The October issue of the journal New Phytologist contains a commentary article by a group of plant scientists who conducted a survey to identify the 100 most pressing scientific questions facing plant biologists. The article “One Hundred Important Questions Facing Plant Science Research” is very thought provoking.
I’ve replicated the questions here for you to read and ponder. I know the list is heavy on the text, but I think these questions are worthy of the space. You should definitely then read their article (and supplementary commentary) and see how they have collectively addressed these questions. They may have addressed these questions in their commentary, but these questions are far from answered and may demand many careers to answer fully.
I already mentioned (here and here) the New Phytologist Symposium on Bioenergy Trees, but I’d like to let you know that my meeting commentary has been published in the journal. I highly recommend attending one of the many New Phytologist Symposia based on their intimate size and the excellent quality of speakers.
This week, it’s been hard to miss the new paper, “How many species are there on Earth and in the Ocean?” published by Mora et al. in the August 2011 issue of the journal PLOS Biology. There have been commentaries or news articles printed in the New York Times, The Economist, The Guardian, Damian Carrington’s Guardian Blog, National Geographic, Yahoo News, AlterNet, MSNBC, Reuters, UNEP, NewsDaily and Ed Yong has posted a commentary on his Google+ page. Furthermore, some well respected scientists who study biological diversity have joined the debate too: Jonathan Eisen has devoted two blog posts to the paper (one about the actual paper in PLOS Biology and another on the National Geographic commentary) and there is a commentary from Robert May in PLOS Biology about the study and its significance. Since there is ample information on the study elsewhere, let me communicate a brief summary of the study and some of my feelings about the paper.
It’s quite embarrassing that we have really no clue how much biological diversity is found on this planet. Adding insult to injury is the fact that we have no concept of the current magnitude of the loss of diversity due to human induced mass extinctions. This paper seeks to predict total global biological diversity by documenting current taxonomic numbers and extrapolating consistent patterns to estimate the number of species that have yet to be identified.
The methods of the authors essentially consisted of three parts. First, the authors compiled a list of approximately 1.2 million species pulled from numerous biological databases. Second, they surveyed a little over 500 taxonomists who were asked to identify the validity of current scientific names and comment on the intensity of current taxonomic efforts to describe new species. Third, the authors analyzed this data to find the estimated global numbers of biological taxa for each phylum.
The authors show a predictable pattern in the classification of species (at the phylum, class, order, family, and genus level) at least consistently for animals. By evaluating these patterns using regression, the authors validated this by closely examining 18 taxonomic groups that we think we understand their total biological diversity. By doing this, the authors come up with a total estimate of 7.7 million species of animals (mostly insects), close to 300,000 species of plants, more than 600,000 species of fungi, and a total estimate of roughly 9 million eukaryotes on Earth. The authors estimate that 86% of species on Earth and 91% of species in the oceans still have not been formally described. Previous estimates of species diversity have been wide: anywhere between 3 million to a 100 million species.
This paper is a novel and worthwhile attempt to determine the total amount of species diversity on this planet. Despite this, I think – and the authors have their own reservations – that there are some serious problems with some of their calculations.
One problem is that the study is based mainly on using animals, and vertebrates for that matter – which are the best described of any phylum, as the baseline for measuring the completeness of species diversity. I would argue that plants and fungi, and obviously bacteria, archaea, and “the protists” are clearly not well known enough to extrapolate any serious estimate species numbers especially when considering vertebrate animals as a baseline and whose numbers are largely skewed.
Another problem is in our collective definition of species, as well as taxonomic subjectivity of the categorization of other taxonomic hierarchies, which are based on the on the homology of shared characters and, I would argue, are largely incomparable outside of each phylum. For example, what one taxonomist calls an order in one grouping may not be equivalent to what another taxonomist calls a completely different order in another completely different grouping.
I should point out that the authors don’t ignore these caveats, but they still exist in their study. In any event, this paper is important because it adds to the dialogue concerning species diversity, the need to estimate, inventory and preserve the massive amount of diversity we share on the planet.
The recently established website extention.org is a agricultural cooperative extention collective of 74 land grant universities which seeks to serve the public though education and service.
This fall there will be a plant breeding and genomics webinar series for plant breeders, breeding assistants, lab personnel, post docs, and graduate students. These webinars will focus on how to use specific tools, such as software for genetics and mapping techniques, and on laboratory techniques across various topics of genomics and plant breeding. For more information or to sign up to view a webinar go here or here. Join the Plant Breeding and Genomics eXtension community of practice this fall for a webinar series to learn how to use tools, software, and techniques.
With next-generation sequencing technologies dropping in price and increasing in throughput, it’s not surprising to find multiple genomes published every week in scientific journals. Most of these articles don’t qualify for publication in the top tier of journals like they did at the onset of the next-generation sequencing boom, but some genome sequencing projects, such as the potato genome, are high profile enough to warrant publication in top tier journals.
In the July 14th issue of the journal Nature, a draft of the potato (Solanum tuberosum) genome was described in a paper authored by the Potato Genome Sequencing Consortium – a huge group of researchers from 26 institutions.
The potato is the world’s fourth most consumed food crop, the most commonly grown vegetable crop, and a member of the economically important Solanaceae family –otherwise known as the nightshades – which include tomato, peppers, aubergine (eggplant if you live in the United States), tobacco, and petunia. Widely distributed in western South America, tuber forming Solanum species are highly morphologically diverse and easily cross with other varieties for breeding purposes.
It’s been a bumpy road sequencing the potato genome since the project was started in 2006. The potato genome is an extremely heterozygous autotetraploid, which translates to four highly variable copies of each of the 12 chromosomes. It’s also the first sequenced Eudicot genome in the Asterid clade, so there are no close genetic relatives to provide the basis for a guided genome assembly.
The consortium began the sequencing by creating a bacterial artificial chromosome (BAC) library of 78,000 clones from a well studied diploid line providing high quality potatoes, named RH89-039-16. The group used the BAC library and 10,000 AFLP markers to create more than 7000 contigs which were constructed into a physical map. The group then identified up to 150 BACs for every chromosome on the potato genome, and verified their locations using fluorescent in situ hybridization.
Heterozygosity was so high in the RH line that after thorough sequencing the group hit an impasse with the assembly of the genome. In an attempt to complement the sequencing of the RH line, the consortium began sequencing a doubled monoploid potato clone, DM1-3 516R44, derived from a diploid wild South America accession. The DM line has a simpler genome than the RH line and is highly homozygous.
Using both the Illumina Genome Analyzer II and Roche 454 pyrosequencing platforms, and supplementing this data with traditional Sanger sequencing, approximately 96 Gb of data was acquired for the DM line. The group then used the SOAPdenovo computer program to assemble the reads with a final assembly of 727 Mb for the DM line and a final estimation of 844 Mb for the genome.
The consortium generated more than 31 Gb of transcriptome data from both the DM and RH line libraries. These 48 libraries represented major tissue types, developmental stages, and included various responses to abiotic and biotic stresses. All the reads from the RNA-Seq libraries were mapped to the assembled DM genome. Using gene prediction methods, along with protein and EST data, the potato genome was predicted to contain 39,000 protein coding genes, an amount which is in agreement with other plant genomes. Within these genes, there were an estimated 2,642 asterid-specific and 3,372 potato-lineage-specific genes. Some of the predicted asterid-specific genes include many novel transcription factors, self-incompatibility factors, and defence-related proteins. The draft assembly of the genome consists of more than 60% repeated elements. The largest class of the transposable elements is the long terminal repeat retrotransposons (LTRs) which are estimated at 30% of the potato genome.
The potato is notorious for being susceptible to many pathogens and pests. This well known susceptibility was one of the priorities for sequencing the genome and determining genes responsible for disease resistance and pathogen defense. The DM genome assembly contains more than 800 putative R genes, responsible for conferring disease resistance, including 408 NBS-LRR-encoding genes, 57 Toll/interleukin-1 receptor (TIR) domains, and 351 non-TIR type resistance genes. An extreme number of pseudogenes – attributed to indels, frameshift mutations, and misplaced stop codons –were identified within known R gene motifs, which possibly explains the potato’s inability to fight off some specific diseases.
One such well known disease, Late Blight, caused by Phytophthora infestans, was responsible for the Irish Potato Famine in the 1840s.. Using information from this genome sequencing project and other studies, we now know the variety brought to Europe in the late 16th century happens to lack specific disease resistance genes for Phytophthora infestans. One could speculate that unbridled transposon jumping caused the inactivation of many R genes in this potato variety.
Unique for the potato is the formation of tubers (the actual potatoes) through the modification of a stolon. The tomato is very closely related to potato, but does not produce stolons or modified tubers. The group used transcript data from both potato and tomato to address genetic regulation of the formation of stolons and the transition of stolons to tubers. Quite interestingly, the formation of stolons and tubers coincides with an up-regulation of genes associated with starch biosynthesis, protein storage, and Kunitz protease inhibitor genes associated with pests and pathogens.
Possibly due to extremely high levels of heterozygosity, it has been difficult to improve the potato through traditional breeding efforts. It’s estimated that there is a worldwide economic loss of 4.5 billion US dollars to potato crops from diseases each year. Just to attempt to suppress these diseases copious amounts of pesticides and fungicides are applied to potato crop land each year. The potato cyst nematode, for example, is an important pest that researchers hope to improve resistance to via breeding initiatives. Having this draft potato genome sequence will aid in the characterization of existing germplasm collections and description of allelic variance in breeding efforts to avoid diseases. The potato genome will also serve as a resource for breeders wanting to improve the quality of other economically important Solanaceous plants such as tomato, pepper, eggplant, and tobacco.
Published in the June 2011 issue of the journal Nature Biotechnology was a paper reporting on the genome sequence of the data palm, Phoenix dactylifera. This paper, authored by Al-Dous et al., addressed the genome sequencing and de novo assembly of this agriculturally important monocot tree, along with comparative genomics with other plants.
Dates have been found in the tombs of pharaohs estimated at 8,000 years old. Fields of agriculturally planted trees, estimated to be older than 5,000 years, suggest the date palm is one of the oldest cultivated plants in the world. Dates are the most important agricultural crop in the hot and arid regions surrounding the Arabian Gulf and their global production is close to 7 million tons yearly.
Despite a prolonged emphasis on their agriculture, there are a few problems to deal with if you are a date grower. Typical of tree crops, there is a long generation time from seedling to fruit harvesting. Additionally, only the female date palm provides fruit and it takes at least 5 years after seed germination to tell if you have a male or female plant. To make it even harder for a date grower, there are more than 2000 date varieties, each exhibiting its own color, flavor, size, shape, and ripening schedule, and they are all really hard to keep track of based on conventional techniques.
In an effort to provide genetic resources for date growers and breeders, the authors of this study – who were mainly located in Qutar – sequenced and assembled 380 Mb of the estimated 658 Mb genome of the Khalas cultivar, which is known for high fruit quality. Generated using short reads from the Illumina Genome Analyzer IIx platform, this partial sequence excluded numerous large repeated regions, includes a predicted 28,890 genes, and represented 18 pairs of chromosomes. The authors estimate that this draft genome represents roughly 90% of the total genes and 60% of the total genome.
This genome resource also serves a comparative genomics purpose by being the first member of the widespread monocot order Arecales. To this date, the only Monocots with sequenced genomes – for example: Corn, Rice, and Sorghum – have all been in the grass order, the Poales.
This report is missing some vital information: in addition to an incomplete genome assembly, there is no metabolic, developmental, or gene network pathway reconstruction for the date palm provided in this paper (and unfortunately this paper also includes some glaring typos in the citation section). In place of these expected analyses, the authors conducted a throughout survey of SNPs in this Khalas cultivar, along with eight additional cultivars common in breeding programs for the date palm. Within these nine cultivars, 3,518,029 SNPs were determined, but quite interestingly, a total of 32 SNPs could be used to differentiate the cultivars.
In addition to the throughout SNP analysis, the researchers then did a full parentage analysis of the cultivars used in this study, which includes the famous date varieties such as Deglet Noor, Dayri, and Medjool. Here‘s an article in Nature Middle East on the importance of understanding this parentage and gender analysis.
Although this is a draft genome still being completed and undergoing resequencing, namely the tools provided by the authors, the SNP and parentage analysis, should provide date palm breeders with many resources for improved fruit quality and this genome represents an exciting piece of the monocot evolutionary puzzle.
In an effort to alleviate this bottleneck, a group of researchers has organized the PhenoDays 2011 International Symposium which will be held October 12th to 14th in Wageningen, The Netherlands. Symposium presentation talks will be given by researchers from both institutional and academic plant breeding groups, as well as industry representatives from the seed production industry. In addition, there will be plant phenotyping workshops. See the symposium website for more information and registration.
I’m just returning from the New Phytologist “Bioenergy Trees” symposium, which just took place from May 17th to 19th at INRA in Nancy, Lorraine, France, and I am pleased to say was a very productive meeting. Due to technical difficulties, I was not able to contribute to the online updates via Twitter, but if you’d like to follow the meeting developments you can read the Twitter feeds using the hashtag #26NPS or following @NewPhyt.
Thanks to next-generation sequencing, the number of genomes that been deciphered is rapidly increasing. Plants have somewhat lagged behind other organisms – due to very large and complex genomes requiring both sequencing and computational energy – but despite these hurdles the number of completed plant genomes are starting to increase rapidly (just look at Phytozome for more evidence of this).
In order to deal with the increasingly large amount of genomic data, the Plant Genome Evolution Meeting, held this year in Amsterdam, The Netherlands, seeks to gather researchers studying plant evolution and comparative genomics. This symposium is sponsored by the Current Opinion series of scientific journals. An early conference program has been announced here and registration is located here.
ChloroFilms is nonprofit project which seeks to develop plant biology education through the promotion of video content about the wonders of plants and plant associated life. ChloroFilms provides cash awards for videos produced about plants. Initial funding for the project came from grants from the American Society of Plant Biologists, the Botanical Society of America, Penn State Institutes for Energy and the Environment, and the Canadian Botanical Association.
Get your cameras ready and start filming!
Here are three award winning films:
The XV International Congress on Molecular Plant-Microbe Interactions has shaped up to be an amazing meeting. A stellar group of researchers will be presenting at the meeting. Registration is open now.
Directly from the meeting website: “The XV International Congress on Molecular Plant-Microbe Interactions is recognized as the most important international meeting for plant-microbe interactions to discuss research and network with colleagues from around the world. This meeting is the global venue for presenting and discussing new research and developments in molecular plant-microbe interactions. Through plenary lectures, concurrent sessions, special workshops and various events, attendees experience innovative plant-microbe interactions research. The meeting features hundreds of abstracts and provides networking and professional development opportunities.”
I’ve already talked about mycorrhizal associations numerous times (here and here), so if you’re not already used to hearing about mycorrhizae, you will if you continue to read this blog. In this recent paper, entitled “Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza“, published online in the journal Nature, the authors Maillet et al address plant and fungal interactions of arbuscular mycorrhizal associations. Using the Glomus intraradices – Medicago truncatula model system, the researchers identify diffusible chemical signals produced by the fungus during initiation of the mycorrhizal association with the plant.
It has been hypothesized that both fungi and bacteria interacting with plant roots do so using similar genetic mechanisms. It has already been shown that rhizobial bacteria – particularly the nitrogen fixing microbes associated with leguminous plants – produce lipochitooligosaccharide (LCO) signals used in the communication with host plants. The authors of this study discovered that the fungus Glomus intraradices, like the nitrogen-fixing bacteria, secretes an array of sulfated and non-sulfated simple LCOs which stimulated the formation of arbuscular mycorrhizae in disparately related plants, such as Medicago (Fabaceae), Daucus carota (Wild Carrot; Apiaceae), and Tagetes patula (French Marigold; Asteraceae). These compounds were found in Glomus intraradices both interacting with plant roots and in free-living resting spores in the soil.
Comparing the genes involved in the transduction of the LCO signals in both rhizobial bacteria associated with legumes and arbuscular mycorrhizal fungi associated with land plants yielded similar gene expression pathways. In order to validate the role of LCOs in mycorrhizae formation, the researchers genetically engineered non-plant interacting bacteria to produce the LCOs from Glomus. These engineered bacteria increased mycorrhizae formation in plants already associated with Glomus. Fungal LCOs were also found to induce root branching, a trait long associated with the formation of mycorrhizae in plants. There is a nice commentary on this research article located here.
Genome sequencing has provided us with an amazing amount of information regarding organismal biology and mycorrhizal fungi are some of the most interesting of the organisms who have had their genomes sequenced. Maybe I am a little partial to these fungi because I study them intimately, but new sequencing technology has made this an exciting time for people like me.
Ectomycorrhizal fungi are a polyphyletic group of organisms which form a symbiotic association with the roots of tree species (the word ‘mycorrhizal’ literally means plant-fungal unions). This association has typically been recognized by the exchange of nutrients and water from the fungus to the plant and the exchange of sugars derived from photosynthesis from the plant to the fungus. Although ectomycorrhizal fungi only form mycorrhizae with 3% of plant species (arbuscular and other mycorrhizal fungi associate with approximately 92% of plants), these associations are with a diverse array of plant lineages, including the Betulaceae, Cistaceae, Dipterocarpaceae, Fabaceae, Fagaceae, Myrtaceae, Pinaceae, and Saleceae. Plants in these families cover almost the entire portion of boreal, temperate, Mediterranean, and sub-tropical woodlands, so their importance is significant. It’s very interesting to note that these associations have independently arisen at least eight times within the angiosperms and between six and eight times in the gymnosperms. Mycorrhizal associations are thought to have originated when plants and fungi climbed onto land together (more on that here).
The sequencing of both fungal and plant genomes over the last few years has led to greater understanding of how these organisms interact during their mutualistic associations. Although genome sequencing has addressed some long established questions, there are many more questions that have arisen from these sequencing efforts. This recent review in Trends in Genetics by Jonathan Plett and Francis Martin of INRA-Nancy, two of my collaborators, addresses the current state of our knowledge of the ectomycorrhizal symbiosis and poses directions for future research in this vital research area.
Currently, only two ectomycorrhizal fungal genomes (Basidiomycete mushroom Laccaria bicolor & Ascomycete truffle Tuber melanosporum) have been sequenced, but other fungi (see the Mycorrhizal Genomes Project) are scheduled to be sequenced by the Martin Lab through JGI. With a genome size of 65 Mb Laccaria bicolor has the largest amount of protein coding regions of any sequenced fungus, and Tuber melanosporum has the largest genome of any sequenced fungus at 125 Mb but has one of the least dense genomes.
The nature of mutualistic symbiotic relationships imply that both organisms benefit from the association and both ectomycorrhizal fungi and their host plants fulfill this criteria. Unlike saprotrophic fungi, ectomycorrhizal fungi are very poorly suited to degrade cellulosic plant material, but they are able to access soil nutrients via a large biological toolbox of secreted proteases and phosphorus transporters. Both Laccaria bicolor and Tuber melanosporum, which have very different genomes, exhibit a very similar suite of symbiosis-induced nutrient cycling enzymes, which suggest that providing nutrients to the host plant is a key defining feature of ectomycorrhizal fungi. Interestingly, Laccaria bicolor and Tuber melanosporum rely on differing mechanisms of interacting with their host and acquiring carbon from the environment. Laccaria bicolor appears to be less dependent on the host and more active at acquiring carbon from the soil substrates and, as a result, may act as a weak saprotroph in the environment. Tuber melansporum is more aggressive in its colonization of plant roots and does not appear to be able to acquire carbon from the soil and therefore is more dependent on the host for its survival.
Information gathered from fungal genomes suggests that a majority of the biochemical and genetic control over the initiation of the mycorrhizal association comes from the fungal partner, which makes sense given that the fungus has more energy to gain from the association. Most mycorrhizal fungi are unable to acquire carbon from the environment so they are completely reliant on hand outs from their host plants. It appears that mutualistic fungi share similar mechanisms with pathogenic fungi and bacteria when interacting with plants, including the use of small secreted proteins which interact directly with plant cells.
With the sheer amount of genomic data being generated it’s an exciting time to be a scientist, especially one who studies mycorrhizal fungi. Over the next few years, especially with sequencing projects scheduled for completion, we will have even more data to shed light on the amazing biological associations of plants and microbes.
(Above Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA)
Fuels derived from cellulosic biomass are increasingly becoming a priority as we focus both on reducing the large amount of greenhouse gases we introduce into the atmosphere and our dependence on unsustainably sourced fossil reserves. Liquid or solid biofuels derived from cellulosic materials, such as trees, will address these criteria while also assisting agricultural development in rural areas by promoting sustainable coppice harvesting on marginal lands not suitable for consumption crop production. The use of next-generation genomics technologies, as well as more traditional biological research methods, will help develop and enhance tree growth in no- to low-input environments. Additionally, genomic resources will contribute to understanding the process of cell wall formation in woody plants and allow researchers to optimize the composition of plant cell walls for bioenergy concerns.
In the upcoming meeting “Bioenergy Trees” – sponsored by the journal The New Phytologist in their ongoing series of symposia – will address the development of trees and other woody biomass for bioenergy purposes. This meeting will be held at INRA-Nancy, in Nancy/Champenoux, France, from May 17th to 19th, 2011. Registration is now open. In addition to this very pertinent research topic, Nancy is truly a magical place, so it’s with great excitement that I tell you about this meeting.
In addition, The New Phytologist has announced the next round of symposia for 2012 here.
I’ll be presenting some papers I find interesting here on the blog. This is mainly as a way for me to semi-formalize my thoughts about research and communicate these thoughts with you, but also to keep me on track with my reading. There is so much amazing science happening it’s almost too much effort to keep track of, but I am going to attempt to, at least in this public forum. These posts will be just as much for my benefit as they will be as ways for you, as the reader, to find out about what is new and interesting, at least what is new and interesting to me…
I’d like to first focus on a paper co-authored by some of my colleagues at Penn State. The Kao Lab has long studied self-incompatibility in plants, mainly using Petunia as a model species for this work. Petunia is a member of the Solanaceae and shares close common relatives with Tomatoes, Potatoes, and Eggplants. The Kao lab has co-authored numerous papers with the Takayama Lab at the Nara Institute of Science and Technology in Japan. This latest paper was published in the journal Science this month.
Plants, of course, can’t move from one place to another to look for a suitable mate with genes for advantageous traits. As the apple doesn’t fall far from the tree, many plants in a specific area will be defined by very similar sets of genes. Plants that breed with genetic relatives may face some of the same fates as those noted in the animal kingdom: predominance of genetic diseases, a decrease in fitness and overall health, and an inability to survive against stresses and pathogens. Therefore, plants have evolved specific mechanisms for reducing or preventing inbreeding depression.
Prior research from the Kao Lab had elucidated two gene types responsible for the prevention of inbreeding, in what has become known as self-incompatibility. One gene first identified in 1994, is an S-RNase, and is responsible for stopping gene expression in pollen grains similar to the flower it arrives at. Another set of genes identified in 2004, SLFs (S-Locus F-box proteins), are found expressed in pollen and regulate self-incompatibility by specifically “disengaging” the S-RNase found in the flower pistil. These two groups of genes work in collaboration to initiate self-incompatibility in the Petunia flower.
This new paper in the journal Science by Kubo et al. identifies a larger suite of SLF genes and adds more detail to the picture of self-incompatibility. In addition to the SLF protein described in 2004, an additional 5 types of SLF genes have been elucidated in this paper. The increased diversity of SLF proteins explains how elaborate this mechanism of self-incompatibility is. There is a commentary on this research here in the same journal.
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