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The Week in Botany 150

May 18, 2020

Normally, I try to see what people following @botanyone on Twitter have been sharing on a Friday afternoon. This week, it's being done on a Sunday night, just before I go to bed. It's been a busy week.
We have fourteen articles on Botany One this week. We also have a new look. I'm hoping this is the last time I say this for a while. The aim is to make the site faster to download on mobile and low-bandwidth connections. I'm pleased, because I've squashed a bug that prevented the site from crediting guest authors properly. I should update the guest author page this week.
I expect to remain busy as later this week, we should have articles on Plant Science's Next Top Models and on Orchid Conservation among other things. Until then, I hope you stay safe and well.
Alun (webmaster@botany.one)

From Botany One

Pattern-oriented modelling a useful tool for FSP models when experimental data is lacking
POM parameter estimation led to a model that converged on manual parameterization.

Job-sharing by the barley cuticle
In addition to preventing water loss, plant cuticles must also regulate nutrient loss, leaching. The eceriferum mutants in Hordeum vulgare (barley) potentially influence these functions by altering epicuticular wax structure and composition.

New insights on the role of cytokinin in nodule formation
Cytokinins may have a role in controlling both bacterial accommodation and tissue differentiation related to nodule formation.

Bloody plants! How soybean uses haemoglobins to obtain nitrogen
Excess nitrogen significantly accelerated nodule senescence and the production of green leghaemoglobin in nodules.

Reconsidering the conservation of an endangered tree in Brazil: one species or a hybrid?
Muniz and colleagues used genetic methods to reveal that a critically endangered tree in an ecotone is actually a hybrid between two other species from different habitats. 

‘Two households, both alike …’? How differences between sexes varies with time in flowering plants
Moquet and colleagues investigate variation over time of sexual dimorphism using the dioecious plant species Silene dioica.

Scientific study shows you can garden your way to health
The act of gardening is one of the key correlates with wellbeing, a survey finds.

The importance of quantitative trait differentiation in habitat restoration
Yoko et al. established a common garden experiment using the widespread North American perennial Geum triflorum to examine trait differences attributable to regional or population environments.

How do plants work?
Beauty is more than skin deep in this book explaining how plants function.

‘Out of Iberia’: How Bristol rock cress got to where it is today
Is a population of rare cress found near Bristol, UK, a remnant of an ice age population, or is it part of a wider European population that survived in refugia somewhere?

V-Mango model: an intricate 3D simulation of the King of Fruits
The computer-modelled mangoes could identify when their real-life counterparts were most at risk from mango blossom gall midge.

Success the hard way: iron-dependent cell death in a rice pathogen
Qing Shen and colleagues show that an iron-dependent form of programmed cell death is required for the infection process of the major plant pathogen rice blast.

Larch, still Number 1!
If a tree falls in a forest, can it still insulate people from sound pollution?

The mystery element: building a variable plant cuticle
Cutan must play a role in plant cuticles, but it's not clear how much cutan a cuticle contains.



News and Views

Artificial chloroplasts turn sunlight and carbon dioxide into organic compounds
Just like mechanics cobble together old engine parts to build a new roadster, synthetic biologists have remade chloroplasts, the engine at the heart of photosynthesis. By combining the light-harvesting machinery of spinach plants with enzymes from nine different organisms, scientists report making an artificial chloroplast that operates outside of cells to harvest sunlight and use the resulting energy to convert carbon dioxide (CO2) into energy-rich molecules. The researchers hope their souped-up photosynthesis system might eventually convert CO2 directly into useful chemicals—or help genetically engineered plants absorb up to 10 times the atmospheric CO2 of regular ones.
Science

Cyber-spinach turns sunlight into sugar
Combination of biological membrane and artificial chemistry could power future synthetic organisms.
Nature

Genera Palmarum - The Evolution and Classification of the Palms
Bill Baker says: "Genera Palmarum - the "bible" for devotees of the #palm family is now freely available online! Please spread the news!"
Royal Botanic Gardens, Kew research repository

M.Sc. position in plant systems biology
The M.Sc. student will gain experience with cutting-edge proteomic and metabolomics mass spectrometry technologies and seek to answer a fundamental question in biology related to how different levels of cellular regulation interact to allow complex organisms to grow under changing environmental cues.
Alberta, CA

Women's research plummets during lockdown - but articles from men increase
Many female academics say juggling their career with coronavirus childcare is overwhelming.
The Guardian

Old math reveals new secrets about these alluring flowers
A model developed by Alan Turing can help explain the spots on these astoundingly diverse flowers—and many other natural patterns as well.
National Geographic

Meet this super-spotter of duplicated images in science papers
Elisabeth Bik quit her job to spot errors in research papers — and has become the public face of image sleuthing.
Nature

Include the true value of nature when rebuilding economies after coronavirus
The pandemic is devastating economies. As countries look to revive growth, recovery must go with — not against — the grain of nature.
Nature

The Shape-Shifting Star Chickweed
"Star chickweed (Stellaria pubera) has been called North America’s showiest chickweed and I am inclined to agree. Come mid-spring, this lovely woodland plant produces wonderful white flowers that measure about 1/2 inch across and are ringed by five petals so deeply notched that there appear to be ten."
In Defense of Plants

Plant Science in Avatar
You might not have to travel from one star system to another to experience the joys of Pandora. In this blog post, I hope to show you how the magic of Pandora can be found on our own wonderful, little planet.
Fronds with Benefits



Scientific Papers

Effect of sequence depth and length in long-read assembly of the maize inbred NC358
Ou et al. have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, they show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly.
Nature Communications

Imaging flowers: a guide to current microscopy and tomography techniques to study flower development
Prunet and Duncan review modern light microscopy and computed projection tomography methods, their capabilities and limitations, and they discuss their current and potential applications to the study of flower development and fertilization.
Journal of Experimental Botany

Field courses narrow demographic achievement gaps in ecology and evolutionary biology
Beltran et al. compared the relationships among academic success measures and demographic data (race/ethnicity, socioeconomic status, first‐generation, and gender) for UC Santa Cruz undergraduate students admitted between 2008 and 2019 who participated in field courses (N = 941 students) and who did not (N = 28,215 students). Additionally, they administered longitudinal surveys to evaluate self‐efficacy gains during field‐based versus classroom‐based courses (N = 570 students). They found no differences in the proportion of students matriculating at the university as undecided, proposed EEB, or proposed other majors across demographic groups. However, five years later, under‐represented students were significantly less likely to graduate with EEB degrees, indicating retention rather than recruitment drives disparities in representation.
Ecology and Evolution

The proportion of soil-borne pathogens increases with warming at the global scale
Using data from a global field survey and a nine-year field experiment, Delgado-Baquerizo et al. show that warmer temperatures increase the relative abundance of soil-borne potential fungal plant pathogens. Moreover, they provide a global atlas of these organisms along with future distribution projections under different climate change and land-use scenarios. These projections show an overall increase in the relative abundance of potential plant pathogens worldwide.
Nature Climate Change

Lichens and associated fungi from Glacier Bay National Park, Alaska
Lead author Toby Spribille says: "Nine years after beginning field work on lichens in
@GlacierBayNPS, very pleased to share our team's paper documenting the highest diversity of lichens and associated fungi ever documented in the Americas. 947 species at 59°N!"
The Lichenologist

Forest microclimate dynamics drive plant responses to warming
Microclimates are key to understanding how organisms and ecosystems respond to macroclimate change, yet they are frequently neglected when studying biotic responses to global change. Zellweger et al. provide a long-term, continental-scale assessment of the effects of micro- and macroclimate on the community composition of European forests. They show that changes in forest canopy cover are fundamentally important for driving community responses to climate change.
Science
 

Flowering plant composition shapes pathogen infection intensity and reproduction in bumble bee colonies
Flowering strips are increasingly planted to increase pollinator abundance and diversity in agricultural settings, but flowers can also be disease transmission sites between pollinators. However, the effect of plant species composition on bee disease is unknown. Adler et al. compared the effect of flowering strips with high- or low-infection plant species, or no flowering strips, on bee infection and reproduction in tents. Using high-infection flowering strips doubled bee infection intensity compared to low-infection flowering strips. However, bee reproduction was higher with any flowering strips. Thus, floral resources in flowering strips benefited bees, but certain plants also come with a risk of increased pathogen infection intensity.
PNAS

Late-spring frost risk between 1959 and 2017 decreased in North America but increased in Europe and Asia
Frost in late spring causes severe ecosystem damage in temperate and boreal regions. Zohner et al. analyze late-spring frost occurrences between 1959 and 2017 and woody species’ resistance strategies to forecast forest vulnerability under climate change. Leaf-out phenology and leaf-freezing resistance data come from up to 1,500 species cultivated in common gardens. The greatest increase in leaf-damaging spring frost has occurred in Europe and East Asia, where species are more vulnerable to spring frost than in North America. The data imply that 35 and 26% of Europe’s and Asia’s forests are increasingly threatened by frost damage, while this is only true for 10% of North America.
PNAS

The Moss Physcomitrium (Physcomitrella) patens: A Model Organism for Non-Seed Plants
Since the discovery two decades ago that transgenes are efficiently integrated into the genome of Physcomitrella patens by homologous recombination, this moss has been a premier model system to study evolutionary developmental biology questions, stem cell reprogramming, and the biology of nonvascular plants. P. patens was the first non-seed plant to have its genome sequenced. With this level of genomic information, together with increasing molecular genetic tools, a large number of reverse genetic studies have propelled the use of this model system. A number of technological advances have recently opened the door to forward genetics as well as extremely efficient and precise genome editing in P. patens. Additionally, careful phylogenetic studies with increased resolution have suggested that P. patens emerged from within Physcomitrium. Thus, rather than Physcomitrella patens, the species should be named Physcomitrium patens. Here Rensing et al. review these advances and describe the areas where P. patens has had the most impact on plant biology.
Plant Cell

A molecular framework underlying the compound leaf pattern of Medicago truncatula
He et al. show that the trifoliate leaf pattern of the model leguminous plant Medicago truncatula is controlled by the BEL1-like homeodomain protein PINNATE-LIKE PENTAFOLIATA1 (PINNA1). They identify PINNA1 as a determinacy factor during leaf morphogenesis that directly represses transcription of the LEAFY (LFY) orthologue SINGLE LEAFLET1 (SGL1), which encodes an indeterminacy factor key to the morphogenetic activity maintenance. ReadCube 
Nature Plants

Urban biodiversity management using evolutionary tools
Lambert and Donihue present a framework for categorizing urban biodiversity from a management perspective. They then discuss a suite of example management tools and their potential evolutionary implications—both their opportunities for and potential consequence to management. Urban ecosystems are proliferating but, far from being ecological lost causes, they may provide unique insights and opportunities for biodiversity conservation. Determining how to achieve urban biodiversity priorities while managing pest species requires evolutionary thinking.
Nature Ecology & Evolution

Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin
Borg et al. describe a multi-layered mechanism by which H3K27me3 is globally lost from histone-based sperm chromatin in Arabidopsis. This mechanism involves the silencing of H3K27me3 writers, activity of H3K27me3 erasers and deposition of a sperm-specific histone, H3.10 (ref. 5), which they show is immune to lysine 27 methylation. The loss of H3K27me3 facilitates the transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation. Thus, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome.
Nature Cell Biology

How to trick a plant pathogen?
Plants can get sick too. In fact, they get infected by all types of microbes and little critters. But plants have evolved an effective immune system to fight off pathogen invasion. Amazingly, nearly every single plant cell is able to protect itself and its neighbours against infections.
Zenodo


     

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