A telomere is the region of DNA that marks the end of a chromosome. The protect the ends of the chromosome, and stop one chromosome from fusing with another. So finding something that looks like a telomere in the middle of a chromosome would be odd – but it happens. And no one knows exactly why.
Although interstitial occurrence of telomeric repeat motifs (ITR) has been reported in the genome of a few organisms, the striking level of polymorphism found by Rosata et al. within a single species has not been described before. Rosata and colleagues investigate whether a comparable pattern of dynamism found for another repetitive element, interstitial 45S rDNA sites, in the genus Anacyclus (Asteracea), is linked to ICT and both have the same underlying causes.
This study provides hints that ancient Robertsonian translocations or the amplification of terminal 45S rDNA sites can be involved in the patterns found for both repetitive families, although a wide survey across Asteraceae is needed for a conclusive answer.
While the regions studied are tiny, the effects could be big if you use ITRs to examine plant evolution. The authors say: “Our results suggest caution for those studies using ITRs as markers of species’ phylogenetic relationships without a thorough sampling.”
Rosato, M., Álvarez, I., Feliner, G. N., & Rosselló, J. A. (2018). Inter- and intraspecific hypervariability in interstitial telomeric-like repeats (TTTAGGG)n in Anacyclus (Asteraceae). Annals of Botany, 122(3), 387–395. https://doi.org/10.1093/aob/mcy079
Rosato, M., Álvarez, I., Feliner, G.N., & Rosselló, J. A. (2017). High and uneven levels of 45S rDNA site-number variation across wild populations of a diploid plant genus (Anacyclus, Asteraceae). PLOS ONE, 12(10), e0187131. https://doi.org/10.1371/journal.pone.0187131
If you were to work out what a plant is, then near the top of the list would be things like “they grow in the soil”, “they’re green”, or “they make their own food”. Orchids tend to treat these as guidelines rather than rules, and research in New Phytologist examines how some orchids have learned to feed themselves through fungi, instead of making all of their own carbohydrates. The paper by Félix Lallemand and colleagues looks at these mixtrophic orchids. They’re mixtrophic because they get some carbon from fungi and some from the air through photosynthesis. The reason we know is they’re getting it this way is because not all carbon is the same.
Most carbon is the same, with six protons, six neutrons and six electrons. However, some carbon 13C has an extra neutron, making it a little bit heavier. This difference means that the carbon plants pull from the air is a little bit less likely to have 13C in it compared to the carbon fungi get. If you examine plant tissue and find it has more 13C in it than you’d expect, then you know it’s been getting it from fungi. Lallemand’s team looked at Cephalanthera damasonium to see what the orchid was doing with the mix of carbon.
C. damasonium, White Helleborine, is a good plant to test as it can act in a few ways. An albino form doesn’t photosynthesize, so it’s easy to compare it with the green form and see what differences the varied diets make. What they found is that different parts of the plant have carbon from different sources. The underground organs are built from fungal carbon. For green plants, it’s photosynthesis that supplies the carbon.
Taking this information, the authors are able to put forward a few ideas about why the orchid behaves this way. For a start building a body takes energy and material. You lose this if you’re in the shade, but being able to take what you need from fungi opens up a lot more habitats. If fungi are taking care of the rhizomes then you can put the limited photosynthetic carbon into fruits.
The downside is that the fungal carbon isn’t really enough to support building seeds, and so there are fewer seeds to set. Lallemand and colleagues look at other solutions for reproduction. They say: “[M]ixotrophy predisposes to an evolution of heterotrophy since underground survival is already largely independent of photosynthesis.” Examples they give are orchids sending out stolons (a runner that can take root), or roots that can sprout themselves. These extra methods of reproduction could compensate for reduced seed set, they say. This explains how – once an ability to take food from fungi evolved – full heterotrophy evolved multiple times in related species, eliminating the need to rely directly on sunlight.
Lallemand, F., Figura, T., Damesin, C., Fresneau, C., Griveau, C., Fontaine, N., … Selosse, M.-A. (2018). Mixotrophic orchids do not use photosynthates for perennial underground organs. New Phytologist. https://doi.org/10.1111/nph.15443
Salinity affects plant growth and metabolites in plants, which in turn affect Cd accumulation. Cheng et al. ran a hydroponic experiment to assess the effect of NaCl on the metabolic response to Cd and Cd accumulation in the halophytic Cd-accumulator Carpobrotus rossii (Aizoaceae).
They find NaCl decreased Cd accumulation in the shoot by decreasing Cd root uptake and root-to-shoot translocation even under constant Cd2+ activity. Peptides and organic acids, particularly phytochelatins, play an important role in Cd tolerance and accumulation, but the change of those metabolites is not the reason for the decreased Cd accumulation.
Cheng et al. conclude that C. rossii‘s ability to accumulate cadmium makes it a promising candidate for Cd phytoextraction in Cd-polluted saline soils and estuarine environments.
Cheng, M., Wang, A., Liu, Z., Gendall, A. R., Rochfort, S., & Tang, C. (2018). Sodium chloride decreases cadmium accumulation and changes the response of metabolites to cadmium stress in the halophyte Carpobrotus rossii. Annals of Botany, 122(3), 373–385. https://doi.org/10.1093/aob/mcy077
We’re not usually that big on plant genomes (“the complete set ofgenetic informationin an organism”) in Cuttings items. We know what they are, and appreciate their importance, but until those genomes are translated into known functions for all the genes identified, etc. there’s not as much of a story as we’d like. However, sometimes one simply can’t ignore them. And, lately there’s been such a veritable tsunami of phytogenomic ‘firsts’, it would be remiss of us if we didn’t make some acknowledgement of their existence. However, since there are so many of them to report, we don’t have the space to offer the usual insightful Cuttingsesque commentary. But, here goes…
Another monocot that, like rice, famously also provides calories to humans – albeit from its sugar content whose consequences are more health-threatening, rather than health-promoting and life-sustaining than for rice – is sugarcane, whose genomes was announced by Olivier Garsmeur et al..
What links all of the above genomes is that they are from members of the Plantae, the Plant Kingdom**, i.e. the primarily terrestrial-inhabiting, so-called land plants (or Embryophyta). We’ve not always had such plants on the planet; indeed, the general notion is that a land flora evolved about 500 MYA. But, if evolution is correct, something will have given rise to those first land-dwelling plants, but what?
* The phenomenon whereby two genomes for the same organism are published at more or less the same time is not that rare in plant science – as we covered in 2013 for chickpea (Cicer arietinum), and for pigeon pea (Cajanus cajan) in 2012.
** That, and the fact that they also all happen to have been published in the Nature family of journals…
Li, F.-W., Brouwer, P., Carretero-Paulet, L., Cheng, S., de Vries, J., Delaux, P.-M., … Pryer, K. M. (2018). Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants, 4(7), 460–472. https://doi.org/10.1038/s41477-018-0188-8
Wan, T., Liu, Z.-M., Li, L.-F., Leitch, A. R., Leitch, I. J., Lohaus, R., … Wang, X.-M. (2018). A genome for gnetophytes and early evolution of seed plants. Nature Plants, 4(2), 82–89. https://doi.org/10.1038/s41477-017-0097-2
Raymond, O., Gouzy, J., Just, J., Badouin, H., Verdenaud, M., Lemainque, A., … Bendahmane, M. (2018). The Rosa genome provides new insights into the domestication of modern roses. Nature Genetics, 50(6), 772–777. https://doi.org/10.1038/s41588-018-0110-3
Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., … Foucher, F. (2018). A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nature Plants, 4(7), 473–484. https://doi.org/10.1038/s41477-018-0166-1
Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., … D’Hont, A. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-05051-5
Nishiyama, T., Sakayama, H., de Vries, J., Buschmann, H., Saint-Marcoux, D., Ullrich, K. K., … Lang, D. (2018). The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization. Cell, 174(2), 448–464.e24. https://doi.org/10.1016/j.cell.2018.06.033
Cheng, S., Melkonian, M., Smith, S. A., Brockington, S., Archibald, J. M., Delaux, P.-M., … Wong, G. K.-S. (2018). 10KP: A phylodiverse genome sequencing plan. GigaScience, 7(3). https://doi.org/10.1093/gigascience/giy013
Long terminal repeat-retrotransposons (LTR-RTs) comprise a large portion of plant genomes, with massive repeat blocks distributed across the chromosomes. Eleocharis (Cyperaceae) species have holocentric chromosomes, and show a positive correlation between chromosome numbers and the amount of nuclear DNA.
de Souza et al. present an overview of the diversity and the role of several Copia and Gypsy LTR-RT families in the organization of Eleocharis holocentric chromosomes. Physical location using Copia and Gypsy probes on the chromosomes indicated different distribution patterns of this genomic fractions representing >50% of genomes.
Rapid and unequal changes in the LTR-RTs represent important mechanisms responsible for genomic differentiation, karyotype evolution and speciation, but LTR-RT number variations seem to be a secondary mechanism in comparison to polyploidy when considering DNA C-values.
De Souza, T. B., Chaluvadi, S. R., Johnen, L., Marques, A., González-Elizondo, M. S., Bennetzen, J. L., & Vanzela, A. L. L. (2018). Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes. Annals of Botany, 122(2), 279–290. https://doi.org/10.1093/aob/mcy066
Native and alien trees associate with a wide range of beneficial fungi, but the few studies of these interactions tend to focus only on a few plant species or locations at a time. This approach limits broad scale understanding of functional shifts and changes in interaction network structure that may occur following introduction. An ectomycorrhizal fungal species can associate with multiple, potentially distantly related, plant species. This means that the presence of one plant species may support a population of fungi that serves as inoculum, facilitating the establishment of a second plant species. The interactions of alien trees through shared mutualist species can therefore be analysed through network theory.
In a study published in AoBP (in the special issue on Evolutionary Dynamics of Tree Invasions), Dickie et al. investigate plant–fungal interaction networks using two extensive datasets derived from fungal sporocarp observations and recorded plant hosts in two island archipelago nations: New Zealand (NZ) and the United Kingdom (UK). In New Zealand, fungi on alien trees are less functionally diverse than those associated with natives, whilst in the UK there is no functional difference in fungal associates of alien and native plant genera. In both New Zealand and the United Kingdom, however, the structure of the plant-fungi interaction network is simplified and “nested”, which suggests that beneficial fungi hosted by alien trees may help facilitate further tree invasion. Whether this is driven by fungal traits (e.g. lack of host-specific fungi; expanded host-range) or habitat drivers (e.g. planting into atypical soils) requires more detailed investigation to unravel. Regardless of the cause, the sharing of symbiotic fungi among alien trees may have important implications for the invasion process, if tree species which share fungal associates facilitate each other.
Dickie, I. A., Cooper, J. A., Bufford, J. L., Hulme, P. E., & Bates, S. T. (2016). Loss of functional diversity and network modularity in introduced plant-fungal symbioses. AoB Plants, plw084. https://doi.org/10.1093/aobpla/plw084
There’s a plan to do something with Taxonomy here at Botany One, but we’re not clear what. It seems a pretty good rule of thumb that if a science has taxonomists, then the work of those taxonomists doesn’t get the respect it deserves. So something positive would be a good idea. It would be even better if it were more helpful than tweeting a #HugYourTaxonomist hashtag.
Rather than go through my notes one-by-one I’ll try to pull together some of the themes.
I think the first is Taxonomy matters because it’s a scientific endeavour. I think everyone took for granted that we know what taxonomy is. I think a note I had was that it was the process that names a coyote Eatibus anythingus – but that’s probably exactly wrong. The mock linnaean names you get in Roadrunner cartoons are arbitrary, and the names taxonomists give to species are emphatically not. A Rosa by any other name might smell as sweet, but it wouldn’t be a rose.
Something that came up in multiple talks is that when you know the name of a species, you also know some of its context. A coyote Canis latrans is similar to a dog Canis familiaris, that Canis showing they’re in the same genus, but not the same species. The African wild dog Lycaon pictus is one of the Canidae – but that different genus name shows that the dog and coyote are more closely related. If you called an African wild dog Canis pictus then you’re not simply changing a name – you’re also making a statement about how it relates to other species.
Looking at it that way, taxonomy is critical in understanding scientific relationships. It’s a feature that came out in talks by Alistair Culham and Christophe Eizaguirre on how to integrate taxonomy with scientific training. Taxonomy isn’t simply about names, and I wonder if the Linnaean labels we give to species are best described as names. Would it be better to describe them as addresses on the Tree of Life?
Technology came up a few times in the meeting. Multiple entry keys look like they have a lot of potential. The dichotomous key tends to work by moving through branching decisions. Is the subject tall or short? Fat or thin? Spherical or squished… and so on. Multiple entry keys offer the ability to put in a lot of this data at once and easily change parameters if you’re unsure. For example, when does a small pine cone become a large pine cone?
There was also use of multimedia and I’ll embed a couple of sample videos below.
The Linnean Society videos are a way of getting some of the collections of the Society digitised and out where the public can see it. Public access to taxonomy was a feature of some of the museums talks too. Either getting the public out and classifying, identifying in museums where many items are classified by volunteers. Elsewhere inviting the public behind the scenes as school trips, or late-night openings was seen as a great way to enthuse people.
The final talk on Pokémon could have been depressing, “Do people know more Pokémon than real species?”. The answer for children is yes, by the age of eight. But Joe Burton also pointed out that the basic skills and desire to classify were there. It was during this talk that Ray Heaton made a comment that pulled a lot of the other talks together for me. He pointed out that kids used to collect flowers or birds eggs, and they don’t anymore. That’s generally a good thing, but we classify and sort what we collect and we’re not really collecting nature through childhood.
The trips behind the scenes also, in a way, confer ownership of collections. In one talk visitors were encouraged to handle the cases of type specimens. I think Max Barclay noted in his talk, the loss of the museum in Rio recently wasn’t a loss for Brazil – it was a loss for all humanity. This might highlight the power of technology again. Through phones and apps, people could collect species via photos, like in iNaturalist. This might highlight the power of technology again. Through phones and apps, people could collect species via photos, like in iNaturalist.
After listening to the talks, I no longer think that Taxonomy would be a good topic to cover as a project. As far as science goes, Taxonomy is too tightly bound into other scientific practice to hive it off separately. Instead, you could look at Taxonomy and Invasive Species or Taxonomy and Evolution. Biodiversity or Conservation seems a difficult topic to discuss without acknowledging the importance of Taxonomy. Also the importance of the public in recording data and classifying observations seems like a topic worth exploring. So while Taxonomy might not be a suitable subject in itself for blogging, Taxonomy and… could be very fruitful.
Diurnal changes in solar position plus occlusion caused by overlapping foliage means that throughout a day, leaves alternate between periods where they are either sunlit or shaded. Describing these patterns for real plant canopies is difficult and computationally intensive.
Retkute et al. combine high-resolution reconstructions of field-grown plants with ray-tracing to analyse how light dynamics vary for different plant species, planting densities and leaf area indices. They develop a stochastic model which involves two states, sunlit and shaded, where the rates of switching between states are a function of time of day and the depth within the canopy.
Retkute, R., Townsend, A. J., Murchie, E. H., Jensen, O. E., & Preston, S. P. (2018). Three-dimensional plant architecture and sunlit–shaded patterns: a stochastic model of light dynamics in canopies. Annals of Botany, 122(2), 291–302. https://doi.org/10.1093/aob/mcy067
Kew’s State of the World’s Fungi has been published. The aim of the report is to establish a baseline for fungal conservation and research. The report states there are 144,000 species of fungi known, with 2000 being added to the list each year. However, that baseline is rather fuzzy. They also estimate there are between 2.2 and 3.8 million fungi out there. That means we know of about 5% of the species at the moment. And at that rate it’ll take about another thousand years to find them all.
The reason biologists think there are so many fungi is down to advances in DNA. Putting together sequences of DNA and comparing them, it’s possible to see how closely related fungi are, and how diverse fungal species are. This kind of analysis is revealing that very similar looking fungi, for example, pathogens like rusts, are actually surprisingly diverse. They are also hints of fungi with distinctive chemical signatures that we haven’t identified yet – which are called dark taxa.
These new techniques are controversial. Kew reports: “The challenge for the future will be to reach consensus across the community of scientists who work on fungi on how these exciting new discoveries of fungal diversity, based purely on DNA sequence data, are incorporated into existing fungal classification systems. Only then will it be possible to reach a truly comprehensive understanding of the full extent of global fungal diversity.”
It might seem odd that Kew, a botanic garden, is studying fungi – which are definitely not plants. They differ in a few important ways.
One of the differences for fungi is how they eat. Plants make their food internally (usually). Fungi exude enzymes externally that digest what they’re in contact with and then reabsorb the goo back into their cells. The cells walls are not made of cellulose, but chitin, the same material that insects use to make their shells. They also store food as glycogen and lipids, instead of starch. So in the way they eat, they way their cells work and the way they store energy they are very different from plants.
Mushrooms are not plants.
They belong to their very own biological kingdom, Fungi.
Genetic tests show that is much more closely-related to our own kingdom, Animals.
The Kew report notes that this different biology means they play a very important role in the environment. The report states: “Fungi are also the most significant organisms that break down cellulose, hemicellulose and lignin. These are the tough polymers in plant cell walls that give wood its great strength and durability. Their decomposition by wood-decaying fungi releases key plant nutrients back into the soil, thereby allowing the next generation of seedlings to grow. Without nutrient cycling, life on Earth as we know it would not exist; nutrients would be in such short supply that biological growth would be severely limited right across the globe.”
Endophytes are fungi that live between cells in a plant, in the shoots or roots. Kew reports: “[E]ndophytic fungi such as Trichoderma (Ascomycota), used as a seed treatment in agriculture, can induce plant resistance to diseases, water deficits, salinity and also heat stress. They do this by altering the expression of the genes involved in root growth, nutrient uptake or protection against oxidative damage.”
The other popular fungal organisms are Mycorrhizas. Kew says: “It is estimated that around 90% of living plant species have mycorrhizal fungi associated with their roots. In contrast, less than 2% of fungal species enter into mycorrhizal partnerships. Through becoming specialised to co-exist with plants, the fungi involved rely on their plant hosts
for their supply of carbon, having lost the ability of their ancestors to decompose dead organic matter . In return for their photosynthetic carbon, the plants receive water and mineral nutrients from the soil via the fungi. Most mycorrhizal fungi are dependent on their hosts for survival, just as many plants are dependent on their fungal partners.”
Kew also describes some of the fungi as fungal ‘bodyguards’ for plants, changing how plant genes react and helping boost defences against herbivores. Applying fungi to seeds gives the potential for crops to be planted with their own guardians. The report states even treatments as low as 500mg per hectare can have an effect.
In light of this, conservation is important and that is another hole in our knowledge. Kew notes that only 56 species of fungi have had their conservation status globally evaluated. For comparison, the same can be said for 25,452 plants and 68,054 animals.
There are clear problems in creating conservation plans. Because fungi are largely microscopic, there’s a lot of gaps in our understanding of where on the planet they are. They can also change form, or look like other fungi. Kew says that: “Despite the eye- catching and prolific displays of spore-bearing structures (e.g. mushrooms) produced by some species, they are generally regarded as difficult to detect and count because, when not sporulating, most are composed of nothing more substantial than a wispy network of mycelium.”
This lack of knowledge has an impact on discussion in conservation. The report states: “It was noted from a review of papers published in the top twelve mainstream conservation journals that only around 3% discussed fungi.” and Kew estimates that at least 10% of European macrofungi, the fungi that produce bodies big enough to see, are threatened with extinction.
Given the peculiar chemistries of fungi, it would seem to be a bad idea to lose many of them before they could be studied. This report and the associated conference will, over the next few days, give some impetus to studying this neglected Kingdom.
We rightly ponder the problem of future food security – in which plants, plant science, and plant scientists (in the broadest sense of that term) have a big part to play. However, just as pressing is concern over sufficiency of fresh – i.e. clean, disease-free, drinkable – water for thosehungryhumans.
Traditionally, one way of cleaning-up water that’s not fit for human consumption has been to use the moringa plant (Moringaoleifera) as a sort of water–purifier. Although that can be effective, it leaves behind high amounts of dissolved organic carbon (DOC), from the seeds that are used to clean the water. That DOC can act as a food source that permits and sustains the regrowth of bacteria after 24 hours. Thus, water cleaned by the traditional moringa technique is only drinkable for a limited period after treatment, i.e. it has a short ‘shelf-life’.
Taking that good idea and making it better is what Brittany Nordmark et al. have done. They show that proteins extracted from moringa seeds can be adsorbed to the surface of silica particles (‘sand’) where their positive charges act to attract both negatively-charged DOC and micro-organisms that contaminate the water. This f-sand* system thus has great potential as a relatively cheap – but much-improved – version of the traditional moringa water-purification method, which can be readily made (as this video shows) in places where it’s needed.
Well, one I see is that to ‘recharge’ the f-sand for reuse you need to wash out the adhered DOC and other undesirables. Presumably that means with clean water, whose supply is the problem in the first place. And, once reset, what do you do with this now-dirty water? But, there’s even more to moringa than just a natural water-purifier. So much more in fact that it has been called the MiracleTree and is associated with both nutritional and properties, claims and benefits.
One tree that can help solve two of humanity’s greatest insecurities – getting enough of the right kind of food, and access to fresh water (and a third if you include its medicinal virtues…). What’s not to like?
Nordmark, B. A., Bechtel, T. M., Riley, J. K., Velegol, D., Velegol, S. B., Przybycien, T. M., & Tilton, R. D. (2018). Moringa oleifera Seed Protein Adsorption to Silica: Effects of Water Hardness, Fractionation, and Fatty Acid Extraction. Langmuir, 34(16), 4852–4860. https://doi.org/10.1021/acs.langmuir.8b00191
Jerri, H. A., Adolfsen, K. J., McCullough, L. R., Velegol, D., & Velegol, S. B. (2011). Antimicrobial Sand via Adsorption of Cationic Moringa oleifera Protein. Langmuir, 28(4), 2262–2268. https://doi.org/10.1021/la2038262
All images copyright of the artist. All text released under a Creative Commons BY-SA licence.
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