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229 results for “plant genomics”
A root-specific NLR network confers resistance to plant parasitic nematodes - genomic sequences and annotations
<p>Sequence and annotation data associated with "A root-specific NLR network confers resistance to plant parasitic nematodes"</p>
Data From: Oatk - a de novo assembly tool for complex plant organelle genomes
<p>This reposity hosts the data for 195 plant organelle genome assemblies generated in the manuscript "Oatk: a de novo assembly tool for complex plant organelle genomes". The sequence data were produced by the Tree of Life programme at the Sanger Institute, mostly from the Darwin Tree of Life (DToL) project, including 24 monocots, 154 eudicots, 16 mosses and one liverwort. See SAMPLE_LIST file for descriptions of these species.</p> <p>In each species subfolder, below files are included.</p> <ol> <li><code>PLTD.fasta</code> Plastome assembly file in FASTA format</li> <li><code>PLTD.annot.bed</code> Plastome assembly annotation file in BED format</li> <li><code>MITO.fasta</code> Mitogenome assembly file in FASTA format</li> <li><code>MITO.annot.bed</code> Mitogenome assembly annotation file in BED format</li> <li><code>MBG.gfa</code> Genome assembly file in GFA format generated with MBG</li> <li><code>PMAT.gfa</code> Genome assembly file in GFA format generated with OATK</li> <li><code>OATK.gfa</code> Genome assembly file in GFA format generated with PMAT (may not exist)</li> </ol> <p> </p> <p>Updates in the New Version:</p> <p>In the previous version, our raw PacBio HiFi read pre-processing pipeline had screened out some reads that it erroneously thought contained HiFi adapter sequence, which led to the gaps in the Hibiscus plastomes. We now fixed this and have rerun all the assemblies that led to any linear organelle components (37 species). All plastomes remain unchanged except for the three Hibiscuses, which are now also circular. Thirteen mitogenomes changed, with six of them now becoming circular.</p>
Supplemental Material for Genome Editing in Crop Plant Research - Alignment of expectations and current developments
<p>Supplemental Material for Paper "Genome Editing in Crop Plant Research - Alignment of expectations and current developments" as submitted to Plants</p>
Contigs scaffolding with Hi-C for plant genomes
<p>Example contigs fasta file use in the protocol: Contigs scaffolding with Hi-C for plant genomes</p>
Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation
<p><span>How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species <em>Lumnitzera littorea</em> and <em>Lumnitzera racemosa</em> provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species <em>Combretum micranthum</em>. While most mangroves have small genomes, the genomes of both <em>Lumnitzera </em>species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, <em>Lumnitzera</em> species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, <em>Lumnitzera </em>genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower color differentiation between the <em>Lumnitzera </em>species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.</span></p>
Data associated to: Uncovering the genomic basis of an extraordinary plant invasion
<p><span>Invasive species are a key driver of the global biodiversity crisis but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in <em>Ambrosia artemisiifolia</em> (ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related <em>Ambrosia</em> species, escape from specific microbial enemies likely favoured the plant's remarkable success as an invasive species.</span></p>
Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens
<p><span>Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for <em>Phytophthora sojae</em>, <em>Globisporangium ultimum</em>, <em>Pythium oligandrum</em>, and <em>G. spinosum</em>. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with <em>Copia</em>-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in <em>P. sojae</em>. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.</span></p>
Strong gene activation in plants with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator.
<p>This data set correspond to the supporting data generated in the manuscript: Strong gene activation in plants with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator. </p>
Comparative genomics of Helotiales (Leotiomycetes) and in silico analysis of temperature adaptations of plant-associated genes
<p><span>Table S1: Genome assembly size and quality for every species in this study; </span></p> <p><span>Table S2: Genome annotation counts for P450, virulence factors, effectors, and CAZy genes and their temperature adaptation.</span></p>
Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.
Data from: Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae)
<p>Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host-related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.</p>
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
<p>With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage <i>in silico</i>. We tested the performance of four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the <i>Vitis</i> clade at the genus level and Vitaceae at the family level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, coupled with incredibly low sequencing costs, we showcase that deep genome skimming (DGS) is as effective for capturing large datasets of SCNs as the widely used Hyb-Seq approach, in addition to capturing plastomes, mtDNA, and entire nrDNA repeats. DGS may serve as an efficient and economical alternative and may be superior to the popular target enrichment/Hyb-Seq approach.</p>
Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies
<p>Resource specialization and host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the general rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary time scales. We applied genome-wide SNP data obtained through low-coverage genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies collected from seven shared willow (<em>Salix</em>) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their <em>Salix</em> hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species than are most bud gallers. In contrast to bud gallers, leaf gallers also exhibit statistically significant cophylogenetic signal with their <em>Salix</em> hosts. The observed discordant patterns of resource specialization and long-term host use in two related galler groups that have radiated in parallel across a shared resource base indicate a general lack of evolutionary repeatability and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.</p>
Designing a Synthetic Microbial Community through Genome Metabolic Modeling to enhance Plant-Microbe Interaction
<p>Supplementary data 1 - <strong>Reconstructed genome-scale metabolic networks from MAGs and Hosts</strong></p> <p>Supplementary data 2 - P<strong>lant growth-promoting traits among members of the minimal community</strong></p> <p> </p> <p>Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynCom, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and a careful selection of compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed an <em>in-silico</em> approach using genome metabolic modeling to design a synthetic microbial community aimed at improving the yield of important crop plants. We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, EPS production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our selection process for the SymCom, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. Our study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.</p>
Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies
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Data from: Combining experimental evolution and genomics to understand how seed beetles adapt to a marginal host plant
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Data associated to: Uncovering the genomic basis of an extraordinary plant invasion
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Data from: Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae)
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Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
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Data from: Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.