Researchers have developed an improved assembly of the genome for the date palm using long-read sequencing technology. This improvement over the current versions of the genome will help advance further research, and also inform the propagation practices of this essential MENA region food source.
Oaks have a complex evolutionary history that has long eluded scientists. New research, however, provides the most detailed account to date of the evolution of oaks, recovering the 56-million-year history that has made the oaks one of the most diverse, abundant and important woody plant groups to the ecology and economy of the northern hemisphere.
An international team succeeded in assembling the first sequence of the pea genome. This study will, in addition to increasing knowledge of this genome compared to that of other legumes, help to improve traits of interest for peas, such as disease resistance, regularity of yield and nutritional value.
This week’s post was written by Jonathan Ingram, Senior Commissioning Editor / Science Writer for the Journal of Experimental Botany. Jonathan moved from lab research into publishing and communications with the launch of Trends in Plant Science in 1995, then going on to New Phytologist and, in the third sector, Age UK and Mind.
In this week of the XIXth International Botanical Congress (IBC) in Shenzhen, it seems appropriate to highlight outstanding research from labs in China. More than a third of the current issue of Journal of Experimental Botany is devoted to papers from labs across this powerhouse of early 21st century plant science.
Collaborations are key, and this was a theme that came up time again at the congress. The work by Yongzhe Gu et al. is a fine example, involving scientists at four institutions studying a WRKY gene in wild and cultivated soybean: in Beijing, the State Key Laboratory of Systematic and Evolutionary Botany at the Institute of Botany in the Chinese Academy of Sciences, and the University of the Chinese Academy of Sciences; and in Harbin (Heilongjiang), the Crop Tillage and Cultivation Institute at Heilongjiang Academy of Agricultural Sciences, and the College of Agriculture at Northeast Agricultural University. Interest here centers on the changes which led to the increased seed size in cultivated soybean with possible practical application in cultivation and genetic improvement of such a vital crop.
Crops and gardens
Botanic gardens are also part of the picture. In another paper in the same issue, Yang Li et al. from the Key Laboratory of Tropical Plant Resources and Sustainable Use at Xishuangbanna Tropical Botanical Garden in Kunming (Yunnan) and the University of the Chinese Academy of Sciences in Beijing present research on DELLA-interacting proteins in Arabidopsis. Here the authors show that bHLH48 and bHLH60 are transcription factors involved in GA-mediated control of flowering under long-day conditions.
Naturally, research on rice is important. Wei Jiang et al. from the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University (Wuhan) describe their research on WOX11 and the control of crown root development in the nation’s grain of choice, which will be important for breeders looking to increase crop yields and resilience.
The other work featured is either in Arabidopsis or plants of economic importance: Fangfang Zheng et al. (Qingdao Agricultural University, also with collaborators in Maryland) and Xiuli Han et al. (Beijing); Yun-Song Lai et al. (Beijing/Chengdu – cucumber), Wenkong Yao et al. (Yangling, Shaanxi – Chinese grapevine, Vitis pseudoreticulata), and Xiao-Juan Liu et al. (Tai-an, Shandong – apple).
Development of plant science
Shenzehn has grown rapidly and is now highly significant for life science as home to the China National GeneBank (CNGB) project led by BGI Genomics. The vision as set out by Huan-Ming Yang, chairman of BGI-Shenzhen, is profound – from sequencing what’s already here, often in numbers per species, to innovative synthetic biology.
Shenzehn is also home to another significant institution, the beautiful and scientifically important Fairy Lake Botanic Garden. At the IBC, the importance of biodiversity conservation for effective, economically focused plant science, but also for so many other reasons to do with our intimate relationship with plants and continued co-existence on the planet, was a central theme.
The research highlighted in Journal of Experimental Botany is part of the wider, positive growth of plant science (and, indeed, botany) not just in China, but worldwide. The Shenzehn Declaration on Plant Sciences with its seven priorities for strategic action, launched at the congress, will be a guide for the right development in coming years.
Could you begin by telling us a little about your research?
I am a plant physiologist specializing in seed biology. I have a long research record on various aspects of seeds, including the mechanisms and regulation of germination and dormancy, desiccation tolerance, as well as issues in seed technology. Being six years from retirement now, I decided to extend my desiccation tolerance studies from seeds to resurrection plants, which display vegetative desiccation tolerance. I strongly believe that unveiling of the mechanism of vegetative desiccation tolerance may help us create crops that are truly tolerant to severe drought, rather than (temporarily) resistant.
How did you become interested in this field of study, and how has your career progressed?
As with many things in life, it was coincidence. I majored in plant biochemistry and applied for a PhD position in seed biology. After obtaining the degree I was offered a tenure track position in seed physiology by the Laboratory of Plant Physiology at Wageningen University, where I still work as a faculty member. My career has progressed nicely and I am an authority in the field of seed science, editor-in-chief of the journal Seed Science Research, and will become the President of the International Society for Seed Science in September of this year.
I see my current work on vegetative desiccation tolerance as a highlight in my professional life. I have always been more interested in the desiccation tolerance of seeds until about five years ago, when my current collaborator Prof Jill Farrant of the University of Cape Town, South-Africa, made me enthusiastic about these wonderful resurrection plants. We started to work together and published our first study recently in Nature Plants.
Read the paper here ($): A footprint of desiccation tolerance in the genome of Xerophyta viscosa.
In your recent paper, you sequenced the genome of the resurrection plant, Xerophyta viscosa, which can survive with less than a 5% relative water content. How is it possible for a plant to lose so much of its water and still survive?
These plants have a lot of characteristics that we’ve seen in seeds. They display protective desiccation tolerance mechanisms in their leaves, including anti-oxidants, protective proteins, and even dismantle their photosynthetic machinery during periods of drought. Even the cell wall structure and composition of resurrection plants resemble those of seeds. We are currently working on a paper describing the striking similarities between seeds and resurrection plants.
What was the most interesting discovery you made upon sequencing the genome of the resurrection plant?
First, the similarities between resurrection plants and seeds listed above were also apparent at the molecular level. For example, previous work suggested that the “ABI3 regulon”, consisting of about 100 genes regulated by the transcription factor ABI3, is specific to seeds, but we found that it is almost completely present (and active) in the leaves of Xerophyta viscosa too!
Secondly, we found “islands” or clusters of genes specific for desiccation tolerance that aren’t found in other species. Many of these regulate secondary metabolite pathways.
How challenging was it to sequence the genome of this plant? How did you overcome any difficulties?
It was very challenging. First, the species is an octoploid, meaning it has eight copies of each chromosome. This meant that we had to sequence its genome at very high coverage and employing the most advanced sequencing facilities, e.g. PacBio. Getting funding for this complex analysis was another challenge. We then took almost a year to assemble the genome and annotate it at the desired quality.
You identified some of the most important genes involved in desiccation tolerance. Is it possible to translate this work into other species, such as crops that may be threatened by drought as the climate changes?
That will be our ultimate goal. It’s important to remember that desiccation-sensitive plants, including all our major crops, produce seeds that are desiccation tolerant. This implies that the information for desiccation tolerance is present in the genomes of these crops but that it is only turned on in the seeds. We are trying to determine how this is localized, in order to find a method to turn on the desiccation tolerance mechanism in vegetative parts of the (crop) plant too. In parallel we are expressing some of the key transcription factors from Xerophyta viscosa in some important crops to see how this affects them.
Are there any other interesting aspects of Xerophyta viscosa biology?
Contrary to plants that wilt and ultimately die because of (severe) drought, leaves of resurrection species do not show such stress-related senescence. This is related to the engagement of active anti-senescence genes during the drying of the leaves of resurrection species. We are currently investigating these senescence-related mechanisms too.
Do you expect to find that different types of desiccation-tolerant plants use the same subset of genes to survive drought, or could they have developed other pathways to resilience?
We expect that the core mechanism is very similar among the resurrection species but that each species may have adapted to its specific environment.
Funding permitting, we will sequence the genomes of at least another ten resurrection species to further clarify the various evolutionary pathways to desiccation tolerance and, importantly, to discriminate between species-specific and desiccation tolerance-specific genes.
What advice do you have for early career researchers?
Stick to what you believe in, even if you have to (temporarily) be involved in research that you appreciate less, e.g., because of better funding opportunities.
Read Henk’s recent paper in Nature Plants here ($): A footprint of desiccation tolerance in the genome of Xerophyta viscosa.
This week’s post comes to us from Crystal Chan, project manager of the Application of Genomic Innovation in the Lentil Economy project led by Dr. Kirstin Bett at the Department of Plant Sciences, University of Saskatchewan.
Could you begin with a brief introduction to your research?
Our research focuses on the smart use of diverse genetic materials and wild relatives in the lentil (Lens culinaris) breeding program.
Canada has become the world’s largest producer and exporter of lentils in recent years. Lentils are an introduced species to the northern hemisphere and, until recently, our breeding program at the University of Saskatchewan involved just a handful of germplasms adapted to our climatic condition. With dedicated breeding efforts we have achieved noteworthy genetic gains in the past decade, but we are missing out on the vast genetic diversity available within the Lens genus. This is a major dilemma faced by all plant breeders: do we want consistency (sacrificing genetic diversity and reducing genetic gains over time) or diversity (sacrificing some important fixed traits and spending lots of time and resources in “backcrossing/rescue efforts”)?
In our current research, we use genomic tools to understand the genetic variability found in different lentil genotypes and the basis of what makes lentils grow well in different global environments (North America vs. Mediterranean countries vs. South Asian countries). We will then develop molecular breeding tools that breeders can use to improve the diversity and productivity of Canadian lentils while maintaining their adaptation to the northern temperate climate.
What first led you to this research topic?
Dr. Albert (Bert) Vandenberg, professor and lentil breeder at the University of Saskatchewan, noticed one of the wild lentil species was resistant to several diseases that devastate the cultivated lentil. After years of dedicated breeding effort, he was able to transfer the resistance traits to the cultivated lentil, but it took a lot of time and resources. We began looking into other beneficial traits and became fascinated with the domestication and adaptation aspects of lentil – after all lentil is one of the oldest cultivated crops, domesticated by man around 11,000 BC! With the rapid advance in genomic technology, we can start to better understand the biology and develop tools to harness these valuable genetic resources.
You have been involved in the development of tools that assist researchers to build databases of genomics and genetics data. Could you tell us more about projects such as Tripal?
Over the past six years, Lacey Sanderson (bioinformaticist in our group) has developed a database for our pulse research program at the University (Knowpulse, http://knowpulse.usask.ca/portal/). The database is specifically designed to present data that is relevant to breeders, as our group has a strong focus on variety development for the Canadian pulse crop industry. Knowpulse houses genotypic information from past and on-going lentil genomics projects, and includes tools for looking up genotypes as well as comparing the current genome assembly (currently v1.2) and other sequenced legume genomes. The tools are being developed in Tripal, an open-source toolkit that provides an interface between the data and a Drupal web content management system, in collaboration with colleagues at Washington State University.
At the moment we are developing new functionalities that will allow us to store and present germplasm information as well as phenotypic data. We are also working with our colleagues at Washington State University (under the “Tripal Gateway Project” funded by the National Science Foundation) to enhance interconnectivity between Knowpulse and other legume databases, such as the Legume Information Service (LIS) and Soybase, to facilitate comparative genomic studies.
How challenging are pulse genomes to assemble? How closely related are the various crops?
We had the fortune to lead the lentil genome sequencing initiative thanks to the support from producer groups and governments across the globe. The lentil genome is really challenging to assemble! We see nice synteny between lentil and the model legume, medicago, however the lentil genome is much bigger. We see a significant increase in genome size between chickpea and beans versus lentil (and pea for that matter), yet we have evidence to show that genome duplication is not the cause of the size increase. There are a lot of very long repetitive elements sprinkled around the genome, which makes its sequencing and proper assembly very challenging. Not to mention understanding the role of these long repetitive elements in biological functions…
What insights into crop domestication have you gained from these genomes?
That’s what we are working on right now under the AGILE (“Application of Genomics to Innovation in the Lentil Economy”) project. Stay tuned!
Do you work with breeders to develop new cultivars? What sorts of traits are most important?
Breeding is at the core of our work – both Kirstin and Bert are breeders (Kirstin has an active dry bean breeding program when she’s not busy with genomic research). All our research aims to feed information to the breeders so that they can make better crossing and selection decisions. Our work in herbicide tolerance has led to the development and implementation of a molecular marker to screen for herbicide resistance. With that marker we save time (skipping a crossing cycle) and forego the herbicide spraying test for all of our early materials.
Disease resistance and drought tolerance are also important for the growers. Visual quality (seed shape, size, color) are very important too as our customers are very picky as to what sort of lentils they like to buy/eat.
What does the future of legume/lentil agriculture hold?
Lentils have been a staple food in many countries for centuries and have been gaining popularity in North America in recent years as people are looking for plant-based protein sources. Lentils are high in fibre, protein, and complex carbohydrates, while low in fat and calories, and have a low glycemic index. They are suitable for vegetarian/vegan, gluten-free, diabetic, and heart-smart diets. Lentils also provide essential micronutrients such as iron, zinc and folates. Lentils are widely recognized as nutrient-dense food that could serve as part of the solution to combat global food and nutritional insecurity.
In modern agriculture, adding lentil or other leguminous crops in the crop rotation helps improve soil structure, soil quality, and biotic diversity, as well as enhancing soil fertility through their ability to fix nitrogen. Because pulse crops require little to no nitrogen fertilizer, they use half of the non-renewable energy inputs of other crops, reducing greenhouse gas emissions.
Follow us on twitter (@Wildlentils) for research updates!
All images are credited to Mr Derek Wright.
Another fantastic year of discovery is over – read on for our 2016 plant science top picks!
The year began with the publication of the fascinating eelgrass (Zostera marina) genome by an international team of researchers. This marine monocot descended from land-dwelling ancestors, but went through a dramatic adaptation to life in the ocean, in what the lead author Professor Jeanine Olsen described as, “arguably the most extreme adaptation a terrestrial… species can undergo”.
One of the most interesting revelations was that eelgrass cannot make stomatal pores because it has completely lost the genes responsible for regulating their development. It also ditched genes involved in perceiving UV light, which does not penetrate well through its deep water habitat.
Read the paper in Nature: The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.
BLOG: You can find out more about the secrets of seagrass in our blog post.
Plants are known to form new organs throughout their lifecycle, but it was not previously clear how they organized their cell development to form the right shapes. In February, researchers in Germany used an exciting new type of high-resolution fluorescence microscope to observe every individual cell in a developing lateral root, following the complex arrangement of their cell division over time.
Using this new four-dimensional cell lineage map of lateral root development in combination with computer modelling, the team revealed that, while the contribution of each cell is not pre-determined, the cells self-organize to regulate the overall development of the root in a predictable manner.
Watch the mesmerizing cell division in lateral root development in the video below, which accompanied the paper:
Read the paper in Current Biology: Rules and self-organizing properties of post-embryonic plant organ cell division patterns.
In March, a Spanish team of researchers revealed how the anti-wilting molecular machinery involved in preserving cell turgor assembles in response to drought. They found that a family of small proteins, the CARs, act in clusters to guide proteins to the cell membrane, in what author Dr. Pedro Luis Rodriguez described as “a kind of landing strip, acting as molecular antennas that call out to other proteins as and when necessary to orchestrate the required cellular response”.
Read the paper in PNAS: Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling.
In April, we received an amazing insight into the ‘decision-making ability’ of plants when a Swiss team discovered that plants can punish mutualist fungi that try to cheat them. In a clever experiment, the researchers provided a plant with two mutualistic partners; a ‘generous’ fungus that provides the plant with a lot of phosphates in return for carbohydrates, and a ‘meaner’ fungus that attempts to reduce the amount of phosphate it ‘pays’. They revealed that the plants can starve the meaner fungus, providing fewer carbohydrates until it pays its phosphate bill.
Author Professor Andres Wiemsken explains: “The plant exploits the competitive situation of the two fungi in a targeted manner, triggering what is essentially a market-based process determined by cost and performance”.
Read the paper in Ecology Letters: Options of partners improve carbon for phosphorus trade in the arbuscular mycorrhizal mutualism.
The transition of ancient plants from water onto land was one of the most important events in our planet’s evolution, but required a massive change in plant biology. Suddenly plants risked drying out, so had to develop new ways to survive drought.
In May, an international team discovered a key gene in moss (Physcomitrella patens) that allows it to tolerate dehydration. This gene, ANR, was an ancient adaptation of an algal gene that allowed the early plants to respond to the drought-signaling hormone ABA. Its evolution is still a mystery, though, as author Dr. Sean Stevenson explains: “What’s interesting is that aquatic algae can’t respond to ABA: the next challenge is to discover how this hormone signaling process arose.”
Read the paper in The Plant Cell: Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE, a regulator of ABA responses unique to basal land plants and required for desiccation tolerance.
Sometimes revisiting old ideas can pay off, as a US team revealed in June. In 1930, Ernst Münch hypothesized that transport through the phloem sieve tubes in the plant vascular tissue is driven by pressure gradients, but no-one really knew how this would account for the massive pressure required to move nutrients through something as large as a tree.
Professor Michael Knoblauch and colleagues spent decades devising new methods to investigate pressures and flow within phloem without disrupting the system. He eventually developed a suite of techniques, including a picogauge with the help of his son, Jan, to measure tiny pressure differences in the plants. They found that plants can alter the shape of their phloem vessels to change the pressure within them, allowing them to transport sugars over varying distances, which provided strong support for Münch flow.
Read the paper in eLife: Testing the Münch hypothesis of long distance phloem transport in plants.
In July, an international and highly multidisciplinary team published the genome of 6,000-year-old barley grains excavated from a cave in Israel, the oldest plant genome reconstructed to date. The grains were visually and genetically very similar to modern barley, showing that this crop was domesticated very early on in our agricultural history. With more analysis ongoing, author Dr. Verena Schünemann predicts that “DNA-analysis of archaeological remains of prehistoric plants will provide us with novel insights into the origin, domestication and spread of crop plants”.
Read the paper in Nature Genetics: Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.
Another exciting cereal paper was published in August, when an Australian team revealed that C4 photosynthesis occurs in wheat seeds. Like many important crops, wheat leaves perform C3 photosynthesis, which is a less efficient process, so many researchers are attempting to engineer the complex C4 photosynthesis pathway into C3 crops.
This discovery was completely unexpected, as throughout its evolution wheat has been a C3 plant. Author Professor Robert Henry suggested: “One theory is that as [atmospheric] carbon dioxide began to decline, [wheat’s] seeds evolved a C4 pathway to capture more sunlight to convert to energy.”
Read the paper in Scientific Reports: New evidence for grain specific C4 photosynthesis in wheat.
September marked an historic event. Professor Stefan Jansson cooked up the world’s first CRISPR meal, tagliatelle with CRISPRy fried vegetables (genome-edited cabbage). Jansson has paved the way for CRISPR in Europe; while the EU is yet to make a decision about how CRISPR-edited plants will be regulated, Jansson successfully convinced the Swedish Board of Agriculture to rule that plants edited in a manner that could have been achieved by traditional breeding (i.e. the deletion or minor mutation of a gene, but not the insertion of a gene from another species) cannot be treated as a GMO.
Read more in the Umeå University press release: Umeå researcher served a world first (?) CRISPR meal.
*You may also be interested in the upcoming meeting, ‘New Breeding Technologies in the Plant Sciences’, which will be held at the University of Gothenburg, Sweden, on 7-8 July 2017. The workshop has been organized by Professor Jansson, along with the GPC’s Executive Director Ruth Bastow and Professor Barry Pogson (Australian National University/GPC Chair). For more info, click here.*
Phytochromes help plants detect day length by sensing differences in red and far-red light, but a UK-Germany research collaboration revealed that these receptors switch roles at night to become thermometers, helping plants to respond to seasonal changes in temperature.
Dr Philip Wigge explains: “Just as mercury rises in a thermometer, the rate at which phytochromes revert to their inactive state during the night is a direct measure of temperature. The lower the temperature, the slower phytochromes revert to inactivity, so the molecules spend more time in their active, growth-suppressing state. This is why plants are slower to grow in winter”.
Read the paper in Science: Phytochromes function as thermosensors in Arabidopsis.
In November, a Chinese team published the genome of Ginkgo biloba¸ the oldest extant tree species. Its large (10.6 Gb) genome has previously impeded our understanding of this living fossil, but researchers will now be able to investigate its ~42,000 genes to understand its interesting characteristics, such as resistance to stress and dioecious reproduction, and how it remained almost unchanged in the 270 million years it has existed.
Author Professor Yunpeng Zhao said, “Such a genome fills a major phylogenetic gap of land plants, and provides key genetic resources to address evolutionary questions [such as the] phylogenetic relationships of gymnosperm lineages, [and the] evolution of genome and genes in land plants”.
Read the paper in GigaScience: Draft genome of the living fossil Ginkgo biloba.
The year ended with another fascinating discovery from a Danish team, who used fluorescent tags and microscopy to confirm the existence of metabolons, clusters of metabolic enzymes that have never been detected in cells before. These metabolons can assemble rapidly in response to a stimulus, working as a metabolic production line to efficiently produce the required compounds. Scientists have been looking for metabolons for 40 years, and this discovery could be crucial for improving our ability to harness the production power of plants.
Read the paper in Science: Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum.
Another amazing year of science! We’re looking forward to seeing what 2017 will bring!
P.S. Check out 2015 Plant Science Round Up to see last year’s top picks!
The 1000 plants initiative (1KP) is a multidisciplinary consortium aiming to generate large-scale gene sequencing data for over 1000 species of plants. Included in these species are those of interest to agriculture and medicines, as well as green algae, extremophytes and non-flowering plants. The project is funded by several supporters, and has already generated many published papers.
Gane Wong is a Professor in the Faculty of Science at the University of Alberta in Canada. Having previously worked on the Human Genome Project, he now leads the 1KP initiative. Dennis Stevenson, Vice President for Botanical Research, New York Botanical Garden, and Adjunct Professor, Cornell University (USA), studies the evolution and classification of the Cycadales. He became involved in the 1KP initiative as an opportunity to sample the breadth of green plant diversity.
We spoke to both Professor Stevenson (DS) and Professor Wong (GW) about the initiative. Professor Douglas Soltis from Florida Museum of Natural History also contributed to this blog post with input in editing the answers.
What do you think has been the biggest benefit of 1KP?
DS: This has been an unparalleled opportunity to reveal and understand the genes that have led to the plant diversity we see around us. We were able to study plants that were pivotal in terms of plant evolution but which have not previously been included in sequencing projects as they are not considered important economically
GW: The project was funded by the Government of Alberta and the investment firm Musea Ventures to raise the profile of the University of Alberta. Notably there was no requirement by the funders to sequence any particular species. I was able to ask the plant science community what the best possible use of these resources would be. The community was in full agreement that the money should be used to sample plant diversity.
Hopefully our work will change the thinking at the funding agencies regarding the value of sequencing biodiversity.
What techniques were utilized in this project to carry out the research?
GW: Complete genomes were too expensive to sequence. Many plants have unusually large genomes and de novo assembly of a polyploid genome remains difficult. To overcome this problem, we sequenced transcriptomes. However, this made our sample collection more difficult as the tissue had to be fresh. In addition, when we started the project, the software to assemble de novo transcriptomes did not work particularly well. I simply made a bet that these problems would be solved by the time we collected the samples and extracted the RNA. For the most part that’s what happened, although we did end up developing our own assembly software as well!
The 1KP initiative is an international consortium. How has the group evolved over time and what benefits have you seen from having this diverse set of skills?
GW: 1KP would not be where it is today without the participation of scientists around the world from many different backgrounds. For example, plant systematists who defined species of interest and provided the tissue samples worked alongside bioinformaticians who analyzed the data, and gene family experts who are now publishing fascinating stories about particular genes.
DS: One of the great things about this project is how it has evolved over time as new researchers became involved. There is no restriction on who can take part, which species can be studied or which questions can be asked of the data. This makes the 1KP initiative unique compared to more traditionally funded projects.
GW: We continually encouraged others to get involved and mine our data for interesting information. We did a lot of this through word of mouth and ended up with some highly interesting, unexpected discoveries. For example, an optogenetics group at MIT and Harvard used our data to develop new tools for mammalian neurosciences. This really highlights the importance of not restricting the species we study to those of known economic importance.
You aimed to investigate a highly diverse array of plants. How many plants of the major phylogenetic groups have now been sequenced, and are you still working on expanding the data set?
DS: A lot of thought went into the species selection. We aimed for proportional representation (by number of species) of the major plant groups. We also aimed to represent the morphological diversity of those groups.
GW: Altogether, we generated 1345 transcriptomes from 1174 plant species.
Has this project lead to any breakthroughs in our understanding of the phylogeny of plants?
DS: This will be the first broad look at what the nuclear genome has to tell us, and the first meaningful comparison of large nuclear and plastid data sets. However, due to rapid evolution plus extinction, many parts of the plant evolutionary tree remain extremely difficult to solve.
One significant breakthrough was the discovery of horizontal gene transfer from a hornwort to a group of ferns. This was unexpected and very interesting in terms of the ability of those ferns to be able to accommodate understory habitats.
GW: With regard to horizontal gene transfer, there are papers in the pipeline that will illustrate the discovery of even more of these events in other species. We have also studied gene duplications at the whole genome and gene family level. This is the most comprehensive survey ever undertaken, and people will be surprised at the scale of the discoveries. However, we will be releasing our findings shortly as part of a series and it would be unwise for us to give the story away here! Keep a look out for these!
Do you have a genome sequencer in your pocket or are you just happy to see me?
By Nikolai Adamski
On September 4 I attended an event sponsored by Oxford Nanopore Technologies (ONT) at Norwich Research Park, UK, which focused on nanopore technologies. This new technology has been dubbed ‘Next, next-generation sequencing’, and could have really exciting implications for the future of genome sequencing.
ONT has developed a pocked-sized genome sequencing device called the MinION that can sequence genomes in real time. Thanks to recent pop culture this generates visions of cuddly yellow creatures with an overly developed desire to serve super-villains. However, a MinION is actually a new genome sequencing device. To help confused readers, the figure below should help clarify the issue once and for all (Figure 1).
The striking thing about the MinION is its size. Sequencing machines these days vary in size from something that sits on a desktop, to something that fills half a student’s room. The MinION however, fits in the palm of your hand. This is possible thanks to highly miniaturized electronics.
So how does it work?
At the core of the MinION are two biological components: the nanopore protein, which gives the company its name, and a motor protein. The nanopore protein sits on top of an artificial layer and acts a microscopic sluice gate that controls how much of the sample solution passes through it into the lower layer. The sample solution contains DNA, but also ions that pass through the nanopore, thus creating a measurable electrical current. If a big molecule like a strand of DNA passes through the nanopore, the flow of ions is perturbed, which results in a change in the electrical current. These changes are recorded and interpreted to give the sequence of said DNA molecule.
Meanwhile, the motor protein sticks to a DNA molecule, attaches itself to the top of the nanopore, and feeds the DNA through the nanopore as a single strand at a certain speed. This process is similar to a ratchet. Each MinION device has thousands of nanopores allowing for as many molecules to pass through and be sequenced in real time. This is nicely illustrated in a video made by ONT, which you can see here which is well worth a watch!
The sequence data are sent to a cloud server in real time, where they are transformed and analyzed and the final data sent back to the user. This eliminates the need for an expensive computer infrastructure as well as the need for extensive training in bioinformatics.
Limitations of the technology
So far so good, but there are still some issues with the MinION system. One of these is the average length of the DNA molecules that can be sequenced. In theory, the MinION system is able to sequence DNA molecules of any length, although the data from users at last week’s event suggests that, at the moment, the average length of sequence obtained is around 6,000 base pairs (bp). This is still a great value, but there is room for improvement. Another issue is the amount of data generated by a single MinION run, which according to user experience is generally around 1Gb, approximately 200 times the size of the gut bacterium E. coli. Both of these issues can be easily remedied by running several MinION sequencers with the same sample.
A larger problem is the matter of sequencing accuracy, which is now somewhere around 90%, although it can be as low as 75%. This can in part be compensated for by the sheer amount of data generated. However, it would require a lot of sequencing to make up for these mistakes, and is a critical point that needs to be addressed by ONT in the future.
The MinION system has been and is being used worldwide for a number of different applications. Scientists and medical doctors have used the MinION to monitor strains of the Ebola virus in different patients. Thanks to the real time sequencing data and cloud-based data analysis, patients could be screened within a few days as opposed to weeks. Another interesting example of the usefulness of the MinION system was when scientists travelled to the Tanzanian jungle to assess the biodiversity of frogs in the region.
There are many more fascinating applications for the MinION sequencer. Scientists who are interested can join the MinION Access Programme (MAP) to become part of the research and development community.
I very much enjoyed the ONT event and I am hopeful and curious about what the next few years will bring in terms of innovation and development.
About the Author:
Nikolai Adamski is a postdoctoral scientist working at the John Innes Centre in Norwich, UK, in the group of Cristobal Uauy. He studies yield and yield-related traits in wheat, trying to identify the underlying genes to understand the control and regulation of these traits.
You can follow him on Twitter @NikolaiAdamski
Peng Jiang and Hui Guo at the University of Georgia think you can! They are currently raising money via a crowdfunding approach to sequence the first cactus genome – but the question is: why would they want to? Peng explains all in this guest blog post.
A Prickly Proposal: Why Sequence the Cactus?
In these times of growing food insecurity due to climate change and population pressures, the prickly pear cactus (Opuntia ficus) has growing commercial and agricultural importance across much of the world – you will find it growing in Mexico and Brazil, Chile, large parts of India and South Africa, and in Spain and Morocco.
The goal of our proposal is to sequence the genome and transcriptome of the prickly pear cactus, a recognized food and forage crop in these challenging semiarid regions of the world.
With more than 130 genera and 1,500 species of Cactaceae, we will create a draft genomic and transcriptome database that would aid the understanding of this understudied plant family, and provide the research community with valuable resources for molecular breeding and genetic manipulation purposes. Here are some of the reasons why we think a first cactus genome would be so important:
1. Ecological Improvement
The beauty of the drought-tolerance cactus is that it can grow on desert-like wastelands. Nowadays, more than 35% of the earth’s surface is arid or semiarid, making it inadequate for most agricultural uses. Without efforts to curb global warming, “Thermageddon” may hit in 30–40 years time, causing desertification of the US, such that it may become like the Sahara. Opuntia helps create a vegetative cover, which improves soil regeneration and rainfall infiltration into the soil. This cactus genome research may help us to adapt our food crops to a much hotter, drier climate.
2. Food Crops, Feed and Medicine
The fruits of prickly pear cactus are edible and sold in stores under the name “tuna”. Prickly pear nectar is made with the juice and pulp of the fruits. The pads of prickly pears (“Nopalito”) are also eaten as a vegetable. Both the fruits and pads of prickly pears can help keep blood sugar levels stable because they contain rich, soluble fibers. The fruit contains vitamin C and was used as an early cure for scurvy.
Furthermore, there has been much medical interest in the prickly pear plant. Studies [1, 2, 3] have shown that the pectin contained in prickly pear pulp lowers cholesterol levels. Another study  found that the fibrous pectin in the fruit may lower a diabetic’s need for insulin. The plant also contains the antioxidant flavonoids quercetin, (+)-dihydroquercetin (taxifolin), quercetin 3-methyl ether (isorhamnetin) and kaempferol, which have a protective function against the DNA damage that leads to cancer.
3. Biofuels in Semiarid Regions
Planting low water use, Crassulacean acid metabolism (CAM; a water saving mode of photosynthesis) biofuel feedstocks on arid and semiarid lands could offer immediate and sustained biogas advantages. Opuntiapads have 8–12% dry matter, which is ideal for anaerobic digestion. With an arid climate, this prevents the need for extra irrigation or water to facilitate the anaerobic digestion process. Requiring only 300 mm of precipitation per year, Opuntiacan produce a large amount of dry matter feedstock and still retain enough moisture to facilitate biogas production. It’s possible to get as much as 2.5 kWh of methane from 1 kg of dry Opuntia.
4. Phylogenetic Importance
Trained botanists and amateurs alike have held cacti in high regard for centuries. The copious production of spines, lack of leaves, bizarre architecture and impressive ability to persist in the harshest environments on Earth are all traits that have entitled this lineage to be named a true wonder of the plant world.
The cacti are one of the most celebrated radiations of succulent plants. There has been much speculation about their age, but progress in dating cactus origins has been hindered by the lack of fossil data for cacti or their close relatives. Through whole genome sequencing, we help will reveal the genomic evolution of Opuntia by comparing this genome with that of other sequenced plant species.
Cacti are typical CAM plants. We will analyse the evolution of CAM genes in the cactus to help reveal the secret of drought tolerance. Furthermore, plant architecture genes and MADS-box gene family members will be analysed to reveal the specific architecture and structure of cactus.
Crowdfunding the Cactus Genome Project
Cactus has several fascinating aspects that are worth exploring, not just for its biology, but also its relevance to humanity and the global environment. We plan to generate a draft genome for Opuntia, and have launched a crowdfunding campaign to help fund this project – we have already raised $2300 USD (46% of what we need), but we only have 15 days to raise the rest. If you would like to help fund this project, please visit our Experiment page at: https://experiment.com/projects/sequencing-the-cactus-genome-to-discover-the-secret-of-drought-resistance.
If we are successful in raising enough money to initiate the Cactus Genome Project, not only will this be the first plant genome to be sequenced in the Cactaceae family, we will be releasing the results to the plant science community through GeneGarden, an ornamental plant genome database. Our citizen science approach is also allowing us to reach out directly to members of the public, creating exciting opportunities for outreach and engagement with plant science.
If you have any further questions, please contact project leader Dr Peng Jiang at email@example.com.
This blog post is slightly adapted from a post originally appearing on GigaScience Journal’s GigaBlog. Reproduced and adapted with permission, under a CC-BY license.
- Wolfram RM, Kritz H, Efthimiou Y, et al. Effect of prickly pear (Opuntia robusta) on glucose- and lipid-metabolism in non-diabetics with hyperlipidemia – a pilot study. Wien Klin Wochenscr. 2002;114(19–20):840–6.
- Trejo-Gonzalez A, Gabriel-Ortiz G, Puebla-Perez AM, et al. A purified extract from prickly pear cactus (Opuntia fulignosa) controls experimentally induced diabetes in rats. J Ethnopharmacol. 1996;55(1):27–33.
- Fernandez ML, Lin EC, Trejo A, et al. Prickly pear (Opuntia sp.) pectin alters hepatic cholesterol metabolism without affecting cholesterol absorption in guinea pigs fed a hypercholesterolemic diet. J Nutr. 1994;124(6):817–24.
- Frati-Munari AC, Gordillo BE, Altamirano P, et al. Hypoglycemic effect of Opuntia streptacantha Lemaire in NIDDM. Diabetes Care. 1988:11(1):63–66.