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The Week in Botany 147

April 27, 2020

Things seem to be shifting again, looking at what people following @botanyone on Twitter are sharing. I'm seeing more scientific papers, but still not many news stories or blog posts that don't mention a virus. There are, however, quite a few PhD and post-doc positions open, so I've added an extra section for that this week.
We have two new bloggers this starting this week on the site. Laura Skates from Perth, Australia writes about Aquilegia flowers and Liam Elliott from Oxford has written on cell walls and hornworts. It's perfect timing for me, as I move house next Monday, I'll be filing next week's email earlier as I have a lot of packing to do, but it should still be with you at the usual time. Until then, I hope you stay safe and healthy.
Alun (

From Botany One

Single copy genes produce a clearer phylogeny of the Apioideae
Analysis of over 3300 single copy genes has produced a well-supported topology with some significant changes.

Will heather be lucky heather as carbon dioxide concentrations rise?
A rise in carbon dioxide could affect production of plant defences in unexpected ways.

Plants have two ways of giving directions to cell wall builders
When getting cellulose to the cell wall, plant cells don't rely on just one set of directions.

In Lomatia, the pollen is naturally poisoned
Lomatia stores the ingredients for cyanide, somewhere in its flowers.

Can you find genetic echoes of an ancient ancestor in hornworts?
The genes hornworts share with other living plants may tell us something about their ancient common ancestor.

Functional composition of subalpine and alpine vegetation in the Apennine mountains
Stanisci et al. analyse aboveground plant strategies for resource use (conservative vs. acquisitive) and functional diversity syndrome (convergent vs. divergent) in calcareous grasslands of the central Apennines, Italy.

Staminodes of Aquilegia: how an unusual floral organ develops
Why would a flower want sterile stamens? An investigation into their development yields some clues.

Balancing the battle: how oak trees defend against new pathogens
Population genetics may decide if oak can fight off infections it has never seen before.

Morphology is most informative in reconstructing early tracheophyte evolution
More so than reproductive or anatomical features, morphology defines evolutionary relationships among early vascular plants.

News and Views

Ancient recipes led scientists to a long-lost natural blue
Medieval texts and modern techniques helped unveil the blue watercolor’s identity
Science News

The Chicago Guide to College Science Teaching
While I’ve mentioned it briefly in the past, now I’m ready for the full announcement: my book is good to go and is available for pre-order!
Small Pond Science

Plant disease: UK restricts olive tree imports to halt infection
Severe restrictions will be placed on imports of some very popular trees and plants in an effort to halt a deadly infection.
BBC News

Rice genetically engineered to resist heat waves can also produce up to 20% more grain
As plants convert sunlight into sugar, their cells are playing with fire. Photosynthesis generates chemical byproducts that can damage the light-converting machinery itself—and the hotter the weather, the more likely the process is to run amok as some chemical reactions accelerate and others slow. Now, a team of geneticists has engineered plants so they can better repair heat damage, an advance that could help preserve crop yields as global warming makes heat waves more common. And in a surprise, the change made plants more productive at normal temperatures.

Scientists are working to protect invaluable living collections during coronavirus lockdowns
During World War II, a devoted group of botanists guarded the world’s oldest collection of plants over the 28-month-long siege of Leningrad. Nearly a dozen of them starved to death, valuing the survival of the collection over their temptation to eat seeds.
The Conversation

Is a pandemic the time to think about genebanks?
Reasons to consider seeds in the time of the coronavirus.
Landscape News


The evolution of extreme nitrogen uptake in plants
The speed at which plants can take up nitrogen is a key limitation to plant growth rate. Genetic engineering to increase nitrogen use efficiency has met limited success because plants can modify their nitrogen uptake efficiency mechanisms in function of the available nitrogen level. Recently, a farming symbiosis involving ants that cultivate, fertilize, live in and defend epiphytic plants (Squamellaria) has been discovered in the Fiji Islands. In this symbiosis, farming ants have practised a form of ‘precision agriculture’ for millions of years, wherein they actively and exclusively provide nitrogen-rich faeces on particular plant structures called warts, which have evolved an extreme nitrogen uptake rate. This project aims to decipher how these symbiotic plants have this extreme uptake efficiency despite high nitrogen concentration.
Durham (UK)

Postdoc opportunity in modeling spatial dimensions of plant-microbe interactions
I am looking for a motivated postdoctoral researcher to join our plant and microbial ecology group starting August 2020. This project will investigate mechanisms underlying the role of microbes in shrubland-grassland ecotonal dynamics. The prospective postdoc will lead the development of spatially-explicit models of plant-microbe interactions and plant-soil feedbacks. There is also potential to pursue independent projects under the general umbrella of: the ecology of plant-soil feedbacks and plant-microbe interactions, competition and coexistence, and effects of climate variability and elevated CO2 on plants and microbes.
Georgia (US)

PhD position: Plant root gene regulatory networks in host-microbiome interactions (1.0 FTE)
Your research will decipher how plants under pathogen attack engage root microbiota for enhanced protection and contribute to innovations in future agriculture.
Utrecht (NL)

Global plant macroecology and evolution with focus on tropical rainforest
Applications are invited for a PhD fellowship/scholarship at Graduate School of Science and Technology, Aarhus University, Denmark, within the Biology programme. The position is available from 1 August 2020 or later.
Aarhus (DK)

PhD position in plant-microbe interactions
This position takes different approaches on identifying and characterizing plant transporter proteins crucial for plant-microbe interactions. The work includes characterizing Arabidopsis thaliana and Brachypodium distachyon lines deficient of these transporters. This work will involve molecular biology and biochemistry techniques, liquid chromatography-mass spectrometry, analysis of microbiomes, as well as imaging techniques.
Zurich (CH)

Postdoctoral Researcher (Dean Group)
A Postdoctoral Researcher position is available in the Professor Dame Caroline Dean Group to study antisense-mediated transcriptional regulation. The Dean group studies mechanisms of RNA-mediated chromatin regulation using genetic, molecular, and most recently, structural analysis (with MRC, LMB Cambridge). They investigate the sense-antisense circuitry at the Arabidopsis floral repressor locus FLC, how it links to alternative chromatin states that mediate transcriptional output and epigenetic switching, and how this has enabled adaptation to a range of habitats.
John Innes Centre (UK)

Scientific Papers

Teaching R in the undergraduate ecology classroom: approaches, lessons learned, and recommendations
Learning ecology requires training in data management and analysis. Because of its transparent and flexible nature, R is increasingly used for data management and analysis in the field of ecology. Consequently, job postings targeting candidates with a bachelor's degree and a required knowledge of R have increased over the past ten years. In this paper, Auker and Bathelmess begin by presenting data from the last ten years demonstrating the increase in the use of R, an open‐source programming environment, in ecology and its prevalence as a required skill in job descriptions. They then discuss our experiences teaching undergraduates R in two advanced ecology classes using different approaches.

Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision
Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Previously, we used in situ cryo-electron tomography to reveal the native architecture of thylakoid membranes... Wietrzynski et al. leverage technical advances to resolve the individual protein complexes within these membranes. Combined with a new method to visualize membrane surface topology, they map the molecular landscapes of thylakoid membranes inside green algae cells. Their tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains.

Profiling the epigenome at home
Henikoff and Henikoff recently described CUT&Tag, a general strategy for epigenomic profiing in which antibody-tethered Tn5 transposase integrates DNA sequencing adapters at sites of specific chromatin protein binding or histone modification in intact cells or nuclei. They now introduce a simplified CUT&Tag method that can be performed at home to help ameliorate the interruption of bench research caused by COVID-19 physical distancing requirements. All steps beginning with frozen nuclei are performed in single PCR tubes through to barcoded library amplication and clean-up, ready for pooling and DNA sequencing. Their CUT&Tag@home protocol has minimal equipment, reagent and supply needs and does not require handling of toxic or biologically active materials.

Fire as a fundamental ecological process: research advances and frontiers
McLauchlan et al. describe the diversity of ways in which fire operates as a fundamental ecological and evolutionary process on Earth. They explore research priorities in six categories of fire ecology: (1) characteristics of fire regimes, (2) changing fire regimes, (3) fire effects on aboveground ecology, (4) fire effects on belowground ecology, (5) fire behaviour, and (6) fire ecology modelling.
Journal of Ecology

SoilTemp: a global database of near‐surface temperature
Lembrechts et al. highlight a call for temperature time series submissions to SoilTemp, a geospatial database initiative compiling soil and near‐surface temperature data from all over the world. Currently this database contains time series from 7538 temperature sensors from 51 countries across all key biomes. The database will pave the way towards an improved global understanding of microclimate and bridge the gap between the available climate data and the climate at fine spatiotemporal resolutions relevant to most organisms and ecosystem processes.
Global Change Biology

Ligand-induced monoubiquitination of BIK1 regulates plant immunity
Recognition of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) triggers the first line of inducible defence against invading pathogens1,2,3. Receptor-like cytoplasmic kinases (RLCKs) are convergent regulators that associate with multiple PRRs in plants4. The mechanisms that underlie the activation of RLCKs are unclear. Ma et al. show that when MAMPs are detected, the RLCK BOTRYTIS-INDUCED KINASE 1 (BIK1) is monoubiquitinated following phosphorylation, then released from the flagellin receptor FLAGELLIN SENSING 2 (FLS2)–BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) complex, and internalized dynamically into endocytic compartments.

Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis
By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, Sun et al. show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within the KNOT, are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT, the knob, and the upstream and downstream flanking regions of the activated TEs.
Nature Communications

A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition
Seybold et al. present a conceptual framework based on coinfection assays, comparative metabolomics, and microbiome profiling to study the interaction of Zymoseptoria tritici in susceptible and resistant wheat. They demonstrate that Z. tritici suppresses the production of immune-related metabolites in a susceptible cultivar. Remarkably, this fungus-induced immune suppression spreads within the leaf and even to other leaves, a phenomenon that they term “systemic induced susceptibility”.
Nature Communications

[FROM 2013] Detection and Learning of Floral Electric Fields by Bumblebees
Plants and their pollinators have very intimate interactions, as emphasized by the many classic cases of coevolution among species of each. Such close relationships require signaling between plant and pollinator. Coordination between plant signals and pollinator perception has been shown to exist in flower color, shape, and odor. Clarke et al. report the potential for a distinct mode of plant–pollinator communication, electric fields. Natural floral electric fields, which are impacted by visits from naturally charged bees, were easily discriminated by bees, based on their level, pattern, and structure, and improved the rate at which bees remembered the location of a nectar reward.

From the frying pan: an unusual dwarf shrub from Namibia turns out to be a new brassicalean family
Tiganophyton karasense, an evergreen dwarf shrub, is described as a new species. A new genus and family are also proposed for it in the order Brassicales. Phylogenetic analysis of DNA sequence data indicate that Tiganophyton is sister to Bataceae / Salvadoraceae, and all three sister to Koeberliniaceae. First realized to be undescribed in 2010, T. karasense is a rare species known only from three localities in the arid Karas Region, southern Namibia. These small shrubs grow near the edges of seasonal pans on calcareous substrate underlaid by shales and mudstones of the Prince Albert Formation of the Karoo Supergroup.


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