🌻 TWiB July 25, 2022
It turns out an extra dot worked its way into a URL last week, so I'll just mention that the Spanish homepage is at https://botany.one/es and hope this time the link works. I'm still working on the Spanish side of the site so it'll be a little while before other languages return.
In other news, I thought the heatwave was bad in the UK, but there's a message from Twitter, included below, showing that it had more dangers in parts of Europe. I expect dealing with unexploded ordnance is a tough job anyway, but doing it in the middle of a bush fire is a whole other level of difficulty.
Another issue of the newsletter should be with you at the same time next week. Until then, take care.
Alun (webmaster@botany.one)
In Botany One
Where does a hemiparasite's food come from? — botany.one A parasitic plant's ability to steal carbon rests in their haustoria, specialised organs they use to tap into a host plant.
When invasive plants move in, where do native pollinators go? — botany.one Invasive plants change the opportunities for pollinators, helping some but harming others.
News & Views
‘Avalanche of fires’: what the front pages around the world say From Portugal’s ‘panic and despair’ to ‘Hell’ in Croatia, newspapers in many countries are dominated by the wildfires
In Ecuador's Amazon, indigenous forest defense gains legal ground — longreads.trust.org Deep in Ecuador's Amazon rainforest, indigenous leader Marcelo Lucitante deftly climbs a tree and attaches a camera trap, camouflaged among thick jungle foliage, to record footage of trespassing illegal gold miners.
ggdensity: A new R package for plotting high-density regions — www.business-science.io As data scientists, it can be downright impossible to drill into messy data. Fortunately, there’s a new R package that helps us focus on a “high-density region”, which is simply an area in a scatter plot defined by a high percentage of the data points. It’s called ggdensity.
GitHub - kevinsblake/NatParksPalettes: Color palette package inspired by National Parks. Color palettes inspired by National Parks. Structure of this package is based on code from the MetBrewer package.
Light pollution is disrupting the seasonal rhythms of plants and trees, lengthening pollen season in US cities — theconversation.com
City lights that blaze all night are profoundly disrupting urban plants’ phenology – shifting when their buds open in the spring and when their leaves change colors and drop in the fall. New research Yuyu Zhou coauthored shows how nighttime lights are lengthening the growing season in cities, which can affect everything from allergies to local economies.
Lab Life: When your PhD (almost) falls apart | eLife As a chance observation threatens to unravel several years of work, a PhD student must choose what to do next.
Why I don’t have trouble finding peer reviewers I see this very often in social media, and also in conversation with other academic editors: it’s getting harder and harder to get find people who agree to review manuscripts.
Open science to tackle plant health emergencies: enough excuses, please! — kamounlab.medium.com The thorny politics of the global food trade are often an excuse against the application of open science principles to plant disease epidemics. But scientists have often themselves to blame for the slow release of information and data, and there are ways around some of the issues.
This 500-Year-Old Tree in California Has a Story to Tell — www.nytimes.com Deep within the trunk of an ancient tree, traces of drought and deluge.
How to create simple diagrams in Inkscape – a guide for scientists — www.thepostedstamp.com Over the last week I had some fun making a couple of diagrams for our World Congress of Soil Science 2022 poster. Not going to lie, it took me a while to put them together but I’m glad I took on the learning curve. I decided to use Inkscape create my images. I thought it might be useful if shared some of the things I learnt on how to create a diagram in Inkscape, so if you fancied using Inkscape too, you’ve got somewhere to start from. I’m definitely not an expert, not by any stretch of the imagination, but from one novice to another this is how I approached it.
Scientific Papers
Environmental strigolactone drives early growth responses to neighboring plants and soil volume in pea — www.cell.com
Wheeldon et al. test whether strigolactones act as either cues or signals for neighbor detection. We show that peas detect neighbors early in the life cycle through their root systems, resulting in strong changes in shoot biomass and branching, and that this requires strigolactone biosynthesis. We demonstrate that uptake and detection of strigolactones exuded by neighboring plants are needed for this early neighbor detection, and that plants that cannot exude strigolactones are outcompeted by neighboring plants and fail to adjust growth to their soil volume.
Supra-organismal regulation of strigolactone exudation and plant development in response to rhizospheric cues in rice — www.cell.com
Since flowering plants have an endogenous perception system for strigolactones, strigolactones are obvious candidates to act as a cue for neighbor presence, but have not been shown to act as such. To test this hypothesis in rice plants, Yoneyama et al. quantified two major strigolactones of rice plants, orobanchol and 4-deoxyorobanchol, in root exudates by using LC-MS/MS (MRM) and examined feedback regulation of strigolactone biosynthesis and changes in shoot branching phenotypes in rice plants grown at different densities in hydroponics and soil culture.
Structural Plastome Evolution in Holoparasitic Hydnoraceae with Special Focus on Inverted and Direct Repeats — academic.oup.com
Jost et al. study Hydnoraceae, one of the oldest and least investigated parasitic angiosperm lineages. Plastome comparative genomics, using seven out of eight known species of the genus Hydnora and three species of Prosopanche, reveal a high degree of structural similarity and shared gene content; contrasted by striking dissimilarities with respect to repeat content [inverted and direct repeats (DRs)]. They identified varying inverted repeat contents and positions, likely resulting from multiple, independent evolutionary events, and a DR gain in Prosopanche. Considering different evolutionary trajectories and based on a fully resolved and supported species-level phylogenetic hypothesis, they describe three possible, distinct models to explain the Hydnoraceae plastome states.
Mapping peat thickness and carbon stocks of the central Congo Basin using field data — www.nature.com
Crezee et al. present the first extensive field surveys of peat in the Democratic Republic of the Congo, which covers two-thirds of the estimated peatland area, including from previously undocumented river-influenced settings. They use field data from both countries to compute the first spatial models of peat thickness (mean 1.7 ± 0.9 m; maximum 5.6 m) and peat carbon density (mean 1,712 ± 634 MgC ha−1; maximum 3,970 MgC ha−1) for the central Congo Basin. They show that the peatland complex covers 167,600 km2, 36% of the world’s tropical peatland area, and that 29.0 PgC is stored below ground in peat across the region (95% confidence interval, 26.3–32.2 PgC).
A diverse group of underappreciated zygnematophytes deserves in-depth exploration
The conjugating green algae (Zygnematophyceae) are the closest relatives of land plants and hence are of great evolutionary interest. Besides the popular placoderm desmids and the filamentous species, there is an underappreciated diversity of unicellular zygnematophytes with a much “simpler” morphology and smooth cell walls – traditionally referred to as “saccoderm desmids”. These saccoderm desmids have a broad geographic distribution and are ecologically diverse. Many species inhabit terrestrial habitats such as dead wood, rock surfaces and glacial ice. Furthermore, several of the saccoderm genera have turned out to be highly polyphyletic and are typically poorly captured by environmental sequencing approaches. One of these genera is Mesotaenium Nägeli, with ~70 described species and infraspecific taxa united only by a relatively simple (plate- or ribbon-like) chloroplast structure. Busch and Hess shed some light on these inconspicuous yet important members of the algal flora and present an updated rbcL gene phylogeny of the conjugating green algae, including several new lineages of Mesotaenium-like zygnematophytes.
Trutzenberg et al. performed phylogenetic analyses and annotated barley PRONE-GEFs. The leaf epidermal-expressed PRONE-GEF HvGEF14 undergoes a transcriptional down-regulation on inoculation with B. graminis f. sp. hordei and directly interacts with the ROP GTPase and susceptibility factor HvRACB in yeast and in planta. Overexpression of activated HvRACB or of HvGEF14 led to the recruitment of ROP downstream interactor HvRIC171 to the cell periphery. HvGEF14 further supported direct interaction of HvRACB with a HvRACB-GTP-binding CRIB (Cdc42/Rac Interactive Binding motif) domain-containing HvRIC171 truncation. Finally, the overexpression of HvGEF14 caused enhanced susceptibility to fungal entry, while HvGEF14 RNAi provoked a trend to more penetration resistance.
The rice blast fungus Magnaporthe oryzae causes a devastating disease which threatens global rice production. In spite of intense study, the biology of plant tissue invasion during blast disease remains poorly understood. Yan et al. report a high resolution, transcriptional profiling study of the entire plant-associated development of the blast fungus. Their analysis revealed major temporal changes in fungal gene expression during plant infection.
Agrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation — www.nature.com
Agrobacterium-mediated plant transformation (AMT) is the basis of modern-day plant biotechnology. One major drawback of this technology is the recalcitrance of many plant species/varieties to Agrobacterium infection, most likely caused by elicitation of plant defense responses. Raman et al. develop a strategy to increase AMT by engineering Agrobacterium tumefaciens to express a type III secretion system (T3SS) from Pseudomonas syringae and individually deliver the P. syringae effectors AvrPto, AvrPtoB, or HopAO1 to suppress host defense responses.
To help EEB researchers adopt useful features from GitHub in their own workflows, Crystal-Ornelas et al. review twelve practical ways to use the platform. We outline features ranging from low to high technical difficulty: storing code, managing projects, coding collaboratively, conducting peer review, and writing a manuscript.
Jointly Modeling the Evolution of Discrete and Continuous Traits
Whether modeling the evolution of a discrete or continuous character, the focal trait of interest does not evolve in isolation and require comparative methods that model multivariate evolution. Progress along these lines has involved modeling multivariate evolution of the same class of character and there are fewer options when jointly modeling traits when one character is discrete and the other is continuous. Boyko et al. develop such a framework to explicitly estimate the joint likelihood for discrete and continuous characters.
Light regulates xylem cell differentiation via PIF in Arabidopsis — www.cell.com
In this study Ghosh et al. show that the accumulation of PIF transcription factors in the dark promotes TDIF signaling and inhibits vascular cell differentiation. On the contrary, PIF inactivation by light leads to a decay in TDIF activity, which induces vascular cell differentiation.
Studies focused solely on single organisms can fail to identify the networks underlying host–pathogen gene-for-gene interactions. Sugihara et al. integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik.
Replicated radiation of a plant clade along a cloud forest archipelago — www.nature.com
Donoghue et al. document the repeated evolution of a set of leaf ecomorphs in a group of neotropical plants. The Oreinotinus lineage within the angiosperm clade Viburnum spread from Mexico to Argentina through disjunct cloud forest environments. In 9 of 11 areas of endemism, species with similar sets of leaf forms evolved in parallel. They reject gene-flow-mediated evolution of similar leaves and show, instead, that species with disparate leaf forms differ in their climatic niches, supporting ecological adaptation as the driver of parallelism.
Increases in vein length compensate for leaf area lost to lobing in grapevine
Migicovsky et al. used homologous landmarking techniques to measure 2632 leaves across 2 years in 476 unique, genetically distinct grapevines from five biparental crosses that vary primarily in the extent of lobing. They determined to what extent leaf area explained variation in lobing, vein length, and vein to blade ratio.
Careers
Postoctoral researcher (w/m/d) For our team, we are looking for a postdoctoral researcher with experience in analyzing genomic data sets in non-model species and with an interest in working with trees. The postdoctoral researcher will have the opportunity to establish his/her own profile in forest genetics research and teaching.
Research Assistant (postdoctoral position) The position is offered for a period of 4 years, if no former times of qualification must be considered. The starting date is as soon as possible. The position is full-time with salary and benefits commensurate with a public service position in the state Hesse, Germany (TV-H E 13).
Horticultural Educator (Grow & Learn in Nature Award) The Caley currently has a fantastic opportunity for someone to join our ranks as a Horticultural Educator working as part of the GLiN Award/ CRT project.
Postdoctoral Scholar in Plant Genomics We seek a postdoctoral researcher to work on a project investigating the role of network biology and quantitative genomic variation (both host and pathogen) in controlling the evolution of plant/biotic interactions across eudicots.
Assistant Professor The Department of Entomology & Plant Pathology at North Carolina State University invites applications for two 12-month tenure-track positions at the Assistant Professor level in Extension Plant Pathology. Both faculty positions are located on the main campus in Raleigh, and incumbents are responsible for extension engagement and research related to their extension responsibilities.
Scientific Officer Flora The team at the Australian Biological Resources Study (ABRS) are seeking an enthusiastic and qualified person to undertake a range of duties in the Flora Team. You will be helping to lead development and expansion of botanical treatments into online platforms (e.g., Flora of Australia and National Species List), in line with nomenclatural codes, accepted taxonomic concepts and our flora standards.
Research Fellow (Cellular Biochemistry of CO2 fixation) This is an opportunity to study the biochemistry and cell biology of “superior” red-type Rubiscos from marine phytoplankton. These enzymes are able to operate in our current atmosphere more efficiently than those found in our crop species, but we are not able to harness their potential due to their inability to fold and assemble in plant chloroplasts. The goal of the programme is to unlock their potential for biotechnology.
Doctoral student position available immediately on transcriptional regulation of arbuscular mycorrhiza. The position is available immediately in the lab of Caroline Gutjahr at the Weihenstephan Campus of the Technical University in Freising, close to Munich. In 2023, the laboratory will move to the Max Planck Institute of Molecular Plant Physiology (MPI-MP) in Potsdam. The position (income level German 65% TVL E13) is initially for 1 year with planned extension for up to 4 years.
GIS, Research and Monitoring Officer We are looking to recruit a GIS, Research and Monitoring Officer to provide technical expertise to facilitate the Trust’s research and monitoring programme.
Postdoc Researcher We are looking for a highly motivated team member with a strong interest in plant development, molecular and cell biology. A number of approaches, including plant histology, high-resolution microscopy, gene editing and transcriptomics-based approaches will be employed during this project. Applicants must be willing to apply to international fellowships (e.g. EMBO, Marie Curie).
Assistant Forum Editor The New Phytologist Foundation is seeking an enthusiastic and proactive individual to join our team as Assistant Forum Editor for New Phytologist. This post holder will support the Forum Editor by aiding in all aspects of the reimaging and delivery of the New Phytologist Forum as a community hub for those with a fascination for plants and their role in society and the natural world.
Associate or Senior Editor, Plant Sciences We are looking for someone with a strong research background in Plant Sciences (at the post-doctoral level) with broad interests in plant growth, reproduction, evolution, adaptation, and use, particularly at the molecular and cellular level, to complement our current expertise in plant ecology. An interest in environmental microbiology is an advantage. We seek applicants who love science and are able to rigorously and critically evaluate scientific work.
Privacy Policy
We store your email in order to know who to send the emails to. We have to share that list with Revue because they’re the company that actually sends the emails out. We get information about how many emails open, so it might be 50% one week, but we wouldn’t be able to tell if you were in the half that opens the email or the half that didn’t. Revue have their own longer privacy policy.
The email is funded by the Annals of Botany Company.
How to create simple diagrams in Inkscape – a guide for scientists — www.thepostedstamp.com Over the last week I had some fun making a couple of diagrams for our World Congress of Soil Science 2022 poster. Not going to lie, it took me a while to put them together but I’m glad I took on the learning curve. I decided to use Inkscape create my images. I thought it might be useful if shared some of the things I learnt on how to create a diagram in Inkscape, so if you fancied using Inkscape too, you’ve got somewhere to start from. I’m definitely not an expert, not by any stretch of the imagination, but from one novice to another this is how I approached it.