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552 results for “Utricularia”
The terrestrial carnivorous plant Utricularia reniformis sheds light on environmental and life-form genome plasticity: Annotation, Gene Ontology and raw data
<p><strong>Description:</strong> In this work, we deeply sequenced (genome and transcriptome of different organs), assembled, and analyzed the 311-Mbp genome of the terrestrial carnivorous plant <em>U. reniformis</em> (Lentibulariaceae). This project presents great importance to the understanding of genomic, evolutive and functional aspects of<em> U. reniformis</em>, which may, with the next-generation sequencing and computational biology approaches shed light to a better understanding not only for the biology and evolution of <em>Utricularia</em> genus, but also for other genera and lineages of the Lentibulariaceae family. Here we present all the raw data generated, including annotation and gene ontology files.</p> <p><strong>External Information</strong></p> <p><a href="https://genomevolution.org/coge/GenomeInfo.pl?gid=54799">Genome Browser</a> avaliable at CoGe Portal (https://genomevolution.org/coge/GenomeInfo.pl?gid=54799)</p> <p><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">GenBank </a><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">Bioproject</a> (https://www.ncbi.nlm.nih.gov/bioproject/290588) for raw genomic and transcriptomic reads</p> <p><a href="https://bv.fapesp.br/en/auxilios/84264/genomics-and-transcriptomics-of-utricularia-reniformis-lentibulariaceae-an-evolutive-and-function/">FAPESP grant website</a> contaning the project abstract and other information.</p> <p><strong>Papers published related to <em>Utricularia reniformis</em> genome</strong></p> <pre><strong>[1]</strong> Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, MichaelTP, Varani AM. <strong>The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family</strong>. PLoS One. 2016 Oct 20;11(10):e0165176. doi:<strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/27764252">10.1371/journal.pone.0165176</a></strong>. </pre> <pre><strong>[2] </strong>Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM. <strong>The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.</strong> PLoS One. 2017 Jul19;12(7):e0180484. doi: <strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/28723946">10.1371/journal.pone.0180484</a></strong>.</pre> <pre><strong>[3] </strong>Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. <strong>The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity.</strong> Int J Mol Sci. 2019 Dec 18;21(1). pii: E3. doi: <strong><a href="https://www.ncbi.nlm.nih.gov/pubmed/31861318">10.3390/ijms21010003</a></strong>.</pre> <p><strong>Acknowledgements</strong></p> <p>This work was supported by Sao Paulo Research Foundation FAPESP, Grant ID: [1325164-6]</p> <p> </p> <p><strong>---------------------------------------------------------</strong><br> <strong>FILES DESCRIPTION</strong><br> <strong>---------------------------------------------------------</strong><br> <br> ----------------<br> <strong>ANNOT-vFinal.sql: </strong>MySQL database containing all integrated annotation information of Urenif and Ugibba<br> ----------------<br> <strong>TABLE fields description</strong><br> gene_name gene name generated by EVidence Modeler + PASA<br> length gene lenght<br> status duplicate_gene_classifier status (0:singleton, 1:dispersed, 2:proximal, 3: tandem, 4:WGD)<br> product gene product <br> GOterms Blast2GO/OmicsBox GOterms<br> GO_mapping Blast2GO/OmicsBox GOterms derived from direct mapping (UniProt)<br> GO_annotation Blast2GO/OmicsBox annotated GOterms<br> GO_interpro Blast2GO/OmicsBox derived from InterProScan<br> EC Blast2GO/OmicsBox EC number<br> EC_name Blast2GO/OmicsBox enzyme name<br> NOG_annot EggNOG annotation description<br> NOG_EC EggNOG EC number<br> NOG_GO EggNOG GOterms<br> NOG_class EggNOG COG/KOG classfication<br> KEGG_Pathway EggNOG KEGG pathyways<br> KEGG_ko EggNOG KEGG ko<br> CAZy EggNOG CAZy enzymes<br> TAIR_gene Closest A. thaliana gene name (homologous) TAIR database lasted version<br> TAIR_annot Closest A. thaliana gene product (homologous) TAIR database lasted version <br> ortho MCL clustering among Vvinifera, Athaliana, and Slycopersicum (S:singleton, C: clustered, Y: shared)<br> ortho_two MCL clustering among Urenif and Ugibba (S:singleton, C: clustered, Y: shared)<br> -<br> -<br> ----------------<br> <strong>CEGs.zip </strong> 336 shared and concatenated CEGs from Urenif, U. gibba, Genlisea nigrocaulis, G. hispidula, G. aurea, G. pygmaea, and G. repens.<br> ----------------</p> <p><strong>ProcessRepeats_mod</strong> Modified version of RepeatMasker, ProcessRepeats script for detection of plant evolutionary lineages<br> ----------------</p> <p><strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> <em>Utricularia gibba</em> files<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong><br> <strong>Ugibba</strong><strong>-no-masked.fa </strong> Ugibba genome excluding organellar genomes (provided by Lan et al., 2017)<br> <strong>Ugibba-softmasked.fa</strong> Ugibba genome RepeatMasker softmasked and excluding organellar genomes (provided by Lan et al., 2017)<br> <strong>Ug.collinearity </strong> MCScanX collinearity file<br> <strong>Ug-duplicates.txt</strong> MCScanX duplicate_gene_classifier short report<br> <strong>Ug.gene_type </strong> MCScanX duplicate_gene_classifier full report<br> <strong>Ug.tandem </strong> Ugibba tandem genes generated by MCScanX tool<br> <strong>Ugibba_annot.annot </strong> Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim) <strong>Ugibba_annot-</strong><strong>noclean</strong><strong>.</strong><strong>annot</strong><strong> </strong> Blast2GO/OmicsBox annotation file (not filtered)<br> <strong>Ugibba</strong><strong>.cDNA</strong> Ugibba cDNAs fasta file<br> <strong>Ugibba</strong><strong>.CDS </strong> Ugibba CDSs fasta file<br> <strong>Ugibba</strong><strong>-EVM.all-no-TEs-PASA-ANNOTATED.gff3</strong> Ugibba GFF3 file fully annotated (including gene products and GO terms)</p> <p><strong>Ugibba</strong><strong>-EVM.all-no-TEs-PASA.gff3</strong> Ugibba GFF3 file fully annotated (genes only)<br> <strong>Ugibba_export.txt</strong> Blast2GO/OmicsBox full exported table<br> <strong>Ugibba_fasta.fasta</strong> Blast2GO/OmicsBox Ugibba fasta proteins containg annotation (product and GO terms)<br> <strong>ugibba_frozen_cleaned-validated.box</strong> Full Blast2GO/OmicsBox file</p> <p><strong>ugibba_frozen.box</strong> Full Blast2GO/OmicsBox file (containing TEs genes annotation)</p> <p><strong>ugibba_nogs_emapper_annotations.box</strong> Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation)</p> <p><strong>Ugibba_GAF.txt</strong> GAF file<br> <strong>Ugibba</strong><strong>.gene</strong> Ugibba gene fasta file<br> <strong>Ugibba_GOstat.txt </strong> GOstat file<br> <strong>Ugibba</strong><strong>-PASA-assemblies.fasta </strong> Ugibba PASA assemblies<br> <strong>Ugibba</strong><strong>-PASA.stats </strong> Ugibba annotation STATS<br> <strong>Ugibba</strong><strong>.</strong><strong>prot</strong><strong> </strong> Ugibba protein fasta file<br> <strong>Ugibba</strong><strong>-RepeatMasker.gff </strong> Ugibba RepeatMasker gff file<br> <strong>Ugibba</strong><strong>-RepeatMasker.gff3 </strong> Ugibba RepeatMasker gff3 file<br> <strong>Ugibba</strong><strong>-RepeatMasker.tbl </strong> Ugibba RepeatMasker results<br> <strong>Ugibba</strong><strong>-RepeatMasker-v2.gff3</strong> Ugibba RepeatMasker gff3 second version file<br> <strong>Ugibba</strong><strong>-RNAseq-assembled.fasta </strong> Ugibba RNAseq assembled transcriptome (Trinity)<br> <strong>Ugibba_TEs_DANTE_2019.fa </strong> Ugibba TEs library, detected by REPET and annotated by PASTEC and DANTE<br> <strong>Ugibba_WEGO.txt </strong> WEGO file</p> <p><strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> <em>Utricularia reniformis</em> files<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong><br> <strong>Urenif</strong><strong>-no-masked.fa </strong> Urenif genome excluding organellar genomes<br> <strong>Urenif</strong><strong>-</strong><strong>softmasked</strong><strong>.fa</strong> Urenif genome RepeatMasker softmasked and excluding organellar genomes<br> <strong>Ur.collinearity </strong> MCScanX collinearity file<br> <strong>Ur-duplicates.txt </strong> MCScanX duplicate_gene_classifier short report<br> <strong>Ur.gene_type</strong> MCScanX duplicate_gene_classifier full report<br> <strong>Ur.tandem</strong> Urenif tandem genes generated by MCScanX tool<br> <strong>Urenif_annot.annot</strong> Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim)<br> <strong>Urenif_annot-</strong><strong>noclean</strong><strong>.</strong><strong>annot</strong> Blast2GO/OmicsBox annotation file (not filtered)<br> <strong>Urenif</strong><strong>.cDNA</strong> Urenif cDNAs fasta file<br> <strong>Urenif</strong><strong>.CDS </strong> Urenif cDNAs fasta file<br> <strong>Urenif</strong><strong>-EVM.all-no-TEs-PASA-ANNOTATED.gff3</strong> Urenif GFF3 file fully annotated (including gene products and GO terms)</p> <p><strong>Urenif</strong><strong>-EVM.all-no-TEs-PASA.gff3</strong> Urenif GFF3 file fully annotated (genes only)<br> <strong>Urenif_export.txt</strong> Blast2GO/OmicsBox full exported table<br> <strong>Urenif_fasta.fasta</strong> Blast2GO/OmicsBox Urenif fasta proteins containg annotation (product and GO terms)<br> <strong>urenif_frozen_cleaned-validated.box</strong> Full Blast2GO/OmicsBox file</p> <p><strong>urenif_frozen.box</strong> Full Blast2GO/OmicsBox file (containing TEs genes annotation)</p> <p><strong>urenif_nogs_emapper_annotations.box</strong> Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation)<br> <strong>Urenif_GAF.txt </strong> GAF file<br> <strong>Urenif</strong><strong>.gene</strong> Urenif gene fasta file<br> <strong>Urenif_GOStat.txt </strong> GOstat file<br> <strong>Urenif</strong><strong>-PASA-assemblies.fasta</strong> Urenif PASA assemblies<br> <strong>Urenif</strong><strong>-PASA.stats </strong> Urenif annotation STATS<br> <strong>Urenif</strong><strong>.</strong><strong>prot</strong><strong> </strong> Urenif protein fasta file<br> <strong>Urenif</strong><strong>-RepeatMasker.gff </strong> Urenif RepeatMasker gff file<br> <strong>Urenif</strong><strong>-RepeatMasker.gff3 </strong> Urenif RepeatMasker gff3 file<br> <strong>Urenif</strong><strong>-RepeatMasker.tbl </strong> Urenif RepeatMasker results<br> <strong>Urenif</strong><strong>-RepeatMasker-v2.gff3 </strong> Urenif RepeatMasker gff3 second version file<br> <strong>Urenif</strong><strong>-RNAseq-assembled.fasta </strong> Urenif RNAseq assembled transcriptome (Trinity)<br> <strong>Urenif_TEs_DANTE_2019.fa </strong> Urenif TEs library, detected by REPET and annotated by PASTEC and DANTE<br> <strong>Urenif_WEGO.txt </strong> WEGO file<br> <strong>----------------------------------------------------------------------------------------------------------------------------------------------<br> ----------------------------------------------------------------------------------------------------------------------------------------------</strong></p>
Linked collectors and determiners for: Unveiling Utricularia amethystina's true colours: a taxonomic revision of one of the largest species complexes (U. sect. Foliosa, Lentibulariaceae).
Natural history specimen data linked to collectors and determiners held within, "Unveiling Utricularia amethystina's true colours: a taxonomic revision of one of the largest species complexes (U. sect. Foliosa, Lentibulariaceae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e182c4cc-2536-4f6c-bdb0-be4704e50e4d">https://bionomia.net/dataset/e182c4cc-2536-4f6c-bdb0-be4704e50e4d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e182c4cc-2536-4f6c-bdb0-be4704e50e4d">https://gbif.org/dataset/e182c4cc-2536-4f6c-bdb0-be4704e50e4d</a>. Formatted as a Frictionless Data package.
Utricularia sp. (BR0000011306771)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia sp. (BR0000011306603)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia sp. (BR0000011306610)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia sp. (BR0000012337316)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293096)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia sp. (BR0000011306788)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293812)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293065)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293751)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000012350797)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010292891)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010292679)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293942)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000024514712)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293546)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia sp. (BR0000022412690)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000022412584)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Utricularia vulgaris L. (BR0000010293164)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
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