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.
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!"
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.
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.
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.
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.
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
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.