Black Forest Summer School on Bioinformatics for Molecular Biologists, September 2013

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Here’s another course for the summer aimed at PhD students and early career molecular biologists on mastering the use of pre-existing bioinformatics tools.  The venue sounds amazing and it looks like the perfect place to learn or hone your existing bioinformatics skills.  Francis Martin will be giving the keynote lecture so there is more incentive to attend!

Just What Is A “Gleba”?

I’m in the process of organizing some of my old teaching materials and I have a few VHS tapes of clips of mycologically related videos for teaching about fungi. Since I don’t have a working VHS tape recorder — and don’t expect many departments to maintain one either — I’ve been trying to find some of the videos online. Here’s a short video clip that I usually show when teaching about the Gastromycetes. The students always remember what a gleba is for their exam.

Summer 2013 Bioinformatics Workshop Roundup Part Two

Here’s a couple more promising bioinformatics workshops taking place in the summer of 2013:

Metagenomics: From The Bench To Data Analysis, Heidelberg, Germany, April 14th to April 20th, 2013

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Joint EU-US Training in Marine Bioinformatics, Newark, Delaware, USA, June 16th to June 29th, 2013

EU-US Course Header

Summer 2013 Bioinformatics Workshop Roundup Part One

The summer is a great time to learn some new skills and really hone data analysis techniques.  I think it’s best to learn some topics — bioinformatic tools and data analysis scripting in particular — as intense multi-day workshops or a week- or two-week long short courses.  Here’s a few courses that are being held this summer that may be of interest to you.  I’ll be sure to post more as I hear about them.

Programming for Evolutionary Biology, Leipzig, Germany, April 3rd to April 19th, 2013

course one

Informatics for RNA-sequence Analysis, Toronto, Canada, June 3rd to June 4th, 2013

course two

Pathway & Network Analysis of -Omics Data, Toronto, Canada, June 10th to June 12th, 2013

course two

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.

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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.

Watermelons

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.

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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.

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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.