The terrestrial carnivorous plant Utricularia reniformis sheds light on environmental and life-form genome plasticity: Annotation, Gene Ontology and raw data

Description: In this work, we deeply sequenced (genome and transcriptome of different organs), assembled, and analyzed the 311-Mbp genome of the terrestrial carnivorous plant U. reniformis (Lentibulariaceae). This project presents great importance to the understanding of genomic, evolutive and functional aspects of U. reniformis, 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 Utricularia 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. External Information Genome Browser avaliable at CoGe Portal (https://genomevolution.org/coge/GenomeInfo.pl?gid=54799) GenBank Bioproject (https://www.ncbi.nlm.nih.gov/bioproject/290588) for raw genomic and transcriptomic reads FAPESP grant website contaning the project abstract and other information. Papers published related to Utricularia reniformis genome [1] Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, MichaelTP, Varani AM. The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PLoS One. 2016 Oct 20;11(10):e0165176. doi:10.1371/journal.pone.0165176. [2] Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM. The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. PLoS One. 2017 Jul19;12(7):e0180484. doi: 10.1371/journal.pone.0180484. [3] Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. Int J Mol Sci. 2019 Dec 18;21(1). pii: E3. doi: 10.3390/ijms21010003. Acknowledgements This work was supported by Sao Paulo Research Foundation FAPESP, Grant ID: [1325164-6] --------------------------------------------------------- FILES DESCRIPTION --------------------------------------------------------- ---------------- ANNOT-vFinal.sql: MySQL database containing all integrated annotation information of Urenif and Ugibba ---------------- TABLE fields description gene_name gene name generated by EVidence Modeler + PASA length gene lenght status duplicate_gene_classifier status (0:singleton, 1:dispersed, 2:proximal, 3: tandem, 4:WGD) product gene product GOterms Blast2GO/OmicsBox GOterms GO_mapping Blast2GO/OmicsBox GOterms derived from direct mapping (UniProt) GO_annotation Blast2GO/OmicsBox annotated GOterms GO_interpro Blast2GO/OmicsBox derived from InterProScan EC Blast2GO/OmicsBox EC number EC_name Blast2GO/OmicsBox enzyme name NOG_annot EggNOG annotation description NOG_EC EggNOG EC number NOG_GO EggNOG GOterms NOG_class EggNOG COG/KOG classfication KEGG_Pathway EggNOG KEGG pathyways KEGG_ko EggNOG KEGG ko CAZy EggNOG CAZy enzymes TAIR_gene Closest A. thaliana gene name (homologous) TAIR database lasted version TAIR_annot Closest A. thaliana gene product (homologous) TAIR database lasted version ortho MCL clustering among Vvinifera, Athaliana, and Slycopersicum (S:singleton, C: clustered, Y: shared) ortho_two MCL clustering among Urenif and Ugibba (S:singleton, C: clustered, Y: shared) - - ---------------- CEGs.zip 336 shared and concatenated CEGs from Urenif, U. gibba, Genlisea nigrocaulis, G. hispidula, G. aurea, G. pygmaea, and G. repens. ---------------- ProcessRepeats_mod Modified version of RepeatMasker, ProcessRepeats script for detection of plant evolutionary lineages ---------------- ---------------------------------------------------------------------------------------------------------------------------------------------- Utricularia gibba files ---------------------------------------------------------------------------------------------------------------------------------------------- Ugibba-no-masked.fa Ugibba genome excluding organellar genomes (provided by Lan et al., 2017) Ugibba-softmasked.fa Ugibba genome RepeatMasker softmasked and excluding organellar genomes (provided by Lan et al., 2017) Ug.collinearity MCScanX collinearity file Ug-duplicates.txt MCScanX duplicate_gene_classifier short report Ug.gene_type MCScanX duplicate_gene_classifier full report Ug.tandem Ugibba tandem genes generated by MCScanX tool Ugibba_annot.annot Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim) Ugibba_annot-noclean.annot Blast2GO/OmicsBox annotation file (not filtered) Ugibba.cDNA Ugibba cDNAs fasta file Ugibba.CDS Ugibba CDSs fasta file Ugibba-EVM.all-no-TEs-PASA-ANNOTATED.gff3 Ugibba GFF3 file fully annotated (including gene products and GO terms) Ugibba-EVM.all-no-TEs-PASA.gff3 Ugibba GFF3 file fully annotated (genes only) Ugibba_export.txt Blast2GO/OmicsBox full exported table Ugibba_fasta.fasta Blast2GO/OmicsBox Ugibba fasta proteins containg annotation (product and GO terms) ugibba_frozen_cleaned-validated.box Full Blast2GO/OmicsBox file ugibba_frozen.box Full Blast2GO/OmicsBox file (containing TEs genes annotation) ugibba_nogs_emapper_annotations.box Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation) Ugibba_GAF.txt GAF file Ugibba.gene Ugibba gene fasta file Ugibba_GOstat.txt GOstat file Ugibba-PASA-assemblies.fasta Ugibba PASA assemblies Ugibba-PASA.stats Ugibba annotation STATS Ugibba.prot Ugibba protein fasta file Ugibba-RepeatMasker.gff Ugibba RepeatMasker gff file Ugibba-RepeatMasker.gff3 Ugibba RepeatMasker gff3 file Ugibba-RepeatMasker.tbl Ugibba RepeatMasker results Ugibba-RepeatMasker-v2.gff3 Ugibba RepeatMasker gff3 second version file Ugibba-RNAseq-assembled.fasta Ugibba RNAseq assembled transcriptome (Trinity) Ugibba_TEs_DANTE_2019.fa Ugibba TEs library, detected by REPET and annotated by PASTEC and DANTE Ugibba_WEGO.txt WEGO file ---------------------------------------------------------------------------------------------------------------------------------------------- Utricularia reniformis files ---------------------------------------------------------------------------------------------------------------------------------------------- Urenif-no-masked.fa Urenif genome excluding organellar genomes Urenif-softmasked.fa Urenif genome RepeatMasker softmasked and excluding organellar genomes Ur.collinearity MCScanX collinearity file Ur-duplicates.txt MCScanX duplicate_gene_classifier short report Ur.gene_type MCScanX duplicate_gene_classifier full report Ur.tandem Urenif tandem genes generated by MCScanX tool Urenif_annot.annot Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim) Urenif_annot-noclean.annot Blast2GO/OmicsBox annotation file (not filtered) Urenif.cDNA Urenif cDNAs fasta file Urenif.CDS Urenif cDNAs fasta file Urenif-EVM.all-no-TEs-PASA-ANNOTATED.gff3 Urenif GFF3 file fully annotated (including gene products and GO terms) Urenif-EVM.all-no-TEs-PASA.gff3 Urenif GFF3 file fully annotated (genes only) Urenif_export.txt Blast2GO/OmicsBox full exported table Urenif_fasta.fasta Blast2GO/OmicsBox Urenif fasta proteins containg annotation (product and GO terms) urenif_frozen_cleaned-validated.box Full Blast2GO/OmicsBox file urenif_frozen.box Full Blast2GO/OmicsBox file (containing TEs genes annotation) urenif_nogs_emapper_annotations.box Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation) Urenif_GAF.txt GAF file Urenif.gene Urenif gene fasta file Urenif_GOStat.txt GOstat file Urenif-PASA-assemblies.fasta Urenif PASA assemblies Urenif-PASA.stats Urenif annotation STATS Urenif.prot Urenif protein fasta file Urenif-RepeatMasker.gff Urenif RepeatMasker gff file Urenif-RepeatMasker.gff3 Urenif RepeatMasker gff3 file Urenif-RepeatMasker.tbl Urenif RepeatMasker results Urenif-RepeatMasker-v2.gff3 Urenif RepeatMasker gff3 second version file Urenif-RNAseq-assembled.fasta Urenif RNAseq assembled transcriptome (Trinity) Urenif_TEs_DANTE_2019.fa Urenif TEs library, detected by REPET and annotated by PASTEC and DANTE Urenif_WEGO.txt WEGO file ---------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------------