Biology subjects

Emms, D. M.

Publications and source records attributed to Emms, D. M..

8 recordsLinked to original sources

bioRxiv2025

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinders high accuracy comparative genomic framework to provide substantially enhanced scalability and accuracy. Specifically, we show that enhanced phylogenetic delineation of orthogroups provides a 7% relative increase in orthogroup inference accuracy. We further demonstrate that a new gene assignment method substantially reduces overall runtime RAM usage without compromising accuracy. The latest version of OrthoFinder is available at https://github.com/OrthoFinder/OrthoFinder.

bioinformatics↗

bioRxiv2021

Conditional Stomatal Closure in a Fern Shares Molecular Features with Flowering Plant Active Stomatal Responses

Stomata evolved as plants transitioned from water to land, enabling carbon dioxide uptake and water loss to be controlled. In flowering plants, the most recently divergent land plant lineage, stomatal pores actively close in response to drought. In this response, the phytohormone abscisic acid (ABA) triggers signalling cascades that lead to ion and water loss in the guard cells of the stomatal complex, causing a reduction in turgor and pore closure. Whether this stimulus-response coupling pathway acts in other major land plant lineages is unclear, with some investigations reporting that stomatal closure involves ABA but others concluding that closure is passive. Here we show that in the model fern Ceratopteris richardii active stomatal closure is conditional on sensitisation by pre-exposure to either low humidity or exogenous ABA and is promoted by ABA. RNA-seq analysis and de novo transcriptome assembly reconstructed the protein coding complement of the C. richardii genome with coverage comparable to other plant models, enabling transcriptional signatures of stomatal sensitisation and closure to be identified. In both cases, changes in abundance of homologs of ABA, Ca2+ and ROS-related signalling components were observed, suggesting that the closure response pathway is conserved in ferns and flowering plants. These signatures further suggested that sensitisation is achieved by lowering the threshold required for a subsequent closure-inducing signal to trigger a response. We conclude that the canonical signalling network for active stomatal closure functioned in at least a rudimentary form in the stomata of the last common ancestor of ferns and flowering plants. Significance StatementStomata are valve-like pores that control the uptake of CO2 and the loss of water vapour in almost all land plants. In flowering plants, stomatal opening and closure is actively regulated by a stimulus-response coupling network. Whether active stomatal responses are present in other land plant lineages such as ferns has been hotly debated. Here we show that stomatal responses in the fern Ceratopteris richardii are active but depend on their past growth environment, and demonstrate that fern stomatal closure and sensitisation are associated with the altered expression of genes whose homologs function in the canonical stomatal regulatory network of flowering plants. Genetic pathways for active stomatal regulation therefore most likely evolved before the divergence of ferns and flowering plants.

plant biology↗

bioRxiv2020

RuBisCO adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analysed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically-resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover ([~]21-37 %), and between the Michaelis constants for CO2 and O2 ([~]9-19 %), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9 %) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints (most likely caused by a slow rate of molecular evolution) have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all such trade-offs.

plant biology↗

bioRxiv2020

A role for neutral variation in the evolution of C4 photosynthesis

Convergent trait evolution is a recurrent phenomenon in all domains of the tree of life. While some convergent traits are caused by simple sequence changes, many are associated with extensive changes to the sequence and regulation of large cohorts of genes. It is unknown how organisms traverse this expansive genotype space to assemble such complex convergent phenotypes. C4 photosynthesis is a paradigm of large-scale phenotypic convergence. Conceptual and mathematical models propose that C4 photosynthesis evolved from ancestral C3 photosynthesis through sequential adaptive changes. These adaptive changes could have been rapidly assembled if modifications to the activity and abundance of enzymes of the C4 cycle was neutral in C3 plants. This neutrality would enable populations of C3 plants to maintain genotypes with expression levels of C4 enzymes analogous to those in C4 species and thus enable rapid assembly of a functional C4 cycle from naturally occurring genotypes given shared environmental selection. Here we show that there is substantial natural variation in expression of genes encoding C4 cycle enzymes between natural accessions of the C3 plant Arabidopsis thaliana. We further show through targeted transgenic experiments in the C3 crop Oryza sativa, that high expression of the majority of C4 cycle enzymes in rice is neutral with respect to growth, development, biomass and photosynthesis. Thus, substantial variation in the abundance and activity of C4 cycle enzymes is permissible within the limits of operation of C3 photosynthesis and the emergence of component parts of this complex convergent trait can be facilitated by neutral variation.

plant biology↗

bioRxiv2019

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves

Rhizomorphic lycopsids are the land plant group that includes the first giant trees to grow on Earth and extant species in the genus Isoetes. Two mutually exclusive hypotheses account for the evolution of terminal rooting axes called rootlets among the rhizomorphic lycopsids. One hypothesis states that rootlets are true roots, like roots in other lycopsids. The other states that rootlets are modified leaves. Here we test predictions of each hypothesis by investigating gene expression in the leaves and rootlets of Isoetes echinospora. We assembled the de-novo transcriptome of axenically cultured I. echinospora. Gene expression signatures of I. echinospora rootlets and leaves were different. Furthermore, gene expression signatures of I. echinospora rootlets were similar to gene expression signatures of true roots of Selaginella moellendorffii and Arabidopsis thaliana. RSL genes which positively regulate cell differentiation in roots were either exclusively or preferentially expressed in the I. echinospora rootlets, S. moellendorffii roots and A. thaliana roots compared to the leaves of each respective species. Taken together, gene expression data from the de-novo transcriptome of I. echinospora are consistent with the hypothesis that Isoetes rootlets are true roots and not modified leaves.

plant biology↗

bioRxiv2019

A Musashi-Related Protein Is Essential For Gametogenesis In Arabidopsis

Musashi (Msi) proteins are an evolutionarily conserved group of RNA-binding proteins, required for targeted control of mRNA translation during many important developmental processes in animals. Most notably, Msi proteins play important roles during both spermatogenesis and oogenesis. Msi proteins also exist in plants but these are largely uncharacterized. Here we report the functional characterization of an Arabidopsis Msi ortholog ABORTED GAMETOPHYTE 2 (AOG2), which encodes a protein containing two RNA recognition motifs and an ER-targeting signal. AOG2-GFP translational fusions were localized to the ER in transient assays, suggesting that AOG2 most likely binds to ER-targeted mRNAs. We show that disrupted AOG2 function leads to a high rate of both ovule and seed abortion, and that homozygous loss of function mutants are embryo lethal. Furthermore, we demonstrate that AOG2 is required to establish asymmetry during pollen mitosis I, and that loss of AOG2 function leads to loss of pollen viability. Collectively the results reveal that AOG2 is required for the establishment of polarity and/or the progression of mitosis during gametophyte development in Arabidopsis, and thus Msi-related proteins have an evolutionarily conserved role in gametogenesis in both animals and plants.\n\nSIGNIFICANCE STATEMENTABORTED GAMETOPHYTE 2 (AOG2) encodes a Musashi-related RNA-binding protein that is required for gametogenesis and embryogenesis in Arabidopsis. AOG2 is required for the establishment of polarity and/or the progression of mitosis during gametophyte development in Arabidopsis, and thus Musashi-related proteins have an evolutionarily conserved role in gametogenesis in both animals and plants.

plant biology↗

bioRxiv2018

OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinders high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted genes trees, gene duplication events, the rooted species tree, and comparative genomic statistics. Each output is benchmarked on appropriate real or simulated datasets and, where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinders comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.

bioinformatics↗

bioRxiv2017

STRIDE: Species Tree Root Inference From Gene Duplication Events

The correct interpretation of a phylogenetic tree is dependent on it being correctly rooted. A gene duplication event at the base of a clade of species is synapamorphic, and thus excludes the root of the species tree from that clade. We present STRIDE, a fast, effective, and outgroup-free method for species tree root inference from gene duplication events. STRIDE identifies sets of well-supported gene duplication events from cohorts of gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of the true root. We show that STRIDE infers the correct root of the species tree for a large range of simulated and real species sets. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for datasets where information is limited. Furthermore, application of STRIDE to inference of the origin of the eukaryotic tree resulted in a root probability distribution that was consistent with, but unable to distinguish between, leading hypotheses for the origin of the eukaryotes. In summary, STRIDE is a fast, scalable, and effective method for species tree root inference from genome scale data.

evolutionary biology↗