David Emms
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View article: OrthoFinder: scalable phylogenetic orthology inference for comparative genomics
OrthoFinder: scalable phylogenetic orthology inference for comparative genomics Open
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy comparative genomic framework to provide substantially enhanced scalability and accuracy. Specifically, we show that enhanced phylogenetic…
View article: Rubisco is evolving for improved catalytic efficiency and CO <sub>2</sub> assimilation in plants
Rubisco is evolving for improved catalytic efficiency and CO <sub>2</sub> assimilation in plants Open
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of…
View article: GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes Open
The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple g…
View article: Rubisco is evolving for improved catalytic efficiency and CO<sub>2</sub>assimilation in plants
Rubisco is evolving for improved catalytic efficiency and CO<sub>2</sub>assimilation in plants Open
Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of…
View article: Author response: GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
Author response: GENESPACE tracks regions of interest and gene copy number variation across multiple genomes Open
Article Figures and data Abstract Editor's evaluation eLife digest Introduction Results and discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract The d…
View article: The Quest for Orthologs orthology benchmark service in 2022
The Quest for Orthologs orthology benchmark service in 2022 Open
The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existi…
View article: GENESPACE: syntenic pan-genome annotations for eukaryotes
GENESPACE: syntenic pan-genome annotations for eukaryotes Open
The development of multiple high-quality reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple refer…
View article: Dataset for, "SHOOT: phylogenetic gene search and ortholog inference"
Dataset for, "SHOOT: phylogenetic gene search and ortholog inference" Open
Test data for "SHOOT: phylogenetic gene search and ortholog inference". Files are described in the README.md file within the archive.
View article: SHOOT: phylogenetic gene search and ortholog inference
SHOOT: phylogenetic gene search and ortholog inference Open
Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here we present the phylogenetic search, SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and r…
View article: Ten Years of Collaborative Progress in the Quest for Orthologs
Ten Years of Collaborative Progress in the Quest for Orthologs Open
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whethe…
View article: Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off
Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off Open
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, thes…
View article: Conditional Stomatal Closure in a Fern Shares Molecular Features with Flowering Plant Active Stomatal Responses
Conditional Stomatal Closure in a Fern Shares Molecular Features with Flowering Plant Active Stomatal Responses Open
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 dr…
View article: Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench Open
Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert-curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup infe…
View article: Supplemental Dataset for, "Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench" - updated published version
Supplemental Dataset for, "Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench" - updated published version Open
The supplemental dataset for, "Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench". This is the updated dataset for the article published in Genome Biology and Evolution.
View article: <i>NO GAMETOPHORES 2</i>is a novel regulator of the 2D to 3D growth transition in the moss<i>Physcomitrium patens</i>
<i>NO GAMETOPHORES 2</i>is a novel regulator of the 2D to 3D growth transition in the moss<i>Physcomitrium patens</i> Open
SUMMARY The colonization of land by plants was one of the most transformative events in the history of life on Earth. The transition from water, which coincided with and was likely facilitated by the evolution of 3-dimensional (3D) growth,…
View article: Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench Open
Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup infe…
View article: A role for neutral variation in the evolution of C<sub>4</sub>photosynthesis
A role for neutral variation in the evolution of C<sub>4</sub>photosynthesis Open
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…
View article: The Quest for Orthologs benchmark service and consensus calls in 2020
The Quest for Orthologs benchmark service and consensus calls in 2020 Open
The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resour…
View article: Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions
Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions Open
The influence of wheat (modern wheat, both bread and pasta, their wild ancestors and synthetic hybrids) on the microbiota of their roots and surrounding soil is characterized. We isolated lines of bread wheat by hybridizing diploid (Aegilo…
View article: Gene expression data support the hypothesis that <i>Isoetes</i> rootlets are true roots and not modified leaves
Gene expression data support the hypothesis that <i>Isoetes</i> rootlets are true roots and not modified leaves Open
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 root…
View article: Supplementary information: Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves
Supplementary information: Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves Open
Supplementary information for paper "Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves"
View article: Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles
Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles Open
Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of …
View article: Supplemental Dataset For: Orthofinder2: Fast And Accurate Phylogenomic Orthology Analysis From Gene Sequences.
Supplemental Dataset For: Orthofinder2: Fast And Accurate Phylogenomic Orthology Analysis From Gene Sequences. Open
The complete supplemental dataset for "OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences."
View article: OrthoFinder: phylogenetic orthology inference for comparative genomics
OrthoFinder: phylogenetic orthology inference for comparative genomics Open
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted genes trees, gene duplication events, the rooted species tree,…