Peter M. Hollingsworth
A5102827640- Genetic diversity and population structure
- Plant and animal studies
- Plant and Fungal Species Descriptions
- Plant Diversity and Evolution
- Genomics and Phylogenetic Studies
- Ecology and Vegetation Dynamics Studies
- Plant Taxonomy and Phylogenetics
- Environmental DNA in Biodiversity Studies
- Species Distribution and Climate Change
- Identification and Quantification in Food
- Plant Parasitism and Resistance
- Botany and Plant Ecology Studies
- Plant Pathogens and Fungal Diseases
- Lichen and fungal ecology
- Conservation, Biodiversity, and Resource Management
- Aquatic Ecosystems and Phytoplankton Dynamics
- Botany, Ecology, and Taxonomy Studies
- Mycorrhizal Fungi and Plant Interactions
- Mediterranean and Iberian flora and fauna
- Bryophyte Studies and Records
- Plant Ecology and Taxonomy Studies
- African Botany and Ecology Studies
- Plant Pathogens and Resistance
- Forest Insect Ecology and Management
- Plant Reproductive Biology
Royal Botanic Garden Edinburgh
2016-2025
Museum für Naturkunde
2023
Royal Museum for Central Africa
2023
Institute of Natural Sciences
2023
Meise Botanic Garden
2023
University of New Caledonia
2019
Royal Botanic Gardens, Kew
2004-2018
Southern Illinois University Carbondale
2003
University of Leicester
1999
University of Glasgow
1995-1998
Six DNA regions were evaluated as potential barcodes for Fungi , the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region mitochondrial cytochrome c oxidase subunit 1 used animal barcode was excluded marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from nuclear ribosomal RNA cistron compared together with three representative protein-coding genes (largest...
DNA barcoding involves sequencing a standard region of as tool for species identification. However, there has been no agreement on which region(s) should be used land plants. To provide community recommendation plant barcode, we have compared the performance 7 leading candidate plastid regions (atpF-atpH spacer, matK gene, rbcL rpoB rpoC1 psbK-psbI and trnH-psbA spacer). Based assessments recoverability, sequence quality, levels discrimination, recommend 2-locus combination rbcL+matK...
Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial aquatic ecosystems. Here, as part the One Thousand Plant Transcriptomes Initiative, we sequenced vegetative transcriptomes 1,124 species that span a broad sense (Archaeplastida), including green (Viridiplantae), glaucophytes (Glaucophyta) red algae (Rhodophyta). Our analysis provides robust phylogenomic framework for examining evolution plants. Most inferred...
Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more contiguous genomes. In eukaryotes the mitochondrial is sequenced alongside nuclear often at very coverage. A dedicated tool for using HiFi still missing. Results MitoHiFi was developed within Darwin Tree Life Project assemble genomes from generated target species. The input either raw or...
Species richness in the tropics has been attributed to gradual accumulation of species over a long geological period stable equatorial climates or, conversely, speciation response late Tertiary events and unstable Pleistocene climates. DNA sequence data are consistent with recent diversification Inga , species-rich neotropical tree genus. We estimate that was concentrated past 10 million years, many arising as recently 2 years ago. This coincides more major uplifts Andes, bridging Isthmus...
Abstract We propose in this paper to use three regions of plastid DNA as a standard protocol for barcoding all land plants. review the other markers that have been proposed and discuss their advantages disadvantages. The low levels variation make necessary; there are no regions, coding or non‐coding, evolve rapidly mitochondrial generally does animals. outline two, three‐region options, (1) rpoC1, rpoB 1matK (2) matK psbA‐trnH viable plant barcoding.
Abstract DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of establishing massive scale databases for few barcode loci is continuing to change our understanding species diversity patterns, and continues enhance human abilities distinguish among species. Capitalizing the developments next generation sequencing technologies decreasing costs genome sequencing, there now opportunity concept be extended new kinds genomic data. We illustrate benefits capacity do...
There has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on common set samples. In this study, we evaluated the seven main plastid regions (rpoC1, rpoB, rbcL, matK, trnH-psbA, atpF-atpH, psbK-psbI) in three divergent groups plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single showed high...
Internal transcribed spacer (ITS nuclear rDNA) data have been obtained from 190 terrestrial orchid species, encompassing all genera and the great majority of widely recognized species Orchidinae, a heterogeneous selection Habenariinae, single Satyriinae Disinae (the latter serving as outgroup). The resulting parsimony-based phylogeny reveals 12 well-resolved clades within based on Anacamptis s.l., Serapias, Ophrys, Steveniella–Himantoglossum s.l. (including 'Comperia' 'Barlia', most being 2n...
Societal Impact Statement There is increasing awareness that plants and fungi, as natural solutions, can play an important role in tackling ongoing global environmental challenges. We illustrate how understanding current projected threats to fungi necessary manage mitigate risks, while building of gaps bias assessment coverage essential adequately prioritize conservation efforts. highlight the state art science point methods future studies needed species extinction. Summary Plant fungal...
Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development implementation for Darwin Tree Life Project (DToL), aims to sequence assemble high quality genomes all eukaryotic Britain Ireland. We present a standardised...
An in silico screen of 41 the 81 coding regions Nicotiana plastid genome generated a shortlist 12 candidates as DNA barcoding loci for land plants. These were evaluated amplification and sequence variation against reference set 98 plant taxa. The deployment multiple primers modified multiplexed tandem polymerase chain reaction yielded 85–94% across taxa, mean differences between sister taxa 6.1 from 156 bases accD to 22 493 matK. We conclude that should be combined effective diagnosis,...
The goals of the Earth Biogenome Project-to sequence genomes all eukaryotic life on earth-are as daunting they are ambitious. Darwin Tree Life Project was founded to demonstrate credibility these and deliver at-scale genome sequences unprecedented quality for a biogeographic region: archipelago islands that constitute Britain Ireland. is collaboration between biodiversity organizations (museums, botanical gardens, institutes) genomics institutes. Together, we have built workflow collects...
Abstract Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding their evolution early diversification. The plastome, typically mapped as a circular genome, has been most important molecular data source for plant phylogeny reconstruction decades. Results Here, we assembled by far largest plastid dataset angiosperms,...
The world's herbaria contain millions of specimens, collected and named by thousands researchers, over hundreds years. However, this treasure has remained largely inaccessible to genetic studies, because both generally limited success DNA extraction the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities prospects for historical have changed dramatically, as most NGS methods are actually designed taking short fragmented...
<ns4:p>The vision of the <ns4:ext-link xmlns:ns5="http://www.w3.org/1999/xlink" ext-link-type="uri" ns5:href="https://www.earthbiogenome.org/">Earth BioGenome Project</ns4:ext-link><ns4:sup>1</ns4:sup> is to complete reference genomes for all planet’s ~2M described eukaryotic species in coming decade. To contribute this global endeavour, ns5:href="https://protect-us.mimecast.com/s/JGLTC82o95fXARy0XI1hqWb?domain=darwintreeoflife.org/">Darwin Tree Life Project </ns4:ext-link>...
Abstract Understanding the effects of cash crop expansion on natural forest is fundamental importance. However, for most crops there are no remotely sensed global maps 1 , and deforestation impacts estimated using models extrapolations. Natural rubber an example a principal commodity which have been highly uncertain, with estimates differing more than fivefold 1–4 . Here we harnessed Earth observation satellite data cloud computing 5 to produce high-resolution (10 m pixel size) associated...