Leaf shape is spectacularly diverse. As a major component of plant architecture and an interface for light capture, gas exchange, and thermoregulation, the potential contributions of leaves to plant ...fitness are innumerable. Particularly because of their intimate association and interaction with the surrounding environment, both the plasticity of leaf shape during the lifetime of a plant and the evolution of leaf shape over geologic time are revealing with respect to leaf function. Leaf shapes arise within a developmental context that constrains both their evolution and environmental plasticity. Quantitative models capturing genetic diversity, developmental context, and environmental plasticity will be required to fully understand the evolution and development of leaf shape and its response to environmental pressures. In this review, we discuss recent literature demonstrating that distinct molecular pathways are modulated by specific environmental inputs, the output of which regulates leaf dissection. We propose a synthesis explaining both historical patterns in the paleorecord and conserved plastic responses in extant plants. Understanding the potential adaptive value of leaf shape, and how to molecularly manipulate it, will prove to be invaluable in designing crops optimized for future climates.
Leaf shape is spectacularly diverse. Here, Chitwood and Sinha discuss recent literature demonstrating that distinct molecular pathways are modulated by specific environmental inputs, the output of which regulates leaf dissection. A synthesis explaining both historical patterns in the paleorecord and conserved plastic responses in extant plants is also proposed.
Chimeras – organisms that are composed of cells of more than one genotype – captured the human imagination long before they were formally described and used in the laboratory. These organisms owe ...their namesake to a fire-breathing monster from Greek mythology that has the head of a lion, the body of a goat, and the tail of a serpent. The first description of a non-fictional chimera dates back to the middle of the seventeenth century when the Florentine gardener Pietro Nati discovered an adventitious shoot growing from the graft junction between sour orange (Citrus aurantium) and citron (Citrus medica). This perplexing chimera that grows with sectors phenotypically resembling each of the citrus progenitors inspired discussion and wonder from the scientific community and was fittingly named the 'Bizzaria’. Initially, the ‘Bizzaria’ was believed to be an asexual hybrid that formed from a cellular fusion between the grafted parents; however, in-depth cellular analyses carried out centuries later demonstrated that the ‘Bizzaria’, along with other chimeras, owe their unique sectored appearance to a conglomeration of cells from the two donors. Since this pivotal discovery at the turn of the twentieth century, chimeras have served both as tools and as unique biological phenomena that have contributed to our understanding of plant development at the cellular, tissue, and organismal level. Rapid advancements in genome sequencing technologies have enabled the establishment of new model species with novel morphological and developmental features that enable the generation of chimeric organisms. In this review, we show that genetic mosaic and chimera studies provide a technologically simple way to delve into the organismal, genetic, and genomic inner workings underlying the development of diverse model organisms. Moreover, we discuss the unique opportunity that chimeras present to explore universal principles governing intercellular communication and the coordination of organismal biology in a heterogenomic landscape.
•The first chimera was discovered more than four centuries ago.•Chimeras are heterogenomic organisms composed of cells of more than one genotype.•Heterogenomicity is a powerful tool for uncovering core principles of development.
Violin design has been in flux since the production of the first instruments in 16th century Italy. Numerous innovations have improved the acoustical properties and playability of violins. Yet, other ...attributes of the violin affect its performance less, and with fewer constraints, are potentially more sensitive to historical vagaries unrelated to quality. Although the coarse shape of violins is integral to their design, details of the body outline can vary without significantly compromising sound quality. What can violin shapes tell us about their makers and history, including the degree that luthiers have influenced each other and the evolution of complex morphologies over time? Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history. Specific shape attributes, which discriminate instruments produced by different luthiers, strongly correlate with historical time. Linear discriminant analysis reveals luthiers who likely copied the outlines of their instruments from others, which historical accounts corroborate. Clustering of averaged violin shapes places luthiers into four major groups, demonstrating a handful of discrete shapes predominate in most instruments. Violin shapes originating from multi-generational luthier families tend to cluster together, and familial origin is a significant explanatory factor of violin shape. Together, the analysis of four centuries of violin shapes demonstrates not only the influence of history and time leading to the modern violin, but widespread imitation and the transmission of design by human relatedness.
Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the ...environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features—connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub‐disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data‐driven era where the meaningful interpretation of large data sets is a limiting factor.
Efforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that ...persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (
). We find that compared with some commonly used conventional traits, (1) persistent-homology-based methods can more comprehensively capture morphological variation; (2) these techniques discriminate between genotypes with a larger normalized effect size and detect a greater number of unique quantitative trait loci (QTLs); (3) multivariate traits, whether statistically derived from univariate or persistent-homology-based traits, improve our ability to understand the genetic basis of phenotype; and (4) persistent-homology-based techniques detect unique QTLs compared to conventional traits or their multivariate derivatives, indicating that previously unmeasured aspects of morphology are now detectable. The QTL results further imply that genetic contributions to morphology can affect both the shoot and root, revealing a pleiotropic basis to natural variation in tomato. Persistent homology is a versatile framework to quantify plant morphology and developmental processes that complements and extends existing methods.
Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene ...sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
Summary
The iconic, palmately compound leaves of Cannabis have attracted significant attention in the past. However, investigations into the genetic basis of leaf shape or its connections to ...phytochemical composition have yielded inconclusive results. This is partly due to prominent changes in leaflet number within a single plant during development, which has so far prevented the proper use of common morphometric techniques.
Here, we present a new method that overcomes the challenge of nonhomologous landmarks in palmate, pinnate, and lobed leaves, using Cannabis as an example. We model corresponding pseudo‐landmarks for each leaflet as angle‐radius coordinates and model them as a function of leaflet to create continuous polynomial models, bypassing the problems associated with variable number of leaflets between leaves.
We analyze 341 leaves from 24 individuals from nine Cannabis accessions. Using 3591 pseudo‐landmarks in modeled leaves, we accurately predict accession identity, leaflet number, and relative node number.
Intra‐leaf modeling offers a rapid, cost‐effective means of identifying Cannabis accessions, making it a valuable tool for future taxonomic studies, cultivar recognition, and possibly chemical content analysis and sex identification, in addition to permitting the morphometric analysis of leaves in any species with variable numbers of leaflets or lobes.
Mobile small RNAs serve as local positional signals in development and coordinate stress responses across the plant. Despite its central importance, an understanding of how the cell-to-cell movement ...of small RNAs is governed is lacking. Here, we show that miRNA mobility is precisely regulated through a gating mechanism polarised at defined cell-cell interfaces. This generates directional movement between neighbouring cells that limits long-distance shoot-to-root trafficking, and underpins domain-autonomous behaviours of small RNAs within stem cell niches. We further show that the gating of miRNA mobility occurs independent of mechanisms controlling protein movement, identifying the small RNA as the mobile unit. These findings reveal gate-keepers of cell-to-cell small RNA mobility generate selectivity in long-distance signalling, and help safeguard functional domains within dynamic stem cell niches while mitigating a 'signalling gridlock' in contexts where developmental patterning events occur in close spatial and temporal vicinity.
Cassava (Manihot esculenta) feeds c. 800 million people world-wide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest ...deterioration and the roots contain low nutritional content.
Here, we provide molecular identities for 11 cassava tissue/organ types through RNA-sequencing and develop an open access, web-based interface for further interrogation of the data.
Through this dataset, we consider the physiology of cassava. Specifically, we focus on identification of the transcriptional signatures that define the massive, underground storage roots used as a food source and the favored target tissue for transgene integration and genome editing, friable embryogenic callus (FEC). Further, we identify promoters able to drive strong expression in multiple tissue/organs.
The information gained from this study is of value for both conventional and biotechnological improvement programs.
Despite a long-standing interest in the genetic basis of morphological diversity, the molecular mechanisms that give rise to developmental variation are incompletely understood. Here, we use ...comparative transcriptomics coupled with the construction of gene coexpression networks to predict a gene regulatory network (GRN) for leaf development in tomato and two related wild species with strikingly different leaf morphologies. The core network in the leaf developmental GRN contains regulators of leaf morphology that function in global cell proliferation with peripheral gene network modules (GNMs). The BLADE-ON-PETIOLE (BOP) transcription factor in one GNM controls the core network by altering effective concentration of the KNOTTED-like HOMEOBOX gene product. Comparative network analysis and experimental perturbations of BOP levels suggest that variation in BOP expression could explain the diversity in leaf complexity among these species through dynamic rewiring of interactions in the GRN. The peripheral location of the BOP -containing GNM in the leaf developmental GRN and the phenotypic mimics of evolutionary diversity caused by alteration in BOP levels identify a key role for this GNM in canalizing the leaf morphospace by modifying the maturation schedule of leaves to create morphological diversity.
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