Abstract
This contribution contains data related to the research article entitled “The 18S-25S ribosomal RNA unit of yerba mate (Ilex paraguariensis A. St.-Hil.)” (Aguilera et al., 2016) [1]. Through a bioinformatic approach involving NGS data, we provide information of the transcribed 45S ribosomal RNA (rRNA) sequence of yerba mate, the first reference for the Ilex L. genus. This dataset (Supplementary file 1) comprises information regarding the assembly and annotation of this rRNA unit. The generated data is applicable for comparative analysis and evolutionary studies among Ilex and related taxa. The raw sequencing data used here is available at DDBJ/EMBL/GenBank (NCBI Resource Coordinators, 2016) [2] Sequence Read Archive (SRA) under the accession SRP043293 and the consensus 45S ribosomal RNA sequence has been deposited there under the accession GFHV00000000.
Keywords: Ilex, Transcriptomics, Assembly, Annotation, RNA unit
Specifications Table
| Subject area | Biology |
| More specific subject area | Evolutionary biology |
| Type of data | Transcriptomics, assembly of reads and sequence annotation |
| How data was acquired | Bioinformatics approach |
| Data format | Analyzed |
| Experimental factors | RNA, used for library construction and Illumina sequencing, was isolated from leaf samples at emerging, young, fully expanded, and early and late senescent stages from I. paraguariensis breeding line Pg538 |
| Experimental features | Paired-end 100 nt Raw reads were filtered, de novo assembled and submitted to homology-based searches and annotation |
| Data source location | Misiones, Argentina |
| Data accessibility | Data are within this article and at DDBJ/EMBL/GenBank under the accessions SRP043293 and GFHV00000000 |
Value of the data
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This data provides the first reference sequence of the transcribed 45S rRNA unit in Ilex L.
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Data is applicable for comparative analysis and evolutionary studies among Ilex and related taxa based on the 18S, 5.8S and 25S rRNA genes and ITS and ETS sequences.
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Accessibility of assembly and annotation data allows researchers to perform further analysis via novel approaches.
1. Data, experimental design, materials and methods
Total RNA extracted of five samples of emerging, young, fully expanded, and early and late senescent stages leaves of Ilex paraguariensis breeding line Pg538 were pooled for high throughput sequencing [1].
The attainment of the transcribed 45S rRNA sequence of yerba mate was completed in seven steps:
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1.
The complete raw sequencing data at SRA under the accession SRP043293 was used to generate a full transcriptome assembly employing the Trinity 2.0.6 platform. All raw sequenced reads were quality filtered and then de novo assembled into contigs with optimal parameters of 25 kmer word and group pairs distance of 500.
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2.
The achieved complete list of 44,907 contigs was subsequently scanned by in-house [3; v.8.1.8] homology searches with BLASTN (word size 11, cut off value of 1e-10) using as baits the conserved 18S, 5.8S and 25S rRNA entire gene regions of Helianthus annuus 45S (KF767534). Sunflower was selected, as it is the closest taxon to yerba mate in Euasterids II clade [4] from which complete rRNA sequence information is available yet.
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3.
Three blast hits were obtained and identified as contigs comp17895_c0_seq. 1 (2936 bp), comp17895_c1_seq. 1 (1053 bp) and comp17901_c0_seq. 2 (2994 bp), which assemble in a 6961 bp sequence (Supplementary Figure 1, BAM file).
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This sequence was further aligned to the sunflower rRNA reference sequence regions [3] following the methods of Geneious global alignment with free end gaps (93%, gap open penalty 12, gap extension penalty 3) and progressive Mauve algorithm [5] at default values. The alignments were manually checked previous to the transference of homology-based annotations among sunflower and yerba mate.
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5.
The annotated sequence which in turns spans the complete 45S rRNA unit of yerba mate, shares a consistent pairwise similarity of 54.2%, 97.6%, 54.3%, 96.2%, 66.4%, 95.7% and 49.7% at the 5´ETS, 18S, ITS1, 5.8S, ITS2, 25S and 3´ETS, respectively, with sunflower.
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This first annotation step of the yerba mate rRNA sequence was further curated by subsequent homology searches [3] in non-redundant NCBI Ilex databases by BLASTN (word size 11, cut off value of 1e-10). Supplementary Figures 2–6 (BAM files) illustrate this step for each ribosomal RNA region with blast hits, and the accession of hits and coverage are provided.
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7.
A final yerba mate annotated ribosomal RNA sequence embracing genes (18S, 5.8S, 25S) and spacers (ITS1, ITS2, 5´ETS, 3´ETS) was attained by last integration of sunflower and Ilex annotated features. Suplementary Figure 7 (GFF file) illustrates this final step.
This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank [2] under the accession GFHV00000000. The version described in this paper is the first version, GFHV01000000.
Acknowledgements
This study was funded by the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT-Argentina), Grant no. UNaM PICT 2014-3328 Préstamo BID Nº AR-L 1181.
Footnotes
Transparency data associated with this article can be found in the online version at doi:10.1016/j.dib.2017.04.044.
Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2017.04.044.
Transparency document. Supplementary material
Supplementary material
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Appendix A. Supplementary material
Suppl. Fig. 1. Assembled 45S rRNA unit of yerba mate.
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Suppl. Fig. 2. 18S rRNA region of yerba mate and associated Ilex NCBI blast hits.
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Suppl. Fig. 3. 25S rRNA region of yerba mate and associated Ilex NCBI blast hits.
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Suppl. Fig. 4. 5.8S rRNA region of yerba mate and associated Ilex NCBI blast hits.
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Suppl. Fig. 5. ITS1 rRNA region of yerba mate and associated Ilex NCBI blast hits.
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Suppl. Fig. 6. ITS2 rRNA region of yerba mate and associated Ilex NCBI blast hits.
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Suppl. Fig. 7. Annotated 45S rRNA unit of yerba mate.
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References
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Supplementary material
Suppl. Fig. 1. Assembled 45S rRNA unit of yerba mate.
Suppl. Fig. 2. 18S rRNA region of yerba mate and associated Ilex NCBI blast hits.
Suppl. Fig. 3. 25S rRNA region of yerba mate and associated Ilex NCBI blast hits.
Suppl. Fig. 4. 5.8S rRNA region of yerba mate and associated Ilex NCBI blast hits.
Suppl. Fig. 5. ITS1 rRNA region of yerba mate and associated Ilex NCBI blast hits.
Suppl. Fig. 6. ITS2 rRNA region of yerba mate and associated Ilex NCBI blast hits.
Suppl. Fig. 7. Annotated 45S rRNA unit of yerba mate.