October 25, 2021

🌱TWiB October 25, 2021

It's a lot easier to work on these emails on a Sunday evening when the evenings are light. Next week in the UK the clocks move back, so the evening shall come even sooner. But if you live in the better hemisphere, then you have the comfort of spring being well underway.

While the harvest is coming to an end in the UK, Plants People Planet is sowing the seeds of a special issue on fruit. They're looking for papers on many topics from microbiomes to fruit production to conservation. I think it could be a fascinating issue, as PPP is good at crossing the biology of plants with the social element of how we interact with them.

On my to-do list this week is learn Spanish, and catch up with some of the videos Plantlife has been putting out on YouTube. For example, it looks like they have an interesting introduction to Palaeoecology. And there's also compile another email to send out this time next week. If it turns out that I can learn all Spanish in a week, I'll be sure to let you know.

Until then, take care.

Alun (webmaster@botany.one)

In Botany One

New maize reference genome may help grow genetically modified lines of corn more easily — www.botany.one The ugly duckling of corn may hold the key to having better grains in the future.

3D model of rhizodeposition — www.botany.one A new model simulates rhizodeposition patterns around growing and exuding root systems.

Flowers grow less yellow without sulphur, and that could affect the pollinators that need to see them — www.botany.one Both Van Gogh and Nature like to use sulphur-derived pigments for flowers, but what happens when there's not enough sulphur?

Are species hiding in the Arctic? — www.botany.one Some of the problems that limit the number of species in the Arctic might also contribute to creating new species.

Building a better grapevine model — www.botany.one A new perennial fruit crop accurately depicts phenology, light interception, carbohydrate allocation and reserve dynamics, and yield components.

News & Views

Meet our #PlantSciStory2021 storytellers: Benedetta Gori - The Global Plant Council — globalplantcouncil.org Benedetta Gori is a young scientist with a highly interdisciplinary background. After a degree in Food Science, and two Masters in Ethnobotany and Plant Taxonomy, she is now working at Kew Gardens as part of the Useful Plants and Fungi of Colombia (UPFC) project, focusing on the conservation and revitalisation of neglected edible plants.

Attempt to charge Mexican scientists with ‘organized crime’ prompts international outcry — www.nature.com The Mexican government has accused 31 scientists and officials of organized crime and money laundering — allegations that they deny and that many claim are politically motivated.

Keeping up with the plant killers by KamounLab I gave this talk in 2020, the International Year of Plant Health, to discuss the pathogens that infect our crop plants. You can see that this talk dates to April 2020 — so, while we were all thinking about a viral pandemic, other pandemics, pandemics of plant diseases, were threatening our crops.

Tree-Killing Pests Across the United States Are Increasing the Threats of Climate Change — www.nature.org First-of-its-kind study finds forest insects and diseases are leading to nearly 50 million more tons of carbon dioxide in the atmosphere each year.

The story behind the 100% public GM bean reaching Brazilian plates

“It is a technology that can be used for small farmers and to address local problems and crops. Large companies aren’t going to invest in sweet potatoes, cassava, beans or peanuts. They prefer to invest in crops of large areas that are grown in different countries. That is why developing countries have to make an investment in their own problems.

Wide gap between Canadians’ beliefs about biotech crop safety and the science — geneticliteracyproject.org Consumer opinions, perspectives and views on food and its production do not necessarily reflect what is occurring. For instance, we know from risk assessment and production data that there is no difference in the safety or nutritional value of food products, regardless of the method used to produce the product. 

Loved to death: Australian sandalwood is facing extinction in the wild — theconversation.com The sweet, earthy fragrance of sandalwood oil has made it immensely popular in incense sticks, candles and perfumes. But its beautiful scent may also be its downfall – Australian sandalwood (Santalum spicatum) is facing extinction in the wild.

Scientific Papers

Automatic identification and annotation of MYB gene family members in plants A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application.

Comparison of read mapping and variant calling tools for the analysis of plant NGS data High-throughput sequencing technologies have rapidly developed during the past years and became an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequence and the identification of sequence variants. Since most benchmarking studies of bioinformatics tools for this purpose have been conducted on human datasets, there is a lack of benchmarking studies in plant sciences. In this study, we evaluated the performance of 50 different variant calling pipelines, including five read mappers and ten variant callers, on six real plant datasets of the model organism Arabidopsis thaliana. Sets of variants were evaluated based on various parameters including sensitivity and specificity. We found that all investigated tools are suitable for analysis of NGS data in plant research.

Gene discovery in plant metabolism: Listening to the sound of silence, but where? An essential strategy for studying a gene’s function is to silence its expression in the living organism and observe the resulting phenotype. To this end, virus-induced gene silencing (VIGS) is a popular tool that can selectively and transiently knockdown genes of interest (GOIs; Ratcliff et al., 1997; Courdavault and Besseau, 2020).

Towards predicting photosynthetic efficiency and biomass gain in crop genotypes over a field season

Keller et al. long-term monitored Fq’/Fm’ at the canopy level for twenty-one soybean (Glycine max (L.) Merr.) and maize (Zea mays) genotypes under greenhouse and field conditions using automated chlorophyll fluorescence and spectral scans. Fq’/Fm’ derived under incident sunlight during the entire growing season was modeled based on genotypic interactions with different environmental variables.

Physical disturbance by recovering sea otter populations increases eelgrass genetic diversity — www.science.org Work in sea otters over the last few decades has transformed our understanding of the importance of specific species, or keystones, as drivers of community structure and stability. Foster et al. took the next step and tested whether otter foraging might influence genetic diversity in an eelgrass ecosystem

Unraveling the regulatory network of bamboo lignification

The ability to deposit the complex phenolic polymer lignin in the cell walls of specialized cell types was a key evolutionary step toward the dominance of the terrestrial ecosystem by plants. Lignin confers mechanical strength to supportive tissues and hydrophobicity to xylem cells, allowing the efficient transport of water and nutrients throughout the plant body. Lignin also plays a major role in the response of plants to various biotic and abiotic stresses. Although essential to plant growth and development, lignin constitutes a major hurdle in the conversion of plant biomass into downstream products in biorefineries.

Grapevines under drought do not express esca leaf symptoms — www.pnas.org The world is witnessing a sharp increase in perennial plant dieback. The hypothesized cause is that environmental stresses such as drought are interacting with pathogens fueling plant decline. Global viticulture has seen similar decreases in fruit yield and vine longevity. One of the hypothesized causes is a synergy between drought and the grapevine vascular disease esca, for which there is no known curative treatment. In sharp contrast to this theory, our study demonstrates that drought completely suppresses esca leaf symptoms, and although esca and drought both alter plant water transport and carbon balance, they do so in completely distinct ways. This understanding reveals the complexity and unpredictability of the stress interactions thought to drive plant mortality.

The Plasmodium NOT1-G paralogue is an essential regulator of sexual stage maturation and parasite transmission

Hart et al. show that in Plasmodium parasites, the NOT1 scaffold protein of the CAF1/CCR4/Not complex is duplicated, and one paralogue is dedicated for essential transmission functions. Moreover, this NOT1-G paralogue is central to the sex-specific functions previously associated with its interacting partners, as deletion of not1-g in Plasmodium yoelii leads to a comparable or complete arrest phenotype for both male and female parasites. They show that, consistent with its role in other eukaryotes, PyNOT1-G localizes to cytosolic puncta throughout much of the Plasmodium life cycle. PyNOT1-G is essential to both the complete maturation of male gametes and to the continued development of the fertilized zygote originating from female parasites.

An invasive species erodes the performance of coastal wetland protected areas — www.science.org

The world has increasingly relied on protected areas (PAs) to rescue highly valued ecosystems from human activities, but whether PAs will fare well with bioinvasions remains unknown. By analyzing three decades of seven of the largest coastal PAs in China, including World Natural Heritage and/or Wetlands of International Importance sites, Ren et al. show that, although PAs are achieving success in rescuing iconic wetlands and critical shorebird habitats from once widespread reclamation, this success is counteracted by escalating plant invasions.

A phytobacterial TIR domain effector manipulates NAD+ to promote virulence Pseudomonas syringae DC3000 type III effector HopAM1 suppresses plant immunity and contains a TIR domain homologous to immunity-related TIR domains of plant NLRs that hydrolyze NAD+ and activate immunity. In vitro and in vivo assays were conducted to determine if HopAM1 hydrolyzes NAD+ and if the activity is essential for HopAM1’s suppression of plant immunity and contribution to virulence. HPLC and LC-MS were utilized to analyze metabolites produced from NAD+ by HopAM1 in vitro and in both yeast and plants. Agrobacterium-mediated transient expression and in planta inoculation assays were performed to determine HopAM1’s intrinsic enzymatic activity and virulence contribution.

A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants The genetic basis and evolution of sex determination in dioecious plants is emerging as an active area of research with exciting advances in genome sequencing and analysis technologies. As the sole species within the sister lineage to all other extant flowering plants, Amborella trichopoda is an important model for understanding the evolution and development of flowers. Plants typically produce only male or female flowers, but sex determination mechanisms are unknown for the species. Sequence data derived from plants of natural origin and an F1 mapping population were used to identify sex-linked genes and the nonrecombining region.

Careers

Independent Junior Research Group Leader (m/f/d) Productive candidates with postdoctoral (international) experience will have to demonstrate their potential to develop a vigorous and competitive research program on important contemporary problems in plant biology/chemistry at the molecular, biochemical or systems level.

Full Professorship (W3) for Plant Cell Biology We seek an internationally renowned scientist in the field of plant molecular biology, who preferentially investigates current topics within the field of molecular plant cell biology using biochemical and/or metabolic approaches. Aspects of signal perception and signal transduction should be visible. A research on plant membranes, the cell wall or metabolic signalling pathways are desirable but not mandatory requirements. The scientific profile of the candidate should integrate well into the over-arching thematic focus “Cellular adaptations of plants to varying environmental cues”.

Research Assistant III The CRoPS project aims to develop crop plants that sequester more carbon via extensive root systems containing recalcitrant carbon polymers to fight climate change. A major component of this research is to phenotype plant traits for conducting genetic analysis and confirm trait changes of genetic changes.

Postdoctoral Researcher We’re looking for a Postdoctoral Researcher to join the Penfield Group, working on cutting-edge science in the field of Crop Genetics. The Penfield group works to understand how weather and climate affect plant reproductive development and seed quality.

Laboratory Technician Applications are invited for the position of Laboratory Technician in the research group of Dr. Sebastian Schornack at the Sainsbury Laboratory, Cambridge University (www.schornacklab.net). The group studies processes of plants which permit colonization by filamentous pathogens and symbiotic fungi. Our work is based on genetic, molecular biological, cell biological and developmental approaches.

Post Doctoral Research Fellow #2 Rust Resistance The Department of Plant Sciences at North Dakota State University is seeking a postdoctoral research fellowto work in dry bean breeding/genetics program. Greenhouse, laboratory, and field activities focused towards the genetic analysis of breeding and genetic populations by using genotypic and phenotypic data and its application into dry bean improvement. The successful applicant is also expected to collaborate with scientists in other departments and institutions to better understand the genetic mechanisms of biotic and abiotic stresses. Specifically, the main responsibility of this individual will be the pyramiding of both known and new bean rust resistance genes, the development of molecular/genomic tools for marker assisted selection, and the deployment of those genes into improved germplasm and commercial cultivars.  Reporting and budget management duties will be made in coordination with the project  leader. Project is initially planned for ~2 years with a possibility of a renewal/extension.

Harvard University Herbaria Research Fellowship The Harvard University Herbaria (HUH; http://huh.harvard.edu) invites nominations and direct applications for the Harvard University Herbaria Research Fellowship, a fellowship in plant and/or fungal science. We especially seek outstanding early-career scientists and collections professionals who see new opportunities and innovations for collections-based research. The goal of the program is to facilitate collections-based research using resources at the HUH which include more than five million specimens of algae, bryophytes, fungi, and vascular plants with complementary Libraries and Archives. The collection includes herbarium sheet material of extant species as well as a paleobotanical and archaeobotanical collection and artifacts of economically important plants and fungi. 

Assistant Professor - Ecology and Evolutionary Biology We are interested in applicants whose research is in the area of Ecology and Evolution, with a focus on urban environments. This search is part of a cluster hire in Transforming Ecologies in Urban Environments that also includes the Department of Environmental Studies and will likely expand to other Departments in future years. More information about this cluster can be found here, along with background about NYU's broader Faculty Cluster Hiring Initiative. This search is for tenure track Assistant Professors. Candidates are expected to develop an externally-funded research program and to participate in the teaching mission of the Department.

Upland Carbon Ecologist This post will initially work primarily with the Peatland team, back filling a 50% secondment of the Peatland team lead PI to NatureScot. The post holder will initially work on existing peatland restoration projects measuring carbon fluxes. However, the post holder will be expected to grow the Hutton’s research in the area of carbon cycling and related biological interactions in upland habitats by working with not only the peatland team, but others within the Biodiversity and Ecosystems group, as well as other groups across the institute.

RESEARCH FELLOW (PLANT-SOIL MICROBIOMES) The Research Fellow (Plant-Soil Microbiomes) will play a key role in the ARC Research Hub Theme 3 (Harnessing plant-soil microbiome interactions for optimising nutrient capture and informing fertiliser design) and collaborate with the other Themes across this multi-disciplinary, industry-university partnership.

EASTBIO: Deciphering the role of translation in temperature-controlled development Ambient temperature has profound effects on almost all aspects of plant development, from the onset of seed germination and seedling establishment to flower and fruit production. Consequently, temperature also strongly impacts crop quality and yield. With the progression of climate change, plants in temperate regions are challenged by more frequent heat waves as well as an overall rise in ambient temperature. Gaining insight into a plant’s response to temperature is thus vital to fully understand how climate change will affect plant growth and development in the future and may also indicate ways to mitigate negative effects of rising temperatures on crop production. 

Assistant Professor We are searching for a tenure-track assistant professor position in Ecology and Evolution of Infectious Plant Diseases in the Department of Botany & Plant Pathology. The successful candidate will be expected to establish a robust and extramurally funded research program that will address ecological and evolutionary processes that drive the dynamics of infectious plant diseases. The focus of the program can be on existing and/or emerging plant infectious diseases that are important to the sustainability of agricultural systems in Oregon and the Pacific Northwest. All research topics within the area of ecology and evolution of infectious plant diseases will be considered.

Postdoc of Fungal host-pathogen genomics — employment.ku.dk The Applied Evolutionary Ecology (AEE) group at Department of Plant and Environmental Sciences (PLEN), Section for Organismal Biology at the University of Copenhagen is advertising a two year Postdoctoral fellowship in comparative genomics and evolutionary ecology of plant and insect-associated Colletotrichum fungi starting April 1st 2022 or as soon as possible thereafter.

Decoding gene expression in polyploid wheat. (PhD) We found that 30 % of wheat genes show different expression levels between the A, B and D homoeologs suggesting that the homoeologs may be non-redundant. We hypothesise that the ability to manipulate the relative expression levels of homoeologs may provide a route to reduce functional redundancy and more easily alter phenotypes in wheat. Therefore, in this project we will investigate the mechanisms that control homoeolog expression levels including epigenetic and nonsense-mediate decay pathways, and their effects on phenotype.

Do shared genetic pathways control drought tolerance and senescence in wheat? (PhD) We have recently discovered several transcription factors which delay senescence (ageing) in wheat, which we hypothesise could provide a route to improve drought tolerance, as has been shown in other plant species. We will use a combination genetic variation studies, knock-out mutants and overexpression lines to ask whether these transcription factors can be used to improve drought tolerance. This part of the project will provide opportunities to run greenhouse and field trials in an academic and commercial research environment and gain a wide range of molecular biology skills.

Research Assistant I The Haus Lab in the Department of Horticulture is hiring a Research Assistant I who will provide expert support and assist in overseeing and coordinating root biology research. Major responsibilities include maintaining and enforcing lab safety guidelines, performing routine lab work to support research projects (including ordering, equipment calibration/maintenance, etc.), assisting in planning and designing experiments, running small-scale pilot experiments collecting root data on various plant species, and writing short reports on the analysis of these experiments. The ideal candidate must have a strong expertise in growing diverse plant species in a greenhouse and growth chamber with special interest for candidates who have also worked in a field setting. Some basic wet lab experience is desired but not required.

Research Associate-Fixed Term The Haus Lab in the Department of Horticulture at Michigan State University is hiring a research associate (postdoctoral position) to lead ongoing root biology research identifying root developmental traits associated with the multiple origins of dry bean and investigating legume root responses to abiotic stressors. Dry beans are an important source of plant-based iron and protein, but production is limited by a number of environmental stressors. Our projects aim to mitigate production losses using inherent, but poorly understood root traits. The successful candidate will lead research projects using developmental, quantitative genetics, and bioinformatic-based approaches. Expertise in plant development or bioinformatics (e.g. genetic mapping and transcriptomics) is preferred. The successful applicant should also have strong writing and communication skills and be able to work independently and as part of an interdisciplinary research team.

Hybridization and climate change in Alpine orchids (PhD) The student will have the opportunity for fieldwork in the Alps as well as training in methods in both the field and lab settings. This includes methods in genetics, entomology, botany, and bioinformatics. Professional training in scientific writing and presentation, as well as development of knowledge in the field through reading, are also an integral part of this project.

Faculty Research Assistant The Department of Botany & Plant Pathology invites applications for a full-time (1.0 FTE), 12-month, fixed-term Faculty Research Assistant position. Reappointment is at the discretion of the Department Head.

Assistant/Associate/Full Professor The Department of Biology (https://biology.uncg.edu/about/the-department/) at the University of North Carolina Greensboro (UNCG) seeks an innovative biologist in any biological subdiscipline at the Assistant/Associate/Full Professor rank who studies plant and/or pollinator biology. With nearly all flowering plants requiring pollinators, the pollination crisis is impacting both human and environmental health. Therefore, we are seeking an individual to take an intellectual leadership role in UNCG’s plant and pollinator research including our state of the art Plant and Pollinator Center (PPC;https://biology.uncg.edu/ppc/), integrate their work with our current strengths (e.g., honey bee microbiome, orphan crops, plant physiological and community ecology), and fit into the Department of Biology’s highly collaborative environment.

Post-Doctoral Associate This is a one year renewable appointment up to a maximum of 5 years within the Plant Pathology and Plant Microbe Biology Section of the School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456.  The position is currently available with a start date as soon as possible.   Applications are sought for a post-doctoral research position studying pathogens of hemp (Cannabis sativa <0.3% tetrahydrocannabinol), which is grown for grain, fiber, and cannabinoid production.

Community Biodiversity Officer We are looking for a Community Biodiversity Officer to join our Trees and Landscapes team. The Trees and Landscape section is based within the Community Services Department. The section comprises of a Landscapes and Leisure Development Manager, Principal Tree and Landscape Officer, two Tree & Landscape Officers, Leisure Contracts and Landscapes Projects Officer and the new Community Biodiversity Officer.

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