Harry Brumer

The delicate stalk and pretty white flowers of Triantha occidentalis may seem like the perfect place to perch if you’re an insect, but get trapped in its sticky hairs and it will suck the nutrients from your dead corpse.

That’s the surprising new finding by University of British Columbia and University of Wisconsin-Madison researchers, detailed in PNAS.

Triantha – a species of false asphodel – is the first new carnivorous plant to be identified by botanists in 20 years. It is notable for the unusual way it traps prey with sticky hairs on its flowering stem.

“Carnivorous plants have fascinated people since the Victorian era because they turn the usual order of things on its head: this is a plant eating animals,” said co-author Dr. Sean Graham, a professor in the department of botany at UBC. “We’re thrilled to have identified one growing right here in our own backyard on the west coast.”

The plant grows in nutrient-poor, boggy but bright areas on the west coast of North America, from California to Alaska. For the study, the researchers investigated specimens growing on Cypress Mountain in North Vancouver, British Columbia.

“What’s particularly unique about this carnivorous plant is that it traps insects near its insect-pollinated flowers,” said lead author Dr. Qianshi Lin, a PhD student at UBC botany at the time of the study. “On the surface, this seems like a conflict between carnivory and pollination because you don’t want to kill the insects that are helping you reproduce.”

“We believe that Triantha is able to balance carnivory with pollination because its glandular hairs are not very sticky and can only trap midges and other small insects, so that the much larger and stronger bees and butterflies that act as its pollinators are not captured,” said co-author Dr. Tom Givnish, a professor in the department of botany at the University of Wisconsin-Madison.

The research builds on previous work in Dr. Graham’s lab, which found that Triantha lacked a particular gene that is often missing in other carnivorous plants.

In order to investigate if the plant was indeed partial to snacking on insects, Dr. Lin attached fruit flies labelled with nitrogen-15 isotopes to its flowering stem. The label acted like a tracking device, allowing Dr. Lin to trace changes in nitrogen uptake by the plant.The research builds on previous work in Dr. Graham’s lab, which found that Triantha lacked a particular gene that is often missing in other carnivorous plants.

He then compared the results with those from similar experiments on other species that grow in the same area, including a recognized carnivorous plant (a sundew) and several non-carnivorous plants as controls.

Isotopic analysis showed significant uptake of nitrogen by Triantha, which obtained more than half its nitrogen from prey –comparable to sundews in the same habitat, and other carnivorous plants elsewhere.

The study also found that the sticky hairs on the Triantha flower stalk produce phosphatase, a digestive enzyme used by many carnivorous plants to obtain phosphorous from prey.

The proximity of Triantha to major urban centres in western Canada and the Pacific coast in the United States suggests that other carnivorous plants – and many other ecological surprises – remain to be discovered, even in well-studied ecosystems.

But if you’re tempted to recreate the film, Little Shop of Horrors, or bring Triantha home to deal with pesky summer fruit flies, the researchers warn the plant doesn’t do well outside of its natural environment and advise admiring its quirks from a distance.

Figure 1: Flower of Triantha occidentalis in a bog at Cypress Provincial Park, British Columbia. Photo: Danilo Lima.

Figure 2: Triantha occidentalis traps insects. Photo: Dr. Qianshi Lin

Figure 3: The bog at Cypress Provincial Park. Photo: Dr. Qianshi Lin

Figure 4: The first new carnivorous plant identified by botanists in 20 years. Photo: Danilo Lima

Article by: Miranda Meents (Lacey Samuels lab)

2015 is somewhat of an anniversary in cell biology. 350 years ago, Robert Hooke published the first description of what he called a cell. But it wasn’t until the mid-19^th century that we started to look inside cells.  Then, in 1898, the Italian scientist Camillo Golgi first described, and gave his name to, a cell structure that is the hero of this story, the Golgi Apparatus. We now know that the Golgi is a stack of flattened compartments like a stack of pita bread. Inside the pita pockets hundreds of chemical reactions occur as the Golgi makes, modifies and packages materials for the cell.  Every animal, plant, and fungal cell has a Golgi. In plants, the Golgi is where many key components of the plant cell wall are produced. In humans, defects in Golgi structure or function have been associated with Alzheimer’s and Parkinson’s disease, as well as a growing list of less well-known disorders including neurological, skeletal, developmental, muscular, and more.  But, despite close to 120 years of research, we still don’t really understand the basic mechanism behind Golgi function, and this is the question that my research is helping to address.

If we cut through the middle of the Golgi, in each pocket we would see a mix of what we call residents and cargo. The residents live in the Golgi; they are the workers that make and modify the cargo. The cargo is what is being modified and packaged before it leaves the Golgi to move somewhere else in the cell. It might help to think of the Golgi as a  can of mixed nuts. Some of the nuts are like Golgi cargo, say pecans, and we need to quickly pull them out so they can get to where they need to go. Other nuts are like residents, cashews for example. To carry out their function they have to stay in the mix. But how do we quickly and efficiently remove the pecans while leaving the cashews behind? This question has been extremely difficult to answer because the Golgi is very small, very active, and very efficient. The system I am using, however, allows me to work around these problems and determine how the Golgi functions.

I am mapping the location of residents and cargo within the Golgi. To do this, I have created fluorescently tagged residents that allow me to label the Golgi in plant cells. I can then find these residents and their cargo within the Golgi in high resolution images taken with an electron microscope. I can then compare the location of the residents and cargo and use the information to build a hypothesis about how the Golgi is able to sort through all of its contents, as well as it does. Ultimately, this research could influence an astonishing breadth of disciplines, from medicine to biofuels to beer, simply because the Golgi is such a key player in how all types of organisms function.

Viruses and bacteria fall back to Earth via dust storms and precipitation. 2011 dust storm in the Sahara.

An astonishing number of viruses are circulating around the Earth’s atmosphere – and falling from it – according to new research from scientists in Canada, Spain and the U.S.

The study marks the first time scientists have quantified the viruses being swept up from the Earth’s surface into the free troposphere, that layer of atmosphere beyond Earth’s weather systems but below the stratosphere where jet airplanes fly. The viruses can be carried thousands of kilometres there before being deposited back onto the Earth’s surface.

“Every day, more than 800 million viruses are deposited per square metre above the planetary boundary layer—that’s 25 viruses for each person in Canada,” said University of British Columbia virologist Curtis Suttle (a professor in the Departments of Botany, EOAS, and Microbiology & Immunology, and the Institute for the Oceans & Fisheries), and one of the senior authors of a paper in the International Society for Microbial Ecology Journal that outlines the findings.

The findings may explain why genetically identical viruses are often found in very different environments around the globe.

“Roughly 20 years ago we began finding genetically similar viruses occurring in very different environments around the globe,” says Suttle. “This preponderance of long-residence viruses travelling the atmosphere likely explains why—it’s quite conceivable to have a virus swept up into the atmosphere on one continent and deposited on another.”

Bacteria and viruses are swept up in the atmosphere in small particles from soil-dust and sea spray.

Suttle and colleagues at the University of Granada and San Diego State University wanted to know how much of that material is carried up above the atmospheric boundary layer above 2,500 to 3,000 metres. At that altitude, particles are subject to long-range transport unlike particles lower in the atmosphere. 

Using platform sites high in Spain’s Sierra Nevada Mountains, the researchers found billions of viruses and tens of millions of bacteria are being deposited per square metre per day. The deposition rates for viruses were nine to 461 times greater than the rates for bacteria.

“Bacteria and viruses are typically deposited back to Earth via rain events and Saharan dust intrusions. However, the rain was less efficient removing viruses from the atmosphere,” said author and microbial ecologist Isabel Reche from the University of Granada.

The researchers also found the majority of the viruses carried signatures indicating they had been swept up into the air from sea spray. The viruses tend to hitch rides on smaller, lighter, organic particles suspended in air and gas, meaning they can stay aloft in the atmosphere longer.

An international team of researchers have completed a massive effort to sequence genes from more than 1,100 plant species—an undertaking that saw UBC botanists collect rare mosses from remote corners of BC, and travel to the South Pacific to collect parasitic plants.

“One of the crucial samples we wanted to include was a parasitic conifer shrub, Parasitaxus, which lives by feeding off fungi and another conifer,” says UBC botanist Sean Graham, who coordinated collection of 300 species for the One Thousand Plant Transcriptomes Initiative (1KP). “Instead of using sunlight to fix energy through photosynthesis, it behaves like a plant vampire.”

It was a particularly challenging sample to collect, says Graham. “Local colleague Adrien Wulff collected it from the field in New Caledonia and we set up an international supply chain to bring our frozen sample from the South Pacific, through the US, and on to Shenzhen, China, where the plant transcriptomes were sequenced. Our vampire plant was a very well-seasoned traveller!”

Our study confirms that the ‘impossible’ moss defines one of the two earliest branches of moss evolution.

Many of key plant species belong to moss families and were found closer to home, including the UBC campus. But collecting British Columbia’s so-called ‘impossible moss’ (Takakia lepidozioides) involved a boat trip and some wading up Jervis Inlet, to reach the southern-most population of this BC moss.

“It seems a bit mad to do an expedition to get this one moss, but it was a key plant to include. Takakia is a kind of living fossil that blends features with other ancient branches of plant life,” says Graham. “Our study confirms that the impossible moss defines one of the two earliest branches of moss evolution.”

The findings, published today in Nature, reveal the timing of whole genome duplications and the origins, expansions and contractions of gene families contributing to fundamental genetic innovations enabling the evolution of green algae, mosses, ferns, conifer trees, flowering plants and all other green plant lineages. The history of how and when plants secured the ability to grow tall, and make seeds, flowers and fruits provides a framework for understanding plant diversity around the planet including annual crops and long-lived forest tree species.

“In the tree of life, everything is interrelated,” said Gane Ka-Shu Wong, lead investigator and professor in the University of Alberta’s Department of Biological Sciences. “And if we want to understand how the tree of life works, we need to examine the relationships between species. That’s where genetic sequencing comes in.”

UBC researchers provided 60 plant samples to the study from across British Columbia, including 30 from UBC Botanical Garden.

“UBC Botanical Garden has fantastic collections of wild plants from around the world, including species from the from southern hemisphere,” says Graham. “This study underscores the importance of maintaining strong research collections around the globe, not only for scientific purposes, but as a way to conserve biodiversity.”

Students also helped out by growing fern species as part of undergraduate labs in the UBC biology program.

“Our inferred relationships among living plant species inform us that over the billion years since an ancestral green algal species split into two separate evolutionary lineages, one including flowering plants, land plants and related algal groups and the other comprising a diverse array of green algae, plant evolution has been punctuated with innovations and periods of rapid diversification,” said James Leebens-Mack, professor of plant biology in the University of Georgia Franklin College of Arts and Sciences and co-corresponding author on the study.

“In order to link what we know about gene and genome evolution to a growing understanding of gene function in flowering plant, moss and algal organisms, we needed to generate new data to better reflect gene diversity among all green plant lineages.”

The study inspired a community effort to gather and sequence diverse plant lineages derived from terrestrial and aquatic habitats on a global scale. Over 100 taxonomic specialists contributed material from field and living collections that from around the world, including Canadian collections from the University of British Columbia Botanical Garden and the University of Alberta. Links to some of the UBC living plants used in the study are posted at the UBC Botanical Garden.

By sequencing and analyzing genes from a broad sampling of plant species, researchers are better able to reconstruct gene content in the ancestors of all crops and model plant species, and gain a more complete picture of the gene and genome duplications that enabled evolutionary innovations.

For most of us, microbes mean only one thing: disease. Disease-causing microbes are actually the extreme minority of the most abundant form of life on Earth. But because of their immediate and direct importance to our health, they are much better studied than the rest of the microbial world. Still, new discoveries about the basic biology and evolution of some of the most infamous pathogens can throw us a curveball.

My lab works on the evolution of apicomplexans, a diverse group of parasites that can only survive by infecting and living inside animal cells. For every animal scientists have studied, there’s an apicomplexan that infects it. A number of common and serious human pathogens, most famously the parasite that causes malaria, Plasmodium, are apicomplexans.

Even after 100 years of work, malaria researchers overlooked one bizarre feature of the parasite, a cellular compartment called a plastid, better known as a chloroplast. The plastid is the part of plant and algal cells where photosynthesis takes place. They’re highly-simplified relicts of photosynthetic bacteria that took up residence in an ancient ancestor of plants and algae. Today, plastids have become genetically integrated with their hosts and are an essential part of plant and algae cells.
 
But how did a parasite like malaria, which lives in the blood of humans, come to possess a plastid? They certainly don’t do photosynthesis, so why do they have plastids? To an evolutionary biologist interested in endosymbiosis — cells living within other cells — it’s a hard question to resist. But it’s also a challenging question to study. Apicomplexan plastids are more than a little weird, and both their genomes and structures are severely simplified from their original form, making them hard to compare to those of plants and algae.

The answer to this question came out of the blue, literally. It was the exploration of coral reefs that provided clues to the origin of apicomplexan plastids. Coral reefs are built thanks to an intimate endosymbiotic relationship between the coral animals and an alga called Symbiodinium. Then Australian researchers discovered some corals contain another symbiont, an apicomplexan whose plastid was still photosynthetic. The discovery took my research in an entirely new direction. The new apicomplexan suggested not only an evolutionary link between the parasites and their photosynthetic ancestors but also to coral, one of the most ancient animal lineages. Perhaps apicomplexans began an association with animals in a different context — as beneficial symbionts instead of parasites.

To follow this lead, however, we had to think beyond the initial evolutionary questions about the origin of the parasites. We had to start to use the tools and methods of environmental microbiology to discover more about the diversity, biology and ecology of apicomplexans in coral. We also moved our experiments from the lab into the field. Luckily these major leaps were not so hard because we were part of a microbial biodiversity network that included experts in coral microbiology. It became the start of a long collaboration with the Caribbean Research and Management of Biodiversity research station. 
 
 In 2013, we packed up our microscopes and scuba gear and flew to one of the southernmost islands of the Caribbean, Curaçao. Thus began the first of four expeditions where we examined the microbes associated with corals, including the enigmatic apicomplexans. 
 
 The leap into environmental research paid off, and the expeditions successfully led to our discovery of a widespread and diverse lineage of apicomplexans living inside corals and related animals like anemones, black corals and sea fans. These new coral-associates are not photosynthetic, but surprisingly they still had the primary pigment that collects light — chlorophyll. It was another unexpected glimpse into the transition from symbiont to parasite.

The environmental research gamble paid even more unanticipated dividends. Taking a group of computer-bound molecular biologists, genomics students and postdocs into the field not only heightened their motivation but put our work into a different context. Most members of my lab are now certified scuba divers. For me, this is one of the more rewarding aspects of the project.

None of us became biologists to sit at a computer and respond to emails, but somewhere in the last 40 years, biology has lost some of the sense of adventure and exploration that made Jacque Cousteau and National Geographic staples of what little TV I watched as a kid. But exploration is the backbone of our work. Even today we know so little about the microbial world that surrounds us that it can be difficult to even know what questions we should be asking.
 
 To ask the right questions, you sometimes have to start by looking around.

https://medium.com/ubcscience/dive-into-the-mysterious-connection-between-malaria-and-coral-reefs-84d8f053813c

Article by George Haughn

The primary plant cell wall of land plants is an essential cellular structure needed for support, cell-cell adhesion, signaling and interaction with both the biotic and abiotic environment. It is composed of a complex, dynamic extracellular matrix consisting of a network of carbohydrate polymers (cellulose, hemicellulose and, pectin) and structural proteins. Wall composition can vary dramatically both throughout the life of individual cells and between different cell types. Such variation is necessary given the need for growth and differences in the function of various cell types. Due to its structural complexity, cell-cell variation and the paucity of analytical tools for complex carbohydrates, scientific progress toward understanding the cell wall has been relatively modest leaving large gaps in our knowledge. We are attempting to fill some of these gaps by using molecular genetics as an approach and the Arabidopsis seed coat as a model system.
The Arabidopsis seed coat has a specialized epidermis containing a large quantity of mucilage between a volcano shaped secondary cell wall and the primary cell wall. Upon exposure to water, the mucilage expands, rupturing the outer primary walls and encapsulating the seed to aid in dispersal, protection and/or hydration (Figure 1).

Figure 1. Arabidopsis seed with extruded mucilage stained with a red pectin specific dye.

Like primary cell walls, seed mucilage is composed of cellulose, hemicellulose, pectin and protein. When extruded, mucilage forms dark-staining rays perpendicular to the seed surface.  The rays are adherent to the seed.  Since mucilage has all the major components of the primary cell wall, is produced by a single cell type, is available in large quantities, has a distinct structure and is not required for seed viability, it is well suited as a genetic model for studying cell wall biogenesis, function and regulation.
Cellulose in extruded mucilage is a component of the ray that extends many cell lengths beyond the surface of the seed (Figure 2).  Using molecular genetics we have investigated its function and how it is made and packaged in the seed coat epidermal cells (Mendu et al., 2011, Plant Physiol. 157: 441–453; Griffiths et al., 2015, Plant Physiol. 168: 502-520). 

Figure 2. Arabidopsis seed with extruded mucilage stained with a red cellulose specific dye.

Mucilage matrix components (pectin, hemicellulose) are made in seed coat epidermal cells and secreted to the apoplast forming a mucilage pocket between the cell membrane and the primary cell wall (Figure 3).

Figure 3. Developing seed coat showing an epidermal cell with volcano shaped cytoplasm and a mucilage pocket (purple) between the cytoplasm and the outer primary cell wall.

Similar to cellulose synthesis in other cell walls, the cellulose in seed mucilage is made by cellulose synthase (CESA) complexes in the membrane. CESA3 and CESA5 are CESA subunit polypeptides that are part of the complex in seed coat epidermal cells and are found in the membrane lining the mucilage pocket (Figure 4).

Figure 4. Seed coat epidermal cell showing fluorescent CESA5 in the membrane around the developing mucilage pocket. 

These complexes move in a linear, unidirectional fashion around the cytoplasmic column of the cell, parallel with the surface of the seed presumably synthesizing cellulose that is coiled around the volcano shaped cytoplasmic column. This cellu-lose appears to unravel as the mucilage extrudes, forming a linear ray (Figure 5).

Figure 5. Diagram showing cellulose and pectin in unextruded and extruded mucilage of a seed coat epidermal cell.

Both the speed of extrusion and the adherence of the mucilage are dependent on this cellulose. The fact that normal pectin is also seems to be required for both processes (Griffiths et al., 2014, Plant Physiology, 165: 991-1004) suggests that these unique properties of mucilage require an interaction between the cellulose and pectin components of mucilage. ​

Article by Katy Hind, Sandra Lindstrom, and Patrick Martone

It is estimated that we have described only 10-20% of species diversity on Earth.  In particular, floristic surveys using modern molecular techniques have revealed that we are vastly underestimating the number of seaweed species.  This finding has implications for researchers using classical methods of identification and is likely complicating studies of ecology and physiology. 

At the Hakai Institute, on Calvert Island along the central coast of British Columbia, Drs. Katy Hind, Sandra Lindstrom, and Patrick Martone are using an integrative approach that combines genetics, ecology, biogeography and historical DNA to accurately assess species diversity. Over the last 5 years, more than 220 species of seaweeds have been documented from this region, from microscopic filaments to large habitat-forming kelps. In particular, they have described over 38 species of calcifying red algae, called coralline algae, which play a key role in the ecology of marine ecosystems and have been used increasingly in studies of climate change, ocean acidification and historical sea ice coverage.  Coralline algae dominate the ocean floor in rocky subtidal habitats and comprise a large portion of the kelp forest understory. 

In a recent study Hind and Martone documented three new coralline algal species from Calvert Island, including one that they named after the Hakai Luxvbalis Conservancy region (Bossiella hakaiensis sp. nov.) where robust and abundant collections of this species were made.  In addition, they confirmed using DNA from collections made over the last 100 years that at least three species in the genus Bossiella are widely distributed from Baja California to Alaska.

Hind and Martone plan to continue their research at the Hakai Institute and focus their efforts on the coralline algae that make up the understory of the kelp forest ecosystems.  Kelp forests are highly productive ecosystems that act as nursery grounds for juvenile fish and food and habitat for many marine species.  The Pacific sea otter, Enhydra lutris, in particularhas strong connections with kelp forest ecosystems as they forage on invertebrates (especially sea urchins) in this habitat.  Where sea otters have been present, they have kept the sea urchin population in check and the kelp forests flourish.  However, where the sea otters are absent (either due to migration or human interactions) the sea urchin populations have exploded and consumed much of the kelp, leaving only a ‘pavement’ of robust coralline algae in their wake.  The species diversity of coralline algae that persist and flourish under such intense herbivory is completely unknown, but may be higher than previously thought. 

Hind and Martone plan to study the relationship between kelp density and coralline algal diversity across a gradient of otter occupation in central British Columbia with sample sites ranging from established kelp forests to urchin ‘barrens’. Their study will uniquely incorporate the use of molecular tools to accurately identify coralline algal species.  This research has broad implications for understanding ecosystem dynamics and for ecologists worldwide who are striving to understand the resilience of coralline-dominated communities.

Figure 1.  Seaweed diversity in a rocky intertidal zone on Calvert Island, Hakai Institute.
Figure 2.  Sandra Lindstrom and helpers conduct a seaweed survey at a long term monitoring site at the Hakai Institute, Calvert Island.
Figure 3.  Calcifying red algae (coralline algae) are very abundant in the rocky intertidal zone on Calvert Island, BC.
Figure 4.  Coralline algae are comprised of species having either upright, usually jointed fronds and prostrate, crustose forms.  Over 38 species of coralline algae have been documented at the Hakai Institute. ​

​Article by Carl Douglas

Do plants have different sexes, meaning distinct male and female individual organisms within a species? The separation of male and female sexual function into different individuals is called “dioecy” and is common in eukaryotes, occurring in 94% of animals. Yes – this occurs in plants but in contrast to animals it is uncommon, occurring in only 6% of flowering plant species.  A recent publication from the research groups of Quentin Cronk, Carl Douglas, and collaborators in the journal Molecular Ecology sheds new light on the evolution of dioecy, with practical spin-offs.

The evolution of dioecy is often accompanied by sex chromosome evolution, and theory suggests that sex-determining loci expand to whole sex chromosomes over time, which are structurally and genetically divergent. For example the mammalian Y chromosome evolved about 170 million years ago and is degenerate (contains very few genes) relative to the non-sex related (autosome) chromosomal pair from which it evolved, and human X and Y sex chromosomes are morphologically distinct and easy to tell apart.

Dioecy is thought to be advantageous by ensuring outcrossing and optimal allocation of reproductive resources, but if so, why is it rare in plants? When present, how and why has it evolved in plants? And, in dioecious plant species, what is the molecular mechanism that tells a male plant to make flowers with only male organs, and a female plant flowers with only female organs? So far, definitive answers to these questions are lacking.

Dioecy has evolved independently in many different flowering plant lineages, and is found in some well-known plants such as papaya, Cannabis, persimmons, asparagus and date palm. In most dioecious plants no discernable sex chromosomes are present, and sex-determining genetic systems are imbedded in areas of reduced recombination in chromosomes that are mostly autosomal (non-sex related).

Populus species (poplars, cottonwoods and aspens) are considered to offer an excellent opportunity to study the evolution of sex chromosomes. Populus and Salix (willows), sister genera in the family Salicaceae, are composed exclusively of dioecious species, suggesting a single origin of dioecy around 65 million years ago when the family arose. Confounding such studies, however, “boy” and “girl” poplar trees are impossible to tell apart (they lack any obvious sexual dimorphism) until they reach sexual maturity and begin to flower at age 5 to 8. Also poplars and willows lack sex chromosomes and the exact location of the poplar sex-determining region, as well the genetic basis for dioecy in this group, has remained unknown. This frustrates poplar breeders who can’t tell which trees they can mate for over 5 years of growth, and makes it difficult to control the sexes of poplar trees planted in plantations (e.g. females can produce huge amounts of undesirable cottony seeds and it may be desirable to restrict their numbers) or to study the mechanism of sex determination on poplars and the suspected ecological and physiological differences between the poplar sexes.

Four postdoctoral fellows/research associates working with Department of Botany professors Quentin Cronk and Carl Douglas, together with a number of other collaborators at UBC (in the Genome Canada/Genome BC-funded POPCAN project) and from other institutions, recently collaborated on major breakthrough study of plant sex in a paper published in Molecular Ecology (Geraldes et al., 2015). Using collections of black cottonwood, or poplar, (Populus trichocarpa) trees grown at UBC’s Totem Field, and of balsam poplar (P. balsamifera) trees grown at the Agriculture and Agri-Food Canada Agroforestry Development Centre, Indian Head SK as their study organisms, Drs. Armando Geraldes and Charles Hefer employed genomic and population genetic approaches to pinpoint the genetic position that determines sex in these tree species. Drs. Armando Geraldes and Arnaud Capron used this information to devise a simple but elegant DNA-based assay to accurately determine the sex of any tree of these and related species before they are old enough to flower, or during most of the year when they are not flowering. Dr. Natalia Kolosova coordinated the isolation of over a hundred poplar DNA samples that went into the analyses.

The new information from the UBC Department of Botany team locates the poplar sex-determining region to a single small genetic locus, near its previously suspected chromosomal position. This was accomplished by comparing the full genome sequences of 68 poplar individuals, generated by the POPCAN project, that had started to flower, and by identifying genetic differences in these genomes (Single Nucleotide Polymorphisms, SNPs) that strictly correlated with sex in the same trees. This work shows definitely that, like mammals, poplars use an XY system to determine sex (females are XX, males are XY), and that the region displays a hallmark of sex-determining loci: strongly suppressed recombination (to maintain the integrity of X and Y regions of homologous chromosome pairs that would otherwise be broken up by recombination over multiple generations). There were several surprises in the work – one being the apparent very small size of the poplar sex locus (about 100,000 DNA base pairs, comprising only 13 genes). This is very much smaller than predicted, since theory suggests that over evolutionary time, such loci should expand, eventually to encompass whole chromosomes – and poplars have had plenty of time. Surprisingly, the age of the poplar sex locus was dated at about 6 million years based on the molecular clock, much younger than the presumed origin of dioecy in the Salicaceae (65 million years), indicating either it must have either independently ‘arisen’ several times, or that it has undergone rapid evolution, or “turnover” as documented in many animals. Consistent with both possibilities, while the sex locus is conserved in other poplars and cottonwoods (eastern cottonwood from North America and black poplar from Europe), it is distinct from the sex determining loci recently described for aspen and a willow species, which are also in the Salicaceae.

These mysteries, and the questions of which gene or genes in the poplar sex-determining locus could specify sex after a 5 to 8 year juvenile period and how different combinations of X and Y alleles of this gene(s) in the sex locus lead to development of distinct male or female flowers, will be the subject of future research. In the meantime, researchers can now determine the sex of any poplar tree of any age from which a small amount of DNA can be isolated (e.g., from a small leaf sample – analogous to a human blood sample), opening the door to commercial applications and to new studies on the ecology and biology of sex in wild populations of poplar trees.

This article is featured as a ‘From the Cover’ paper, a Molecular Ecology section that contains papers of exceptional interest to a wide audience that address significant questions in ecology, evolution, behaviour or conservation. 
http://onlinelibrary.wiley.com/doi/10.1111/mec.13126/epdf

Figure 1: UBC Totem Field black cottonwood trial, April 2014 – a mixture of male and female individuals used in the study of Geraldes et al. (2015). Photo, Carl Douglas

Figure 2: Poplar male inflorescence (catkin). Photo courtesy of Raju Soolanayakanahally ​

Article by Bill Harrower, Jenny McCune, and Jeannette Whitton

National level endangered species laws are designed to prevent species from going extinct. Canada’s endangered species law, the Species At Risk Act (or SARA), was enacted almost 13 years ago¹. Associate Professor Jeannette Whitton led a group of 14 students and researchers from the UBC Botany Department, the UBC Department of Zoology, Simon Fraser University and the Beaty Biodiversity Museum has worked to understand what threatens species at risk in Canada, and how recovery planning is proceeding for these species.

Once a species is listed, SARA outlines a specific process with mandated timelines. Recovery strategies are to be finalized within one to two years of a species being listed under the law, depending on whether a species is listed as threatened or endangered. Recovery strategies must be publically available and must include three things. They must identify the threats to a species’ survival, state specific objectives for recovery, and define the area that contains habitat that is critical for the species to survive. We summarised data for all 388 species listed by the end of March 2014, and asked which threats are the most significant, whether the timelines set out in the law are being met, and whether the objectives that are being set are ambitious enough for species recovery.

Human disturbance from recreation, invasive species, and residential or commercial development are the most common threats to species at risk². This likely reflects the fact that plants are the largest group of species listed under SARA, and listed plants occur in areas of high human activity. Our data show that almost 75% of all species at risk occur along Canada’s southern border, and that over 40% of the species at risk in Canada are plants. To protect at risk plants, we must have specific goals to reduce these threats, but we may not be meeting these objectives.

Many species were automatically listed the same year SARA was enacted, and this created a large backlog of species waiting for recovery strategies to be written. We found that since 2009 there has been steady progress made in completing recovery strategies. However, only around 60% of the 380 species that required recovery strategies by the beginning of 2014 had a finalized recovery strategy. One reason why there are so few strategies is because it takes so long to complete them. By the time most strategies were completed they were more than four years overdue. We predict that at the current rate it will take between six and seven years from the time of listing to the completion of a recovery strategy.

Plants (in which we include vascular plants, mosses and even lichens) fare relatively well under SARA. More plant species than other groups have finalized strategies. However, these strategies are often incomplete and over the years their goals for recovery are progressively becoming less ambitious. Almost 50% of finalized strategies did not designate critical habitat as required. Furthermore, the number of species with recovery objectives that aim to increase the number of individuals, populations, or distribution of a species has steadily declined. Low ambition of these objectives means that the outlook for many species is poor, because by the time they are listed, most species have already undergone large declines in their numbers or substantial reductions in their ranges. Simply stopping declining trends is not real recovery. Recovery is the act of restoring healthy and self-sustaining populations, not merely stalling extinction. After examining the data we collected, we worry that meaningful recovery is not being targeted, and will likely not be achieved.

¹ SARA (Species at Risk Act) (2002) An act respecting the protection of wildlife species at risk in Canada. SC 2002, c 29, s 15. Available: http://Laws-lois.justice.gc.ca/PDF/S-15.​3.pdf. 

² McCune JL, Harrower WL, Avery-Gomm S, Brogan JM, Csergő A, et al. (2013) Threats to Canadian species at risk: An analysis of finalized recovery strategies. Biological Conservation 166: 254–265 http://dx.doi.org/10.1016/j.biocon.2013.​07.006.

Caption 1: A Garry oak savannah is one Canada’s rarest ecosystem and home to many of the plants listed under the Species At Risk Act (SARA). Three multi-species recovery strategies are available for Garry oak ecosystems. These include one for Garry oak woodlands, one for maritime meadows associated with Garry oak ecosystems, and one of vernal pools and other ephemeral wetlands. Photo: Jenny McCune

Caption 2:  Carolinian Forest, or Canada’s eastern deciduous forest, is an ecosystem that occurs around Lake Erie that contains many species of plants and animals that occur nowhere else in Canada. The threats to this unique ecosystem include habitat loss to agricultural and residential development. Photo: Jenny McCune

Caption 3: Carl Rothfels, a post-doctoral researcher in UBC’s Biodiversity Research Centre, contemplates the Mexican mosquito-fern (Azolla mexicana). This small fern of wetlands, ponds, and quiet lakes is threatened in Canada by urban and residential development and pollution of its wetland habitat. Mexican mosquito-fern grows in association with the blue-green bacteria that live in cavities on the fern’s leaves. Photo: Marc Johnston

Caption 4: Baikal Sedge (Carex sabulosa) is an at risk plant that occurs in the southern and western Yukon. It is only known from 14 historical sites, but with the help of Aboriginal traditional knowledge other potential sites have been identified and are being surveyed. Baikal Sedge grows only on active sand dunes, and is usually one of the first plants to colonize. Baikal sedge is threatened by invasive species, recreational vehicle use, and residential development. Photo: Syd Cannings ​

Article by Hélène Sanfaçon

Plant viruses can cause significant economic losses in cultivated plants by inducing visual symptoms that affect plant productivity.  However, there are also many viruses that co-exist with their hosts without inducing significant symptoms.  Symptom severity is determined not only by the ability of viruses to multiply and to disrupt the physiology of the plant but also by plant defense responses that attempt, sometimes unsuccessfully, to control virus infection. 

Our lab, which is located at the Pacific Agri-Food Research Centre in Summerland, BC, and is associated with the Department of Botany at UBC, has been interested in studying how plants and viruses interact and how these interactions influence symptom severity.  In particular, we have been studying the molecular mechanisms regulating symptom recovery in Nicotiana benthamiana plants infected with tomato ringspot virus (ToRSV).  ToRSV causes economic losses in fruit trees (apple, peach etc…), grapevine and small fruits (raspberry, blueberry etc…) in North America and also infects a wide variety of non-cultivated herbaceous plants such as N. benthamiana.   After inoculation with ToRSV, N. benthamiana plants develop necrotic symptoms on the inoculated leaves and on leaves immediately above the inoculated leaves.  However, later in infection, plants recover from infection and new leaves emerge that are asymptomatic (often referred to as recovered leaves) (Fig. 1).   

In initial studies, we found that the recovered leaves contain viral nucleic acids (RNA in the case of ToRSV) in concentrations similar to those found in symptomatic leaves (1).  This left us puzzled:  if the virus is still there, why is it no longer inducing symptoms?  Basudev (Basu) Ghoshal (UBC Botany Ph.D. student) started in the lab in May 2009, and was determined to get answers.   He first showed that symptom recovery is temperature-dependent and occurs at 27^oC but not at 21^oC (Fig. 2).   Although viral RNAs are present in similar levels in symptomatic or recovered leaves, the concentration of viral proteins is much decreased in recovered leaves compared to symptomatic leaves.   Further analysis revealed that this is due to a severely reduced rate of translation of the viral RNAs just prior to the onset of symptom recovery (2).   This repression of viral RNA translation is not observed in plants grown at 21^oC, and as a consequence, viral proteins accumulate to high levels and the plants continue to develop severe symptoms.  These results indicate that accumulation of viral proteins, controlled by the rate of translation of viral RNAs, regulates symptom severity.

RNA silencing is a well-characterized plant antiviral response that generally acts by degrading viral RNAs in a sequence-specific manner.  RNA silencing is also known to be more active in plants grown at higher temperature.  Although RNA silencing has been implicated in other symptom recovery phenotypes, we knew that if it was involved in ToRSV-infected plants, it likely used a mechanism distinct from RNA degradation, since viral RNAs were still present in high concentration in recovered leaves.  Basu decided to test the effect of down-regulating the expression of ARGONAUTE (AGO) proteins, which are key enzymes of plant RNA silencing pathways.  We were very excited when he discovered that plants deficient in AGO1, one of the 10 plant AGO proteins, did not recover from infection (Fig. 3).  In addition, these plants are unable to repress the translation of viral RNAs.  Thus, viral proteins accumulate to a high level (2).  These results provided strong evidence that translation repression can function as a novel plant antiviral mechanism and that AGO1 is involved directly or indirectly in this mechanism. 

Basu defended his thesis in July 2014 and the introduction chapter of his thesis was adapted to be published as an authoritative review on the various RNA silencing mechanisms associated with symptom recovery in virus-infected plants (3).  This review, now in press, will be published in conjunction with the 60^th anniversary issue of the journal “Virology” and includes a model for the newly-discovered translation repression mechanism.  We are hoping that the new insights in the molecular mechanisms regulating symptom recovery will lead to improved plant disease management strategies applicable to cultivated plants in the field.

1. Jovel J, Walker M, Sanfacon H. 2007. Recovery of Nicotiana benthamiana plants from a necrotic response induced by a nepovirus is associated with RNA silencing but not with reduced virus titer. J Virol 81:12285-12297.
2. Ghoshal B, Sanfacon H. 2014. Temperature-dependent symptom recovery in Nicotiana benthamiana plants infected with tomato ringspot virus is associated with reduced translation of viral RNA2 and requires ARGONAUTE 1. Virology 456-457:188-197.
3. Ghoshal B, Sanfacon H. 2015. Symptom recovery in virus-infected plants: Revisiting the role of RNA silencing mechanisms. Virology in press.

Figure 1: Symptom recovery in N. benthamiana plants infected with ToRSV.  Inoculated leaves develop symptoms in the form of necrotic rings by five days post-inoculation (5 dpi, left).  At 8 dpi, leaves immediately above the inoculated leaves display necrotic symptoms along the veins (centre).  At late stages of infection, the plant apparently recover from infection and new leaves are asymptomatic (right).
Figure 2: Temperature-dependent symptomatology in N. benthamiana plants infected with ToRSV.  Although necrotic symptoms initially develop on ToRSV-infected plants grown at 21 or 27oC, symptom recovery is only observed at the higher temperature.  At 21oC, infected plants become completely necrotic and eventually die (pictures show plants at 20 dpi).
Figure 3: Symptom recovery depends on AGO1.  Although wild-type plants recover from infection by 16 dpi at 27oC (top panel), plants that are deficient in AGO1 do not (lower panel).  The stunting of AGO1-deficient plants compared to wild-type plants is a well-documented side-effect related to the regulation of plant development by AGO1. ​

Article by Bill Harrower, Lauchlan Fraser and Roy Turkington

Grasslands of British Columbia’s southern interior mountains provide stunning landscapes and host many of the provinces at risk species of plants and animals. Hot dry sagebrush and bunchgrass ecosystems occupy the valley bottoms and grade to the cool wet grasslands with increasing elevation.

The structure of ecosystems varies enormously because of their location and the organisms that live there. The Fraser and Turkington labs have studied the structure and function of many types of ecosystems – deserts, savanna grasslands, boreal forest understory, subtropical forest understory, and grasslands in Yukon and interior British Columbia. Using observations and experiments we have investigated how the plants and animals that live in grasslands interact to produce the abundance and complexity of life we see. One of the major techniques we use is called a removal experiment. We document all the plants and animals in an intact ecosystem and monitor various measures of ecosystem function such as rates of productivity and decomposition, soil nutrient levels and turnover rates. We then remove specific components of the system such as small birds, mice and voles, insects, plant species, and litter to determine how ecosystem composition and function change in response to these removals.  In this way we can predict the consequences of disturbances (such as might be associated with climate change or overgrazing) and species loss on the structure and function of grasslands. We have done this research in grasslands having different amounts of rainfall and ranges in temperature. By comparing the effects of species removals in cool wet grasslands to removals in hot dry grasslands, we gain an understanding of the processes that structure ecosystems, promote biodiversity, and ultimately supply humans with the services we need. We found that the removal of song birds and small mammals can have profound effects on the growth and diversity of plants, and that these effects depend on whether we are in a hot dry grassland or a wet cool grassland. Predation by birds and mammals on insects alters the amount of herbivory on plants. When we remove bird and mammals we change insect communities and this increases plant growth in wet cool grasslands or retards growth in hot dry grasslands. Dead plant material, litter, can influence the degree to which birds or mammals influence plants. This is important because the amount of litter in the ecosystems depends on the amount of wildfire and livestock grazing humans allow.

We chose to do this research in grasslands because of their widespread global distribution and because of their great importance to humans. Grasslands filter water, mitigate flooding, clean air, and we often live in or beside them. Grassland ecosystems provide us with much of our food – – crops, forage and livestock.  This understanding of grassland ecosystems allows us to conserve grasslands and manage the services they provide to humans.

Originally published by UBC Science on August 2, 2022

For the first time, plant biologists have defined the high-efficiency “hacks” that cannabis cells use to make cannabinoids (THC/CBD). Although many biotechnology companies are currently trying to engineer THC/CBD outside the plant in yeast or cell cultures, it is largely unknown how the plant does it naturally. 

“This really helps us understand how the cells in cannabis trichomes can pump out massive quantities of tetrahydrocannabinol (THC) and terpenes—compounds that are toxic to the plant cells at high quantities—without poisoning itself,” says Dr. Sam Livingston, a botanist at the University of British Columbia who led the research. 

“This new model can inform synthetic biology approaches for cannabinoid production in yeast, which is used routinely in biotechnology. Without these ‘tricks’ they’ll never get efficient production.”

For centuries, humans have cultivated cannabis for the pharmacological properties that result from consuming its specialized metabolites, primarily CBD and terpenoids. Today, production within Canada’s $2.6 billion-a-year cannabis industry ($20 billion global cannabis market) largely relies on the biological activity of tiny cell clusters, called glandular trichomes, found mainly on the plant’s flowers. 

The study, published this week in Current Biology, reveals the microenvironments in which THC is produced and transported in cannabis trichomes, and sheds light on several critical points in the pathway of making THC or CBD within the cell. 

Dr. Livingston and co-author Dr. Lacey Samuels used rapid freezing of cannabis glandular trichomes to immobilize the plant’s cellular structures and the metabolites in situ. This enabled them to investigate cannabis glandular trichomes using electron microscopes that revealed cell structure at the nano level, showing that the metabolically active cells in cannabis form a “supercell” that acts as a tiny metabolic biofactory. 

Until now, synthetic biology approaches have focused on optimizing the enzymes responsible for making THC/CBD—like building a factory with the most efficient machinery to make as much product as possible. However, these approaches haven’t developed an efficient way to move intermediate substances from one enzyme to another, or from inside the cell to the outside of the cell where final products can be collected. This research helps to define the subcellular “shipping routes” that cannabis uses to create an efficient pipeline from raw materials to end products without accumulating toxins or waste products.

“For more than 40 years, everything that we thought about cannabis cells was inaccurate because it was based on dated electron microscopy,” says Dr. Samuels, a plant cell biologist at UBC. “This work defines how cannabis cells make their product. It’s a paradigm shift after many years, producing a new view of cannabinoid production. This work has been challenging, partly the result of legal prohibition and also due to the fact that no protocol for the genetic transformation of cannabis has been published.”