Publications

This is a list of peer-reviewed publications that were made possible due to their use of this HPC resource. To cite Crop Diversity HPC in your work, please see our Frequently Asked Questions.

Preprints:

• https://doi.org/10.1111/ejss.13538 - A Deep Learning Approach for High-Resolution Mapping of Scottish Peatland Degradation

• https://doi.org/10.1101/2024.02.14.580321 - Resistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation

• https://doi.org/10.1101/2023.03.24.534090 - THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline

• https://doi.org/10.1101/2022.06.22.497172 - KPop: An assembly-free and scalable method for the comparative analysis of microbial genomes

• https://doi.org/10.1101/2022.09.23.22279632 - Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin resistant Enterococcus faecium

• https://doi.org/10.1101/2022.11.03.515020 - Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

• https://doi.org/10.21203/rs.3.rs-2250881/v1 - Combining phylogenomic and morphological data reveals new patterns of diversity in the national tree of Brasil, Paubrasilia echinata

• https://doi.org/10.1101/2021.09.02.458763 - A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

• https://doi.org/10.21203/rs.3.rs-137842/v1 - QTL Across Fruit Development in Red Raspberry, A Study of A Primocane X Biennial Raspberry Population

• https://doi.org/10.1101/2021.08.12.456076 - Analysis of wild plant pathogen populations reveals a signal of adaptation in genes evolving for survival in agriculture in the beet rust pathogen (Uromyces beticola)

• https://doi.org/10.1101/2022.03.16.484639 - Selection on the fly: short term adaptation to an altered sexual selection regime in Drosophila pseudoobscura

• https://doi.org/10.1101/2022.09.13.507768 - Genomic erosion in the assessment of species extinction risk

2024:

• https://doi.org/10.1111/nph.20263 - A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence

• https://doi.org/10.1016/j.atech.2024.100515 - Leaf Only SAM: A Segment Anything Pipeline for Zero-Shot Automated Leaf Segmentation

• https://doi.org/10.1016/j.cj.2024.09.013 - Transcriptional profiling during infection of potato NLRs and Phytophthora infestans effectors using cDNA enrichment sequencing

• https://doi.org/10.3389/fpls.2024.1490502 - A novel root hair mutant, srh1, affects root hair elongation and reactive oxygen species levels in wheat

• https://doi.org/10.1007/s00122-024-04568-2 - Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data

• https://doi.org/10.1007/s00122-024-04605-0 - Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii

• https://doi.org/10.3389/fpls.2024.1384401 - A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines

• https://doi.org/10.1007/s00122-024-04651-8 - Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato

• https://doi.org/10.5281/zenodo.13385757 - Automated trait extraction from unstructured species descriptions for species ID: a pilot study using a large language model

• https://doi.org/10.1099/mgen.0.001247 - Presence of phage-plasmids in multiple serovars of Salmonella enterica

• https://doi.org/10.1038/s41586-024-07324-0 - Phylogenomics and the rise of the angiosperms

• https://doi.org/10.1093/aob/mcae043 - Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae)

• https://doi.org/10.3389/fpls.2024.1360087 - The origin and the genetic regulation of the self-compatibility mechanism in clementine (Citrus clementina Hort. ex Tan.)

• https://doi.org/10.1007/s00122-024-04577-1 - A new winter wheat genetic resource harbors untapped diversity from synthetic hexaploid wheat

• https://doi.org/10.1038/s41597-023-02850-4 - Genomic resources for a historical collection of cultivated two-row European spring barley genotypes

• https://doi.org/10.1111/nph.19592 - Extinction risk predictions for the world’s flowering plants to support their conservation

• https://doi.org/10.1093/jac/dkae023 - Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium

• https://doi.org/10.1093/aob/mcae022 - Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa

• https://doi.org/10.3389/fpls.2024.1360087 - The origin and the genetic regulation of the self-compatibility mechanism in clementine (Citrus clementina Hort. ex Tan.)

• https://doi.org/10.1093/aob/mcae022 - Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa

2023:

• https://doi.org/10.1002/pld3.490 - Raspberry plant stress detection using hyperspectral imaging

• https://doi.org/10.1111/nph.19421 - Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats

• https://doi.org/10.1093/hr/uhad211 - SMRT–AgRenSeq-d in potato (Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5

• https://doi.org/10.1111/nph.19421 - Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats

• https://doi.org/10.1016/j.ympev.2023.107907 - Frog phylogeny: a time-calibrated, species-level tree based on hundreds of loci and 5,242 species

• https://doi.org/10.1093/molbev/msad109 - Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs

• https://doi.org/10.1186/s12859-023-05335-8 - HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes

• https://doi.org/10.1002/ajb2.16241 - Phylogenomic and morphological data reveal hidden patterns of diversity in the national tree of Brazil, Paubrasilia echinata

• https://doi.org/10.1016/j.virol.2023.109870 - Alternative splicing impacts the rice stripe virus response transcriptome

• https://doi.org/10.1186/s13007-023-01009-x - A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants

• https://doi.org/10.1093/zoolinnean/zlad107 - Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)

• https://doi.org/10.1111/nph.19295 - Re-evaluating the importance of threatened species in maintaining global phytoregions

• https://doi.org/10.1016/j.avrs.2023.100095 - Systematics of the avian family Alaudidae using multilocus and genomic data

• https://doi.org/10.1111/2041-210X.14093 - Modelling density surfaces of intraspecific classes using camera trap distance sampling

2022:

• https://royalsocietypublishing.org/doi/10.1098/rsif.2022.0013 - Exact Bayesian inference of epidemiological parameters from mortality data: application to African swine fever virus

• https://doi.org/10.1093/bioinformatics/btac761 - Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease

• https://doi.org/10.1002/ece3.9537 - Population genomic analyses support sympatric origins of parapatric morphs in a salamander

• http://doi.org/10.26508/lsa.202101255 - The value of genotype-specific reference for transcriptome analyses in barley

• https://doi.org/10.1111/tpj.15871 - BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

• https://doi.org/10.3389/fpls.2022.965217 - Measuring the frequency and distribution of meiotic crossovers in homozygous barley inbred lines

• https://doi.org/10.1111/tpj.15908 - The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication

• https://doi.org/10.1093/sysbio/syab035 - A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

• https://doi.org/10.1111/nph.18257 - Stomata on the abaxial and adaxial leaf surface contribute differently to leaf gas exchange and photosynthesis in wheat

• https://doi.org/10.1007/s00122-021-03991-z - Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley

• https://doi.org/10.1002/csc2.20768 - Genetic resistance to yellow rust infection of the wheat ear is controlled by genes controlling foliar resistance and flowering time

• https://doi.org/10.1111/nph.18554 - Diversity and Divergence: Evolution of secondary metabolism in the tropical tree genus Inga

• https://doi.org/10.1111/nph.18628 - Transcriptional profiling reveals a critical role for GmFT2a in soybean staygreen syndrome caused by the pest Riptortus pedestris

• https://doi.org/10.24823/EJB.2022.398 - Comparative transcriptome analysis of two closely related begonia species reveals divergent patterns in key light-regulated pathways

• https://doi.org/10.24823/EJB.2022.409 - A hybrid capture bait set for begonia

• https://doi.org/10.1126/science.abm7525 - Attenuated evolution of mammals through the Cenozoic

• https://doi.org/10.1007/s00122-021-03967-z - Wheat genetic loci conferring resistance to stripe rust in the face of genetically diverse races of the fungus Puccinia striiformis f. sp. tritici

• https://doi.org/10.3390/agronomy12040782 - Genome-Wide Association Study for Resistance to Rhynchosporium in a Diverse Collection of Spring Barley Germplasm

• https://doi.org/10.3389/fpls.2021.806407 - Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning

• https://doi.org/10.1534/g3.119.401010 - A genome assembly of the barley ‘transformation reference’ cultivar golden promise

• https://doi.org/10.1002/pld3.388 - The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem-driven shoot diversity

• https://doi.org/10.1111/cobi.13992 - Evidence-based guidelines for automated conservation assessments of plant species

• https://doi.org/10.3389/fpls.2021.806407 - Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning

• https://doi.org/10.1038/s41467-022-33300-1 - Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley

• https://doi.org/10.1111/nph.18365 - Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions

• https://doi.org/10.1016/j.funeco.2022.101191 - Nitrogen deposition and temperature structure fungal communities associated with alpine moss-sedge heath in the UK

• https://doi.org/10.1002/ajb2.1827 - Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

• https://doi.org/10.1016/j.gecco.2022.e02308 - Biogeography in the deep: Hierarchical population genomic structure of two beaked whale species

• https://doi.org/10.24823/ejb.2022.1928 - Resolving phylogenetic and taxonomic conflict in Begonia

• https://doi.org/10.1016/j.physa.2022.128261 - Co-evolution of network structure and consumer inequality in a spatially explicit model of energetic resource acquisition

• https://doi.org/10.1093/sysbio/syac042 - Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy

• https://doi.org/10.1098/rspb.2021.2668 - Population viscosity promotes altruism under density-dependent dispersal

• https://doi.org/10.1016/j.cub.2022.08.036 - Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century

• https://doi.org/10.1111/cla.12507 - Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales

• https://doi.org/10.1111/nph.18314 - AirMeasurer: open-source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice

• https://doi.org/10.1098/rsta.2021.0298 - Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm

• https://doi.org/10.1038/s41588-022-01153-5 - A multi-tissue atlas of regulatory variants in cattle

• https://doi.org/10.1186/s12859-022-04755-2 - GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization

• https://dx.doi.org/10.7488/era/2224 - The Land Capability for Agriculture: building a tool to enable climate change assessments

• https://doi.org/10.1016/j.physa.2022.128261 - Co-evolution of network structure and consumer inequality in a spatially explicit model of energetic resource acquisition

• https://doi.org/10.1111%2Fcobi.13918 - Genomic erosion in a demographically recovered bird species during conservation rescue

• https://doi.org/10.1186/s13059-022-02745-4 - Comparative transcriptome in large-scale human and cattle populations

2021:

• https://doi.org/10.1093/plphys/kiab324 - Large-scale field phenotyping using backpack LiDAR and CropQuant-3D to measure structural variation in wheat

• https://doi.org/10.1038/s41597-021-00872-4 - EORNA, a barley gene and transcript abundance database

• https://doi.org/10.48130/FruRes-2021-0007 - Seeing the wood for the trees: hyperspectral imaging for high throughput QTL detection in raspberry, a perennial crop species

• https://doi.org/10.21425/F5FBG49226 - Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae)

• https://doi.org/10.1002/csc2.20692 - Genome-wide association mapping of Hagberg falling number, protein content, test weight, and grain yield in U.K. wheat

• https://doi.org/10.1186/s13059-021-02354-7 - Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

• https://doi.org/10.1038/s41586-020-2961-x - Multiple wheat genomes reveal global variation in modern breeding

• https://doi.org/10.1038/s41598-021-96854-y - Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family

• https://doi.org/10.3390/v13102035 - A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae

• https://doi.org/10.1007/s00122-021-03781-7 - Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A

• https://doi.org/10.1371/journal.pone.0249735 - Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA

• https://doi.org/10.1002/ajb2.1698 - A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae

• https://doi.org/10.1016/j.ympev.2021.107068 - Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

• https://doi.org/10.1111/jse.12757 - A new classification of Cyperaceae (Poales) supported by phylogenomic data

• https://doi.org/10.3389/fpls.2020.619404 - Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

• https://doi.org/10.1093/g3journal/jkab282 - Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae

• https://doi.org/10.1111/mpp.13072 - Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae

• https://doi.org/10.3389/fpls.2021.767324 - State-of-the-Art Technology and Applications in Crop Phenomics

• https://doi.org/10.1002/ajb2.1697 - Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes

• https://doi.org/10.1002/ajb2.1701 - A higher-level nuclear phylogenomic study of the carrot family (Apiaceae)

• https://doi.org/10.1093/sysbio/syab035 - A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

• https://doi.org/10.1073/pnas.2109176118 - Plant–environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere

• https://doi.org/10.1038/s41437-021-00459-0 - Combining conventional QTL analysis and whole-exome capture-based bulk-segregant analysis provides new genetic insights into tuber sprout elongation and dormancy release in a diploid potato population

• https://doi.org/10.1126/sciadv.abg1245 - Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

• https://doi.org/10.1002/ajb2.1693 - An updated infra-familial classification of Sapindaceae based on targeted enrichment data

2020:

• https://doi.org/10.1038/s41467-020-18404-w - Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

• https://dx.doi.org/10.24823/Sibbaldia.2020.289 - Diversity of woody-host infecting Phytophthora species in public parks and botanic gardens as revealed by metabarcoding, and opportunities for mitigation through best practice

• https://doi.org/10.1534/g3.120.401234 - Genetic Characterization of a Wheat Association Mapping Panel Relevant to ian Breeding Using a High-Density Single Nucleotide Polymorphism Array

• https://doi.org/10.1093/botlinnean/boaa099 - Resolving generic limits in Cyperaceae tribe Abildgaardieae using targeted sequencing

• https://doi.org/10.1111/efp.12602 - Detection and spread of Phytophthora austrocedri within infected Juniperus communis woodland and diversity of co-associated Phytophthoras as revealed by metabarcoding

• https://doi.org/10.1016/j.virusres.2019.197837 - RNA sequence analysis of diseased groundnut (Arachis hypogaea) reveals the full genome of groundnut rosette assistor virus (GRAV)

• https://doi.org/10.1080/15476286.2020.1858253 - 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

• https://doi.org/10.1002/csc2.20248 - From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

• https://doi.org/10.1007/s10681-020-02647-1 - QTL dissection of floral traits in Streptocarpus (Gesneriaceae)

• https://doi.org/10.1016/j.molp.2020.08.011 - Mobilizing Crop Biodiversity

• https://doi.org/10.1111/nph.16439 - Moving on up - controlling internode growth

• https://doi.org/10.1111/nph.16736 - SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination

• https://doi.org/10.1111/tpj.14910 - Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari

• https://doi.org/10.3390/f11111223 - Phytophthora austrocedri in Argentina and Co-Inhabiting Phytophthoras: Roles of Anthropogenic and Abiotic Factors in Species Distribution and Diversity

• https://doi.org/10.1111/nph.16810 - Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley

2019:

• https://doi.org/10.3389/fpls.2019.00544 - A Comparison of Mainstream Genotyping Platforms for the Evaluation and Use of Barley Genetic Resources

• https://doi/prg/10.7717/peerj.6931 - Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain

• https://doi.org/10.3389/fevo.2019.00439 - The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques

• https://doi.org/10.1016/j.virusres.2019.03.004 - The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection

• https://doi.org/10.1099/jgv.0.001210 - Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data

• https://doi.org/10.1186/s12864-019-6243-7 - BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

• https://doi.org/10.1186/s13007-019-0486-9 - A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing

• https://doi.org/10.1016/j.enganabound.2019.03.025 - Smoothed particle hydrodynamics for root growth mechanics

• https://doi.org/10.1111/nph.15548 - Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain

• https://doi.org/10.1038%2Fs41598-019-49302-x - Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function