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The Week in Botany 137

February 17, 2020

Normally somewhere in this introduction I plug following @botanyone on Twitter. However, if you're a PhD student, then Plantae is also a good place to be. This week, for example, people have been sharing a webinar on how to prepare a manuscript for submission
However, I will mention the Special issue on Coastal Flooding and Storm Risks from Annals of Botany that is free access for another two and a bit months. I'll probably be doing that again when the newsletter returns next week.
Alun (webmaster@botany.one)

From Botany One

Distribution of Veronica polyploids is influenced by both habitat differentiation and historic glaciation
Species with higher ploidy levels prefer cooler, wetter habitats than diploids.

Gene copy number is associated with phytochemistry in Cannabis sativa
THCA and CBDA were thought to have a simple mode of inheritance; however, a recent study by Vergara et al. describes that in fact multiple gene copies are involved in their production.

The Next Generation of Natural Historians
Recap of the Student Spotlights 2020: Discover the next generation of natural historians event at the Linnean Society.

Climate change threatens the first line of defence against coastal storms
When the storms come in, plants could help secure natural defences. But climate change is giving them problems of their own.

Scaly Tree Ferns Have Slow and Steady Diversification
Did the Cyatheaceae become such a diverse family slowly over time, or in spurts? The largest molecular sampling yet points to gradual accumulation of species.

Nature Table – BBC Radio 4
BBC Radio 4 has a new science-comedy crossover show.

Sodium chloride solutions not a good experimental substitute for sea water
Simulating seawater in the lab is more complicated than just getting the salt concentration right.

Decrypting the tubby-like protein gene family in cassava
Dong et al. identify and characterise the cassava TLP gene family, MeTLP, at the genomic level. 

Does Viagra really help preserve flowers?
It is said that sildenafil citrate can help preserve flowers. Here’s an experiment that you could do at home, but probably shouldn’t, to find out.



News and Views

Plantae Webinar Recording Available | Preparing your Manuscript for Submission with Mary Williams
In this webinar, ASPB Features Editor Mary Williams will outline the key steps in writing a paper, preparing figures, and navigating the submission process.
Plantae Community

World Pulses Day
Pulses, also known as legumes, are the edible seeds of leguminous plants cultivated for food. Dried beans, lentils and peas are the most commonly known and consumed types of pulses.
United Nations

French court rules sweet grapefruit, barley, wheat and 2500 crops, developed by mutagenizing seeds with toxic chemicals or gamma rays yet often sold as organic, are GMO, must be labeled and cultivation banned
Sometimes a headline makes a summary redundant.
Genetic Literacy Project

Just1Action4WIS
"My call for action under the banner #Just1Action4WIS – which of these can you commit to? There should be something for everyone here, whatever their role: as academic, teacher, student, parent or simply a member of the public."
Athene Donald's Blog

Global economic growth will take big hit due to loss of nature
Damage to environment could wipe £368bn a year from growth by 2050 and UK will be hard hit, WWF warns.
The Guardian

Deforested parts of Amazon 'emitting more CO2 than they absorb'
Up to one fifth of the Amazon rainforest is emitting more CO2 than it absorbs, new research suggests.
BBC News

Antarctic temperature rises above 20C for first time on record
Scientists describe 20.75C logged at Seymour Island as ‘incredible and abnormal’
The Guardian

A Growing Presence on the Farm: Robots
A new generation of autonomous robots is helping plant breeders shape the crops of tomorrow.
The New York Times

Drought-tolerant GMO wheat boosts yields up to 22% in field trials, while drought-tolerant soy could launch in 2020
During the latest harvest, drought-tolerant wheat yielded up to 22.1% more, according to tests conducted on 395 hectares, [the biotech firm] Bioceres said.
Genetic Literacy Project

Curiosity is the first step in fighting the climate crisis
"The origin of the word “biologist” is “life-learner”. If you are gazing at life from a window, swimming in water, hiking up a mountain, or experiencing nature via the dulcet tones of Sir David Attenborough, you are a biologist too." Opinion by Alexandre Antonelli.
Evening Standard



Scientific Papers

An inferred fitness consequence map of the rice genome
Joly-Lopez et al. present a fitness consequence (fitCons) map for rice (Oryza sativa). They inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae.
Nature Plants

EXO70D isoforms mediate selective autophagic degradation of Type-A ARR proteins to regulate cytokinin sensitivity
Acheampong et al. describe a mechanistic link between cytokinin signaling and autophagy, demonstrating that plants modulate cytokinin sensitivity through autophagic regulation of type-A ARR proteins. Type-A ARR proteins were degraded by autophagy in an AUTOPHAGY-RELATED (ATG)5-dependent manner. EXO70D family members interacted with Type-A ARR proteins, likely in a phosphorylation-dependent manner, and recruited them to autophagosomes via interaction with the core autophagy protein, ATG8. Consistently, loss-of-function exo70D1,2,3 mutants compromised targeting of type-A ARRs to autophagic vesicles, have elevated levels of type-A ARR proteins, and are hyposensitive to cytokinin.
bioRxiv

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy
In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, Valuchova et al. have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy.
eLife

The hornwort genome and early land plant evolution
Zhang et al. report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance.
Nature Plants

The strength and pattern of natural selection on gene expression in rice
Groen et al. assayed gene expression in rice (Oryza sativa), and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions.
Nature

Genomics of sorghum local adaptation to a parasitic plant | PNAS
Bellis et al. develop a framework to characterize associations between genome variants in global landraces (traditional varieties) of the staple crop sorghum with the distribution of the devastating parasitic weed Striga hermonthica. They find long-term maintenance of diversity in genes related to parasite resistance, highlighting an important role of host adaptation for coevolutionary dynamics in smallholder agroecosystems.
PNAS

The pan-genome effector-triggered immunity landscape of a host-pathogen interaction
Plant pathogens elicit an immune response through effector proteins. In turn, plant genomes encode genes that determine species-specific recognition of these effectors by a process known collectively as effector-triggered immunity (ETI). By examining a range of strains of the pathogen Pseudomonas syringae that infect the model plant Arabidopsis thaliana, Laflamme et al. generated a P. syringae Type III Effector Compendium (PsyTEC) and in turn identified the genes responsible for ETI in Arabidopsis.
Science

TOR dynamically regulates plant cell–cell transport
Brunkard et al. show that the ancient eukaryotic TARGET OF RAPAMYCIN (TOR) metabolic signaling network controls plasmodesmata (PD) transport in plants. TOR is a protein kinase that is activated by nutrients, including sugars, and then coordinates growth with nutrient availability. Our study demonstrates that TOR has evolved new roles in plants by regulating cell–cell connectivity via PD.
PNAS

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff
VanBuren et al. report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows them to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, they detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids.
Nature Communications

Ecological strategies begin at germination: traits, plasticity, and survival in the first four days of plant life
We commonly use trait variation to characterize plant function within and among species and understand how vegetation responds to the environment. Seedling emergence is an especially vulnerable window affecting population and community dynamics, yet trait‐based frameworks often bypass this earliest stage of plant life. Larson et al. assess whether traits vary in ecologically‐meaningful ways when seedlings are just days old. How do shared evolutionary history and environmental conditions shape trait expression, and can traits explain which seedlings endure drought?
Functional Ecology


     

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