Published today is a really nice New York Times Science Tuesday headline feature written by Carl Zimmer on the wonderful world of the Slime Molds. Check it out.
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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.
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 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.
Horizontal Gene Transfer (HGT) goes against what we typically consider the normal transfer of genetic material from parent to offspring. HGT involves the transfer of genetic material from one organism to another. Within the bacteria, whose mode of survival typically depends on phagocytosis, there is a fairly amount of HGT. Events of HGT have been rarely observed in Eukaryotes because numerous barriers exist to prevent foreign nucleotides from entering a cell’s nucleus. Some of these barriers in the Fungi include a substantial cell wall made of chitin, multiple cell and nuclear membranes to cross, and the secretion of metabolic enzymes to the outside of the cells and subsequent uptake of the nutrients. Despite these barriers, there is now evidence of multiple occurrences of HGT in the fungi.
As you can gather from the name, the “100 Plant and Animal Reference Genome Project” seeks to provide a total of 1000 plant and animal genomes for the use of researchers (For more information on the “1000 Plant and Animal Reference Genomes Project” see here).
Some of the top researchers in this newly emerging discipline will be speaking at the Jacques Monod Conference “Integrative Ecological Genomics.” The meeting is held in Roscoff, Brittany, France. Registration is by application (the submission deadline is June 20th 2011) and the number of attendees is capped at 115 people. Information regarding the meeting and registration can be found here and here.
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.
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) We’re only just now starting to get a grasp on the sheer amount of global biological diversity, most of which has been very difficult to observe with conventional observational means. Changes in technology and sampling strategies have resulting in the acquisition of information regarding many previously undocumented forms of biological life. Along with microorganisms associated with plant roots – the strict focus on my research interests – phytoplankton represent a large group of organisms that we still know little about. For selfish reasons I was interested in this study because I wanted to see how these authors addressed ways of learning more about a previously unknown lineage of ocean phytoplankton. As evidenced by next generation sequencing efforts, there are many unknown and undescribed fungi in soils and there is a huge amount of commonality of the diversity of microbial life in soils and oceans. Published in the Proceedings of the National Academy of Sciences, a study entitled “Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life”, by Kim et al, describes a recently identified and previously uncultured marine and freshwater microalgal lineage of Eukaryotic organisms. The researchers title this group of phytoplankton the rappemonads, from the initial paper (authored by Rappé et al 1998) that reported unknown DNA sequences from this lineage. The researchers designed nucleotide primers and fluorescent probes from initial DNA sequences (from the Rappé et al study) and used these molecular diagnostics to observe marine and freshwater samples for their presence or absence of these unknown organisms. Phylogenetic analysis of environmental nucleotide sequences revealed that rappemonads are related to both haptophyte and cryptophyte algae but constitute a diverse and independent lineage. To resolve the phylogenetic position of the rappemonads the authors designed specific nucleotide primers spanning the 18S-ITS1-5.8S-ITS2-28S rRNA genes and sequenced this gene cluster. The authors used maximum likelihood algorithms to construct a phylogeny, which resolved the rappemonads between the haptophyte and cryptophyte algae. It should be made clear that there is low branch support (at around 50) for some of these clades, so more data is needed for strict resolution of the red plastid algae.
Probes for fluorescent in situ hybridization were developed to observe rappemonads. Rappemonads were described to be relatively large in size – approximately 6 µm in diameter versus the smaller picophytoplankton (2 to 3 µm) – significantly larger than open-ocean phytoplankton. Rappemonads appear to contain two to four plastids and are putatively photosynthetic. Using quantitative PCR methods, the authors identified high concentrations of rappemonads in late-winter blooms along the surface waters at a site in the Sargasso Sea. Rappemonads were rare or absent in stratified summertime conditions, when concentrations of chlorophyll containing microorganisms are at their highest in deep waters. Rappemonads were frequently found in North Pacific anticyclonic eddy samples, which are characterized by colder more nutrient-rich waters that have been brought to the sea surface. When considering water characteristics (such as depth, salinity, phosphate, nitrate, and nitrite), there were no statistical significance between samples containing rappemonads and those where they were absent. In addition, rappemonads were found in both marine and freshwater conditions, bringing into question when and where one may find these organisms and which would warrant further study.
I’m not sure if I am going to be able to make this meeting, but I thought I would pass on the information to you. The list of speakers is excellent and it’s in a beautiful location. This is a biannual meeting on the comparative genomics of Eukaryotic microorganisms sponsored by the European Molecular Biology Organization (EMBO). Registration and meeting information is located here. |
I'm a biologist with broad interests, focused mainly on fungal and plant genomics and understanding how these two diverse groups of organisms interact with each other. I am mainly interested in the mycorrhizal fungal symbiosis, the meta-taxonomic and metagenomic assessment of plant-associated environments, and the dissection of interactions of fungus and plant: from cell-to-cell contact to the modification of gene expression resulting from these communications. I typically use laboratory techniques and field studies addressing more specific questions using controlled experiments. I have increasingly turned to bioinformatic techniques to handle the analysis of genomic data so I spend a lot of time in front of a computer.
You can read more about me and my interests at my website. Please get in touch with me by emailing me at josh...@gmail.com |
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How Many Species Are There On Earth And In The Ocean?
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.
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.
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.
UPDATE: More commentaries in the news can be found here, here, and here.
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