Büntgen et al. recently described how climate change may be affecting truffle production, either directly, or by affecting the biology of the truffle’s host trees.  Such measurements are challenging in numerous regards; inspecting climate data is difficult enough, but reports of truffle harvesting are scarce for many reasons, one of which is the fact that many successful truffle collectors are reluctant to give information about their productive grounds.

truffle climate paper figure

The authors correlated climate details from 12 climate models with truffle harvests from various parts of Europe (namely Aragón in Spain, Périgord in southern France, and Piedmont and Umbria in Northern Italy).  They observed that tree ring growth in Oak trees and truffle production were correlated and showed that increased measurements of summer evapotranspiration could explain both the reduction in plant growth and truffle production.

The authors hypothesize that tree and fungus competition for summer soil moisture may be reducing the production on truffle sporocarps.  Unless the present course of climate change is reversed, it is expected that truffle harvests in Europe will continue to decline.  This is bad news not just for the truffles and trees, but the people who enjoy both.

UPDATE: The New York Times have posted an article (December 20th) entitled “$1,200 a Pound, Truffles Suffer in the Heat

The Draft Genome Of Watermelon: Citrullus lanatus

The Cucurbitaceae is an agriculturally important family of plants (think melons, pumpkins, cucumbers, squashes, etc.) and one of the most popular species in this family is Watermelon.  Watermelon has been cultivated for more than 4,000 years and was most probably spread by nomadic people as a portable source of both water and pre-packaged nutrients.  The estimated center of diversity of the Cucurbits is in Southern Africa.  Watermelon has many cultivars – more than 200 in production worldwide – with a wide range of phenotypic diversity and a wide area of production that accounts for 7% of land grown for vegetables.


Unfortunately, Curcubits are generally susceptible to pathogens – most typically in the form of bacterial and fungal pathogens.  The genomes in this group are starting to pile up which makes the family an interesting group for comparative genomics studies –particularly in the development of model species for plant pathogen studies.

watermelon genome paper header

The recently published paper “The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions” by Guo et al. in the journal Nature Genetics, described the draft genome for the Citrullus lanatus East Asian cultivar 97103 and then re-sequenced 20 different watermelon accessions – representing three different sub-species – in order to observe genetic diversity in wild.

Almost 47 Gb of sequence data was generated using Illumina’s sequencing platforms to give 108X coverage on the relatively small estimation of 426 Mb C. lanatus genome, while the draft is approximately 353 Mb or 83.2% of the estimated genome size.  Unmapped reads, totaling almost 20% of the sequencing data, could not accurately be constructed into contigs because of explicit regions of genome duplication.

watermelon figure 1

The authors estimated 23,440 genes in the watermelon genome – very close to both the cucumber genome (no surprise) and the human genome (surprise).  About 85% of the genes from watermelon could be predicted on the basis of homology to other plant genes.  The authors did a throughout assessment of transposable elements, various repeats, and classified functional RNAs from ribosomal RNA subunits to microRNAs.  Like other plants, watermelon shows gene enrichment in subtelomeric regions.  On the basis of comparison to other genome sequences, watermelon possesses the seven paleotriplications shared with the eudicots.

watermelon paper figure 2

The authors assessed genetic diversity across varieties of C. lanatus by sequencing 20 representative accessions anywhere between 5X and 16X coverage.  The estimated diversity of these accessions was considerably lower than similar arrays of accessions in maize, soybean, and rice.  One explanation of the disease susceptibility of the Cucurbitaceae is this low level of genetic diversity.  As a result, one objective of breeding programs for watermelon is to introduce more diversity from wild accessions.

watermelon paper figure 3

Lastly, the authors assessed a number of key features of the C. lanatus genome (along with the other Cucurbitaceae): vascular transport of water and nutrients along vine-like stems, sugar content and accumulation, and the presence of an interesting non-essential amino acid – originally described from watermelons – called Citrulline.

The watermelon genome database is located both here and here.

The Many Stages Of Manuscript Writing

Again, I’ve been in the midst of writing manuscripts and doing data analysis and haven’t been able to put as much time into this blog as I usually like.  I’m also having some trouble with my server, so you’ll have to excuse the slow load times from my service provider.  As well as having lots of papers in the pipeline, I am finishing up a few draft posts for the blog, so stay tuned as there is more on the way.

Speaking of paper writing, the following video has made the rounds on the internet – and with the theme of this post – I’m reproducing it here.  Computer Science graduate student Timothy Weninger recently submitted a paper to a conference and created a video of his writing process.