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
----------------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------------