Category Archives: Article Commentary

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.

Seasonal Trends In Bryophyte-Associated Fungal Communities

I recently returned from the Mycological Society of America annual meeting – this year held at Yale University in New Haven.  There were lots of great talks about fungal genomics, systematics, and ecology – and it’s always good to see old mycological friends and make new ones.

Håvard Kauserud of The University of Oslo, who spoke about recent research from his laboratory, gave one of my favorite talks of the meeting.  His talk took place during a very rewarding afternoon session on fungal ecology.  Already highly prolific, there’s been an increase in the flood of papers to come out of the Kauserud lab over the last year.  Just this month, there’s a nice commentary on the phenomenon of metagenomic tag switching during amplicon sequencing published in the journal Fungal Ecology.

Another paper published this month in the journal New Phytologist is the study “Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing”, authored by Davey et al., a group of researchers both members and affiliates of the Kauserud laboratory, and it is this paper I will address here.

Davey et al 2012 header

Bryophytes represent a portion of the dominant vegetation in boreal forests, but very little is understood about the taxonomy, seasonality, or biomass of the fungi associated with them.  Additionally, microbes associated with mosses may be responsible for nitrogen fixation and nutrient immobilization as epiphytes or on forest soils.  A previous study from the Kauserud lab reported high levels of fungal biomass and active plant cell wall degrading enzymes identified from moss-associated fungi.

Figure One

As I have mentioned here numerous times, fungi are notoriously hard to identify by cultural and morphological means and are extremely diverse.  To understand this diversity, the authors performed 454 pyrosequencing of the ITS2 region of the ribosomal DNA operon for molecular taxonomic identification against a database of known fungal sequences.  This sequencing was done in concert with an ergosterol HPLC assay that is used to estimate living fungal biomass.

Figure Two

The authors identified a large numbers of fungi, some presumably moss associated, and the total amount of fungi recognized was comparable to that found in forest soils.  The majority of fungi were identified as Ascomycetes, which agrees with other studies investigating vascular plant phyllosphere communities using the primer pair ITS3 and ITS4.  Additionally, this study identified a consistent taxonomic profile as a previous study from the Kauserud laboratory using a cloning strategy and Sanger sequencing approach.  Not surprisingly, this study reports orders of magnitude more fungi but identified roughly the same groups of fungi (Helotiales, Chaetothyriales, Agaricales, and Tremellales).

Figure Three

The researchers addressed seasonal variation by sampling every eight weeks between April and January over the course of a year.  Quite interestingly, there is a strong consensus in this study with other research that provides evidence that fungi not only survive under snowpack, but also continue to grow during the winter months.  While the researchers found consistent trends with regard to season, there were fluctuations in fungal biomass when considering host bryophyte.  By using principle component analyses, the authors show that the fungal communities are structured mainly by host plant and secondarily by the type of bryophyte tissue that was sampled.  This paper is an important contribution to the growing literature that show that plant-associated fungi are extremely diverse, dynamic, and show complex relationships with host plants.

Carbohydrate binding gene family expansion in the amphibian pathogen Batrachochytrium dendrobatidis

You’d have to be living under a rock – as some amphibians do – to not be aware of the massive extinction facing our vertebrate friends living within aquatic habitats.  Researchers still don’t fully understand what is causing the amphibian mass-extinction – stress from habitat loss, increased chemical concentrations in the environment, and an auto-immune degrading infection have all been proposed.  What is known is that the chytrid fungus Batrachochytrium dendrobatidis – opportunistic or not – is infecting and killing a large number of amphibians.

What is not fully understood about B. dendrobatidis is its pathogenicity and what mechanisms it employs to cause infection.  A recent paper, “Species-Specific Chitin-Binding Module 18 Expansion in the Amphibian Pathogen Batrachochyrium dendrobatidis”, published in the mBio journal by John Abramyam & Jason Stajich at UC Riverside, begins to address this pathogenicity.  As the authors point out – more than 100,000 species of fungi have been described to date and very few of them are pathogenic.  This means that the ability to be pathogenic is derived from somewhere: genome expansion events, gene family duplication and diversification events – and we’re only starting to understand horizontal gene transfer events in fungi. This paper addresses the expansion of a gene family across two B. dendrobatidis genomes that are associated with pathogenicity.

When comparing the genomes of B. dendrobatidis with the genomes from other chytrid fungi there has been an expansion of genes within the family Carbohydrate-Binding Module Family 18 (CBM18).  The CBM18 family is a large group of proteins that have been implicated in other fungal pathogenic infections on both plants and animals.  The authors here question whether this interesting lineage specific expansion of CBM18 in B. dendrobatidis could be associated with the virulence of its pathogenicity on amphibians.

The authors used the CBM18 protein family domain HMM to search across the B. dendrobatidis genomes and found an increase in the number of domains when comparing it to genome of its closest relative.  When constructing phylogenetic trees of the CBM18 gene family, three monophyletic and strongly supported clades emerged.  When focusing on divergence of the protein domains, the authors determined that individual domain groups were monophyletic and showed a general pattern with regards to their genome locations.

More specifically, clades of the CBM18 family appears to possess different gene functions, some of which appear to be similar to lectins (LL), tyrosinase/catechol oxidases (TL), and chitin deacetylases (DL).  The function of these genes has yet to be experimentally determined, but the authors make some deductions based on DNA sequences.  The lectin-like genes may be involved in the sequestering of chitin, which could then be disrupting the amphibian immune response.  The tyrosinase/catechol oxidase gene family is associated with melanin synthesis, which could be disrupting the electron transport of the infected amphibians.  Lastly, chitin deacetylases may be involved in suppressing defense mechanisms in place to suppress the fungal infection of the host.  The authors plan to continue to elucidate the pathogenicity of B. dendrobatidis in an attempt to understand the ecology and evolution of its infection on amphibians.

A Genome Sequence for Tomato

The average person in the United States eats more than 10 kilograms of tomatoes a year – underscoring the fact that the fruit is one of the most important plant crops in cultivation.  To improve taste, texture, and disease resistance – just to name a few traits – a large consortium of researchers has initiated and provided a draft tomato genome.  In fact, the research consortium has published the genome sequence from two varieties of tomatoes: the domesticated inbred Solanum lycopersicum strain Heinz 1706 – the variety famous for ketchup – and the wild breeding Peruvian ancestor, Solanum pimpinellifolium.

The consortium published the draft genome sequences with a paper entitled “The tomato genome sequence provides insights into fleshy fruit evolution” in the journal Nature.  The consortium started sequencing the genome officially in 2003, but heterozygosity and duplication events made assembling the genome difficult.  The tomato genome is approximately 900 Mb – smaller than the Human genome – but certainly not small by eukaryotic standards.  Genetically and phenotypically diverse, the genus Solanum is one of the largest in the angiosperms.

The genomes of Solanum lycopersicum and S. pimpinellifolium only show 0.6% divergence and there is evidence of recent hybridization between the two species.  Both species show approximately 8% genome divergence compared against close relative potato, Solanum tuberosum.  Across the genus Solanum there has been two genome triplications with subsequent gene loss: one genome triplication is ancient and shared with all the rosid clade and another triplication is shared within the Solanaceae, which appear to be highly syntenic across the family.  The genomes were completed with both Sanger- and Illumina-derived sequences and assembled with the help of physical and genetic maps developed from a long history of tomato breeding efforts.

There are 34,727 and 35,004 genes identified across the genomes of Solanum lycopersicum and S. pimpinellifolium respectively.  These findings are similar to other plant genomes as 8,615 of these genes are found to be common to tomato, potato, rice, grape, and Arabidopsis.  Expression was assessed by replicated RNA-Seq of root, leaf, flower, and fruit tissues.  A total of 18,320 orthologous gene pairs were found in tomato and potato indicating diversifying selection between the two species of Solanum.

The consortium specifically compared tomato to grape in this study, as grape and tomato shared a common ancestor at approximately 100 million years ago, before the first whole genome triplication event that preceded the rosid-asterid divergence.  Additionally, both grape and tomato have similar molecular fruit maturation mechanisms.  When comparing the genomes of tomato and grape, approximately 73% of gene models are orthologous.  By estimating genome triplication events, the researchers conclude that the genome duplication event within the Solanaceae occurred roughly 71 million years ago and approximately 7 million years prior to the tomato-potato divergence.

Having a draft genome sequence is an important mechanism to understanding the molecular biology of the tomato plant.  Genome duplication events gave rise to the diversification of genes responsible for enhanced fruit physiological and chemical development – such as lycopene synthesis – and include photoreceptors and transcription factors that influence fruit ripening.  Additionally, tomato has had a contraction in the number of gene families associated with toxic alkaloid synthesis – the chemical hallmarks of many members of the Solanaceae.  One interesting question not answered by this research is the genomic mechanism by which the tomato regulates nutrient investment in above-ground fruits while the potato regulates starch investment in below-ground tubers.

These two tomato genomes, along with the genomes of fellow Nightshades completed or in the works (potato, pepper, tobacco, petunia, eggplant, etc.), will help breeders to develop traits desired by producers, like long shelf life, and fruit quality traits desired by tomato-consumers, such as taste, color, and texture.  In addition to these benefits, the draft tomato genomes will provide insights into the biology and nutrition of the Solanaceous plants, and provide more information for comparative genomics within this important economic group of plants.

Searching For Candidate Effector Proteins of Rust Fungi

The understanding of effector proteins has advanced by leaps and bounds in the last few years.  Secreted by microorganisms interacting with plants, these small proteins enter a host cell and modify physiological changes, most notably influencing the suppression or activation of host directed immunity.  Fungal effector proteins have been characterized in the pathogen infection process as well as the suppression of host defenses in mutualistic associations such as mycorrhizae.  There is a recently published book, edited by Francis Martin & Sophien Kamoun, which addresses the current state of knowledge on the biology of microbial effector proteins.

Published on January 6th in the journal PLOS One, the paper “Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi” authored by Saunders et al., seeks to describe unknown effector proteins by exploring the diversity of secreted proteins of rust fungi.  The Kamoun Lab has been at the forefront of understanding effector biology in the fungi, and this paper is a significant contribution to understanding how rust fungi invoke pathogenicity on their host plants.

Rust fungi are a monophyletic group of pathogens which cause damage on many important economic crop plants.  In this study, the authors investigated two pathogens with sequenced genomes, Puccinia graminis f. sp. tritici, the cause of wheat stem rust, and poplar leaf rust, Melampsora larici-populina.  By developing an analysis pipeline, the authors inspected the secretome of both fungi to search for putative effector proteins and describe their structure and possible mode of infection into a plant.  Few plant defense mechanisms have been identified for rust fungi.  This study was considered a preliminary step to identify candidate rust effectors in the eventual selection of new resistance (R) genes in plant breeding programs and genome sequencing initiatives.

Eight families of putative effector proteins were identified in the secretomes of P. graminis f. sp. tritici and M. larici-populina, and a total of 6663 proteins were identified by the pipeline, with 2826 proteins containing secretion signal peptide regions.  Analysis of the protein motifs identified several conserved cysteine motifs common to other effector proteins previously characterized from fungal and oomycete plant pathogens.  Not surprisingly, the authors identified many previously unrecognized proteins with domains that exhibited similarity to known pathogenicity-related or haustorial-expressed fungal proteins.  Both P. graminis f. sp. tritici and M. larici-populina showed differences in the types of effectors secreted and the numbers of each putative effector tribe.

As I mentioned before, this study should be considered a first step in the identification of pathogenicity related effector proteins from rust fungi.  Next steps would include wet lab characterization and experimental validation for putative effectors identified in this paper.  Additional studies will be needed to address the functional expression of these proteins, as well as the R genes expressed in planta, during the infection process initiated by the rust fungus.  This paper provides an interesting priority list for further studies in this rapidly advancing area of understanding the biology of the intimacies of the plant-fungus interaction.

Common Toolbox Based On Necrotrophy In A Fungal Lineage

One of the most exciting aspects of the genomic revolution in biology is understanding the genetic mechanisms behind an organisms natural history.  Within the fungi it has been fascinating to begin to tease apart how seemingly similar life histories can be explained by disparate genomic landscapes, or opposingly, how completely different modes of survival can be explained by a common set of genes.  There has been a steady increase in research over the last few years documenting a large array of tools in the genomic toolbox.

A recently published paper in the journal PLOS One, authored by Andrew et al., entitled “Evidence for a Common Toolbox Based on Necrotrophy in a Fungal Lineage Spanning Necrotrophs, Biotrophs, Endophytes, Host Generalists and Specialists” comes from the Kohn Lab at the University of Toronto, which has long studied the fungal family Sclerotiniaceae.  The Sclerotiniaceae is a group of Ascomycetes known for being typically necrotic pathogens which are host generalists or specialists.

This is a great group of fungi to address questions like: why is one species necrotic while another is just biotrophic? …and why are some fungi specialists, while others generally infect plants without regard to taxonomy?  To address these questions the authors sampled across 52 strains of fungi in the Sclerotiniaceae representing 30 taxa covering the spectrum of host specificity/generality and trophic types.  They chose a suite of genes responsible for both general cell housekeeping (controls, etc.) and associated with pathogenicity and constructed phylogenies of these genes to observe relationships between these 52 strains.  Evidence of positive selection acting on these genes, as well as site-specific selection, was also assessed.  Lastly, the authors assessed the pathogenicity of these strains by initiating infection studies on Arabidopsis thaliana plants.

The authors found that there are at least two origins of biotrophy from a necrotrophic ancestor in the Sclerotiniaceae and that there is evidence of selection on all the genes associated with pathogenicity tested in this study.  The housekeeping genes in this study were used to control for the phylogenetic analysis and showed no evidence of positive selection as opposed to the pathogenicity genes.  Furthermore, likelihood analyses showed no statistical differences in the genes of strains from different trophic lifestyles, as well as host generalists and specialists.

Within this study on the Sclerotiniaceae, it appears that there is a common tool box of genes shared by the fungal strains studied here.  The level of expression of genes differed in this study, which could explain trophic and host specificity differences exhibited by these fungi.  It will be interesting when we have more genome sequences from this family to see how genome structure and rearrangements have contributed to the expression and diversity of genes associated with necrotrophy in this family of fungi.