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The Week in Botany 32

January 29, 2018

In Defense of Plants was popular with people following @botanyone on Twitter this week, with two stories getting shared, including one from 2016. If you're interested in these posts you might want to support the Kickstart campaign to produce a video on the Botany of the Cascades, looking at the effect of global warming in this region of the Pacific Coast.

From Botany One

Hypericum hybrids trapped in their polyploid gene pool
The underlying genetic causes of the switch to apomixes are not yet fully understood, but in Hypericum there is good evidence for the existence of ‘apomictic factors’.

Warming and elevated CO2 alter the suberin chemistry in roots
In a recent Editor’s Choice article published in AoB PLANTS, Suseela et al. examined the effects of elevated CO2 and warming on the quantity and composition of suberin in the roots of a C4 and C3 grass species.

Citation Classics in Plant Sciences since 1992
Philip White asks what are the classic papers in plant sciences, and highlights a method that allows you to produce your own lists for your field or sub-field.

Carbohydrate storage and leaf biomass scaling in meadow plants
These findings imply that storage in herbs is probably governed by factors other than just the disturbance regime applied once in a growing season.

Shaping the cline of floral calyx lobe length in Asarum
Divergent selection may have driven the calyx lobe length variation in series Sakawanumtaxa, although the underlying mechanism is still not clear.

What is it that plant pathogens are attacking?
It might seem obvious that plant pathogens attack plants, but a new paper in Molecular Plant Pathology argues that we should be looking at a wider battle in the soil.

What do you know about leaves???
Ever so occasionally one comes across a book that makes one think, “That’s the book I’d like to have written”. Well, for me, David Lee’s Nature’s Fabric: Leaves in Science and Culture, is just such a book. Nigel Chaffey's latest review.

Call for Papers: Special issue on the Ecology and Evolution of Plant Reproduction

Botanists have long been fascinated by the extraordinary diversity in flowering plant reproductive patterns and have sought to understand theecological processes and genetic mechanisms influencing plant mating. Over the last five years, research progress in this discipline has rapidly accelerated. Important new insights in this field often combine elegant theoretical models with innovative field and laboratory experiments. Annals of Botany will release a Special Issue on the Ecology and Evolution of Plant Reproduction in January 2019, and it will highlight papers from 3 symposia at the XIX International Botanical Congress in Shenzhen, China. See the full call for papers for more information.

News and Views

Zoophagous Liverworts?
Are there carnivorous liverworts? This 2016 blog post got a lot of attention this week.
In Defense of Plants

CRISPR crops—exempt from GMO regulations—reaching US market in record time
CRISPR–Cas9-edited plants can be cultivated and sold free from regulation, the US Department of Agriculture (USDA) is making increasingly clear. The agency gave a free pass to Camelina sativa, or false flax, with enhanced omega-3 oil. And more recently, in October, said that a drought-tolerant soybean variety developed with CRISPR falls outside of its regulatory purview. This laissez-faire attitude from the agency shaves years and tens of millions of dollars off the cost of bringing a biotech plant to market.
Genetic Literacy Project

The lost art of looking at plants
Advances in genomics and imaging are reviving a fading discipline.

Hundreds of wildflower species found blooming in midwinter
UK survey finds 532 types – far more than older textbooks suggest should be out
The Guardian

Fast-talking plants increase flower production within 24-hours of soil nutrient application
The molecular mechanisms enabling plants to quickly adapt their rate of flower production in response to changing nutrient levels in soil have been revealed by researchers at the Sainsbury Laboratory at the University of Cambridge.
Sainsbury Lab

How Trees Fight Disease
Plants do not have immune systems like animals. Instead, they have evolved an entirely different way of dealing with infections. In trees, this process is known as the "compartmentalization of decay in trees" or "CODIT." CODIT is a fascinating process and many of us will recognize its physical manifestations.
In Defense of Plants

Stem rust attacks in Sweden heralds the return of a previously vanquished foe
Stem rust or black rust has long been seen as the bubonic plague of wheat farming – a once dreaded pathogen that has now been neutralized and is now hardly worthy of attention, let alone concern. In summer 2017, a vast outbreak occurred in Uppland in Sweden, and the fungus is now feared to have returned to the north.
Sveriges lantbruksuniversitet

'Absurdly small': Taxonomy funds shrivel amid rising threats and discoveries
The latest study on taxonomists– released without fanfare late last year by the Turnbull government – found numbers of taxonomists in Australia have remained in the few hundreds since the 1970s even as the population doubled. Significantly, more than a quarter of the taxonomic workforce in 2016 "identified as being retired/honorary/volunteer positions", compared with 19 per cent in 1975, the report said.
The Sydney Morning Herald

Honeybees Help Farmers, But They Don't Help The Environment
Jonas Geldmann, at the University of Cambridge, says he understands how the honeybee became a symbol of environmental conservation. But he still doesn't like it. "Lots of conservation organizations are promoting local honey, and even promoting sponsorships of honeybees and that kind of stuff, and that increasingly annoyed me," he says. It annoyed him because the honeybee is perhaps the one type of bee that we should worry about the least. Honeybee hives aren't natural, and they don't help the environment. In fact, they may harm it.
NPR The Salt

The curious case of Copper Sulphate
The role of chemicals in agriculture is high on the EU policy agenda these days. A vocal organic lobby claims that outlawing synthetic pesticides is crucial for public health. On the other hand, farmers claim that pesticides and fertilizers are essential for their livelihoods. But in the shadows of Brussels’ opaque comitology process, a chemical treatment has just had its authorisation extended despite EFSA raising numerous health concerns about it.

Call for papers: Developing sustainable bioenergy crops for future climates

Rapid progress has been made over the last five years with respect to emerging new genomic technologies for crop improvement and this Annals of Botany Special Issue will be devoted to highlighting the latest findings and considering the potential of these technologies for the future deployment of bioenergy crops in the face of climate change. At the same time, cutting-edge research that provides insights into the complex plant traits underpinning drought tolerance and response to other abiotic and biotic stresses is required for these relatively new crops. Knowledge in this area will be brought together in this Special Issue, and there will be a focus on recent advances in high throughput phenotyping to unravel these complex responses. See the full call for papers for more information.

Scientific Papers

The genome-wide rate and spectrum of spontaneous mutations differs between haploid and diploid yeast
We report the first direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploid and diploid forms of the budding yeast Saccharomyces cerevisiae. Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that diploidy masks the effects of recessive alleles.

Chemical hijacking of auxin signaling with an engineered auxin–TIR1 pair
We report an engineered, orthogonal auxin–TIR1 receptor pair, developed through a bump-and-hole strategy, that triggers auxin signaling without interfering with endogenous auxin or TIR1/AFBs. A synthetic, convex IAA (cvxIAA) hijacked the downstream auxin signaling in vivo both at the transcriptomic level and in specific developmental contexts, only in the presence of a complementary, concave TIR1 (ccvTIR1) receptor. 
Nature Chemical Biology

High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis
These findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant–Arbuscular mycorrhizal fungi interactions that link AMF genome variation with plant phenotype and fitness.
New Phytologist

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species.
Nature Genetics

Ex Situ Propagation of Philippine Rafflesia in the United States: Challenges and Prospects
We report our attempts in the United States to propagate host cuttings infected with Rafflesia speciosa Barcelona & Fernando and R. lagascae Blanco collected from the Philippines, as well as uninfected host material. We also describe efforts to germinate R. speciosa seeds in vitro using various plant growth regulators (PGRs).
Sibbaldia: the Journal of Botanic Garden Horticulture

A new opening for wheat seed production
Crop plant domestication has targeted a variety of traits, including synchronous development of ovules and stamens to maximize fertilization and seed production. In wheat, with its autogamous, or self-fertilizing, flowers, this is very attractive for guaranteeing yield but extremely frustrating for a researcher trying to cross individuals of distinct genotypes, and even more so for a breeder trying to generate hybrids.

A fast likelihood solution to the genetic clustering problem
We introduce snapclust, a fast maximum-likelihood solution to the genetic clustering problem, which allies the advantages of both model-based and geometric approaches. Our method relies on maximising the likelihood of a fixed number of panmictic populations using a combination of geometric approach and fast likelihood optimization using the Expectation-Maximization (EM) algorithm. It can be used for assigning genotypes to populations and optionally identify various types of hybrids between two parental populations. Several goodness-of-fit statistics can also be used to guide the choice of the retained number of clusters.
Methods in Ecology and Evolution

Hot mitochondria?
Using the thermosensitive mitochondrial-targeted fluorescent dye Mito Thermo Yellow (MTY), Chrétien and colleagues suggest that mitochondria are optimised to nearly 50 °C, 10 °C hotter than body temperature. This extreme value questions what temperature really means in confined far-from-equilibrium systems but encourages a reconsideration of thermal biology.

Quantifying progress toward a conservation assessment for all plants
We consolidated digitally available plant conservation assessments and reconciled their scientific names and assessment status to predefined standards to provide a quantitative measure of progress toward this target. The 241,919 plant conservation assessments generated represent 111,824 accepted land plant species (vascular plants and bryophytes, not algae). At least 73,081 and up to 90,321 species have been assessed at the global scale, representing 21–26% of known plant species. Of these plant species, at least 27,148 and up to 32,542 are threatened. Eighty plant families, including some of the largest, such as Asteraceae, Orchidaceae, and Rubiaceae, are underassessed and should be the focus of assessment effort if the GSPC target is to be met by 2020.
Conservation Biology

Ecology of Floristic Quality Assessment: testing for correlations between coefficients of conservatism, species traits and mycorrhizal responsiveness
Many plant species are limited to habitats relatively unaffected by anthropogenic disturbance, so protecting these undisturbed habitats is essential for plant conservation. Coefficients of conservatism (C values) were developed as indicators of a species’ sensitivity to anthropogenic disturbance, and these values are used in Floristic Quality Assessment as a means of assessing natural areas and ecological restoration. However, assigning of these values is subjective and improved quantitative validation of C values is needed.


Next week and onwards

On the to do list for this week is some work on internationalisation for Botany One, but I doubt that will be finished by Friday. It might mean odd things appear and disappear on the site though. The other thing I have is chasing up some illustrations for posts where we already have the text, so I'm hoping we have a couple of guest posts this week.

Next event: Japanese Society of Plant Physiologists Meeting in Sapporo, March (OUP Stand)



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