An official website of the United States government
Summary Vascular bundles transport water and photosynthate to all organs, and increased bundle number contributes to crop lodging resistance. However, the regulation of vascular bundle formation is poorly understood in the Arabidopsis stem.We report a novel semi‐dominant mutant with high vascular activity,hva‐d, showing increased vascular bundle number and enhanced cambium proliferation in the stem. The activation of a C2H2 zinc finger transcription factor,AT5G27880/HVA, is responsible for thehva‐dphenotype. Genetic, biochemical, and fluorescent microscopic analyses were used to dissect the functions of HVA.HVA functions as a repressor and interacts with TOPLESS via the conserved Ethylene‐responsive element binding factor‐associated Amphiphilic Repression motif. In contrast to the HVA activation line, knockout ofHVAfunction with a CRISPR‐Cas9 approach or expression of HVA fused with an activation domain VP16 (HVA‐VP16) resulted in fewer vascular bundles. Further, HVA directly regulates the expression of the auxin transport efflux facilitatorPIN1, as a result affecting auxin accumulation. Genetics analysis demonstrated that PIN1 is epistatic to HVA in controlling bundle number.This research identifies HVA as a positive regulator of vascular initiation through negatively modulating auxin transport and sheds new light on the mechanism of bundle formation in the stem.
more »
« less
This content will become publicly available on May 1, 2026
habtools : An R package to calculate 3D metrics for surfaces and objects
Abstract Technological advances in three imaging techniques have opened the door to advanced morphological analyses and habitat mapping for biologists and ecologists.At the same time, the challenge of translating complex 3D data into meaningful metrics that can be used in conjunction with biological data currently hinders progress and accessibility.We introducehabtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow.We expect the functionality ofhabtoolsto continue to expand as new metrics and faster methods become available, and we welcome new contributions and ideas.
more »
« less
- Award ID(s):
- 1948946
- PAR ID:
- 10615710
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Methods in Ecology and Evolution
- Volume:
- 16
- Issue:
- 5
- ISSN:
- 2041-210X
- Page Range / eLocation ID:
- 895 to 903
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Ecosystem models offer a rigorous way to formalize scientific theories and are critical to evaluating complex interactions among ecological and biogeochemical processes. In addition to simulation and prediction, ecosystem models are a valuable tool for testing hypotheses about mechanisms and empirical findings because they reveal critical internal processes that are difficult to observe directly.However, many ecosystem models are difficult to manage and apply by scientists because of complex model structures, lack of consistent documentation, and low‐level programming implementation.Here, we present the ‘pnetr’ R package, which is designed to provide an easy‐to‐manage ecosystem modelling framework and detailed documentation in both model structure and programming. The framework implements a family of widely used PnET (net photosynthesis, evapotranspiration) ecosystem models, which are relatively parsimonious but capture essential biogeochemical cycles of water, carbon and nitrogen. We chose the R programming language because it is familiar to many ecologists and has abundant statistical modelling resources. We showcase examples of model simulations and test the effects of phenology on carbon assimilation and wood production using data measured by the Environmental Measurement Station (EMS) eddy‐covariance flux tower at Harvard Forest, MA.We hope ‘pnetr’ can facilitate further development of ecological theory and increase the accessibility of ecosystem modelling and ecological forecasting.more » « less
-
Abstract A prominent challenge for managing migratory species is the development of conservation plans that accommodate spatiotemporally varying distributions throughout the year. Migratory networks are spatially‐explicit models that incorporate migratory assignment and seasonal abundance data to define patterns of connectivity between stages of the annual cycle. These models are particularly useful for widespread application because different types of migratory data can be used to quantify individual and population‐level movement across the annual cycle of migratory species. While there are clear benefits of combining migratory assignment and abundance data for the development of conservation strategies, there is a concurrent need for corresponding user‐friendly software to facilitate the integration of these data for conservation.Here, we presentmignette(migratory network tools ensemble), an R package for developing migratory network models to estimate network connectivity among migratory populations. We demonstrate the functionality ofmignettewith three empirical examples that highlight the use of different types of tracking data for migratory assignment.mignettefacilitates the modelling of migratory networks by providing R functions to: (1) define breeding and nonbreeding nodes, (2) assemble abundance and assignment data and (3) model the migratory network. Additionally,mignetteprovides R functions to visualize modelled migratory networks.With increasing availability of migratory assignment and abundance data,mignetterepresents a valuable tool for developing effective conservation strategies for migratory species.more » « less
-
Summary White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype‐resolved chromosome‐scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data.Despite strongly conserved chromosome synteny and genome size acrossQuercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found thatQ. albahas high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus.The white oak genome represents a major new resource for studying genome diversity and evolution inQuercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution inQuercus.more » « less
-
Summary Plant homeodomain leucine zipper IV (HD‐Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)‐related lipid transfer (START) domain. While the START domain is required for TF activity, its presumed role as a lipid sensor is not clear.Here we used tandem affinity purification fromArabidopsiscell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative member that controls epidermal differentiation, recruits lysophosphatidylcholines (LysoPCs) in a START‐dependent manner. Microscale thermophoresis assays confirmed that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding.We additionally found that PDF2 acts as a transcriptional regulator of phospholipid‐ and phosphate (Pi) starvation‐related genes and binds to a palindromic octamer with consensus to a Pi response element. Phospholipid homeostasis and elongation growth were altered inpdf2mutants according to Pi availability. Cycloheximide chase experiments revealed a role for START in maintaining protein levels, and Pi starvation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity.We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Our data provide insights toward understanding how the lipid metabolome integrates Pi availability with gene expression.more » « less
