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). 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 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) Sequence Read Archive (SRA) under the accession SRP043293 and the consensus 45S ribosomal RNA sequence has been deposited there under the accession GFHV00000000.Fil: Aguilera, Patricia Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentin

Aguilera, Patricia Mabel

Debat, Humberto Julio

Grabiele, Mauro

Data in Brief

English

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.Instituto de Patología VegetalFil: Aguilera, Patricia Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Universidad Nacional de Misiones. Instituto de Biotecnología de Misiones; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Universidad Nacional de Misiones. Instituto de Biotecnología de Misiones; Argentin

Repositorio Institucional – Biblioteca Digital

Contents lists available at ScienceDirectData in BriefData in Brief 12 (2017) 649–651http://d2352-34(http://cn CorrMisioneE-mjournal homepage: www.elsevier.com/locate/dibData ArticleDataset of the transcribed 45S ribosomal RNAsequence of the tree crop “yerba mate”Patricia M. Aguilera a,b,n, Humberto J. Debat c,Mauro Grabiele a,ba Instituto de Biología Subtropical, Universidad Nacional de Misiones (CONICET), 3300 Posadas, Misiones,Argentinab Instituto de Biotecnología de Misiones, Universidad Nacional de Misiones, 3300 Posadas, Misiones,Argentinac Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias (INTA), 5000 Córdoba, Argentinaa r t i c l e i n f oArticle history:Received 21 February 2017Received in revised form4 April 2017Accepted 24 April 2017Available online 6 May 2017Keywords:IlexTranscriptomicsAssemblyAnnotationRNA unitx.doi.org/10.1016/j.dib.2017.04.04409/& 2017 The Authors. Published by Elsereativecommons.org/licenses/by/4.0/).esponding author at: Instituto de Biologías, Argentina.ail address: patriciamaguilera@gmail.com (a b s t r a c tThis contribution contains data related to the research articleentitled “The 18S-25S ribosomal RNA unit of yerba mate (Ilexparaguariensis A. St.-Hil.)” (Aguilera et al., 2016) [1]. Through abioinformatic approach involving NGS data, we provide informa-tion of the transcribed 45S ribosomal RNA (rRNA) sequence ofyerba mate, the first reference for the Ilex L. genus. This dataset(Supplementary file 1) comprises information regarding theassembly and annotation of this rRNA unit. The generated data isapplicable for comparative analysis and evolutionary studiesamong Ilex and related taxa. The raw sequencing data used here isavailable at DDBJ/EMBL/GenBank (NCBI Resource Coordinators,2016) [2] Sequence Read Archive (SRA) under the accessionSRP043293 and the consensus 45S ribosomal RNA sequence hasbeen deposited there under the accession GFHV00000000.& 2017 The Authors. Published by Elsevier Inc. This is an openaccess article under the CC BY license(http://creativecommons.org/licenses/by/4.0/).vier Inc. This is an open access article under the CC BY licenseSubtropical, Universidad Nacional de Misiones (CONICET), 3300 Posadas,P.M. Aguilera).P.M. Aguilera et al. / Data in Brief 12 (2017) 649–651650Specifications TableSMTHDEEDDubject area Biologyore specificsubject areaEvolutionary biologyype of data Transcriptomics, assembly of reads and sequence annotationow data wasacquiredBioinformatics approachata format AnalyzedxperimentalfactorsRNA, used for library construction and Illumina sequencing, was isolated fromleaf samples at emerging, young, fully expanded, and early and late senescentstages from I. paraguariensis breeding line Pg538xperimentalfeaturesPaired-end 100 nt Raw reads were filtered, de novo assembled and submittedto homology-based searches and annotationata sourcelocationMisiones, Argentinaata accessibility Data are within this article and at DDBJ/EMBL/GenBank under the accessionsSRP043293 and GFHV00000000Value of the data This data provides the first reference sequence of the transcribed 45S rRNA unit in Ilex L. Data is applicable for comparative analysis and evolutionary studies among Ilex and related taxabased on the 18S, 5.8S and 25S rRNA genes and ITS and ETS sequences. Accessibility of assembly and annotation data allows researchers to perform further analysis vianovel approaches.1. Data, experimental design, materials and methodsTotal RNA extracted of five samples of emerging, young, fully expanded, and early and latesenescent stages leaves of Ilex paraguariensis breeding line Pg538 were pooled for high throughputsequencing [1].The attainment of the transcribed 45S rRNA sequence of yerba mate was completed in seven steps:1. The complete raw sequencing data at SRA under the accession SRP043293 was used to generate afull transcriptome assembly employing the Trinity 2.0.6 platform. All raw sequenced reads werequality filtered and then de novo assembled into contigs with optimal parameters of 25 kmer wordand group pairs distance of 500.2. 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 conserved18S, 5.8S and 25S rRNA entire gene regions of Helianthus annuus 45S (KF767534). Sunflower wasselected, as it is the closest taxon to yerba mate in Euasterids II clade [4] fromwhich complete rRNAsequence information is available yet.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 bpsequence (Supplementary Figure 1, BAM file).4. This sequence was further aligned to the sunflower rRNA reference sequence regions [3] followingthe methods of Geneious global alignment with free end gaps (93%, gap open penalty 12, gapextension penalty 3) and progressive Mauve algorithm [5] at default values. The alignments weremanually checked previous to the transference of homology-based annotations among sunflowerand yerba mate.P.M. Aguilera et al. / Data in Brief 12 (2017) 649–651 6515. The annotated sequence which in turns spans the complete 45S rRNA unit of yerba mate, shares aconsistent 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.6. This first annotation step of the yerba mate rRNA sequence was further curated by subsequenthomology searches [3] in non-redundant NCBI Ilex databases by BLASTN (word size 11, cut off valueof 1e-10). Supplementary Figures 2–6 (BAM files) illustrate this step for each ribosomal RNA regionwith blast hits, and the accession of hits and coverage are provided.7. A final yerba mate annotated ribosomal RNA sequence embracing genes (18S, 5.8S, 25S) andspacers (ITS1, ITS2, 5´ETS, 3´ETS) was attained by last integration of sunflower and Ilex annotatedfeatures. Suplementary Figure 7 (GFF file) illustrates this final step.This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank [2] underthe accession GFHV00000000. The version described in this paper is the first version, GFHV01000000.AcknowledgementsThis 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.Transparency document. Supporting informationTransparency data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2017.04.044.Appendix A. Supplementary materialSupplementary data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.dib.2017.04.044.References[1] P.M. Aguilera, M. Grabiele, H.J. Debat, R.E. Bubillo, D.A. Marti, The 18S-25S ribosomal RNA unit of yerba mate (Ilex para-guariensis A. St.-Hil.), Plant Biosyst. 150 (2016) 1240–1248.[2] NCBI Resource Coordinators, Database resources of the National Center for Biotechnology Information, Nucl. Acids Res. 44(2016) D7–D19.[3] M. Kearse, R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, et al., Geneious Basic: an integrated andextendable desktop software platform for the organization and analysis of sequence data, Bioinformatics 28 (2012)1647–1649.[4] The Angiosperm Phylogeny Group, An update of the Angiosperm Phylogeny Group classification for the orders and familiesof flowering plants, Bot. J. Linn. Soc. 161 (2009) 105–121.[5] A.C.E. Darling, B. Mau, F.R. Blattner, N.T. Perna, Mauve: multiple alignment of conserved genomic sequence with rear-rangements, Genome Res. 14 (2004) 1394–1403.

Dataset of the transcribed 45S ribosomal RNA sequence of the tree crop “yerba mate”

CONICET Digital

Dataset of the transcribed 45S ribosomal RNA sequence of the tree crop yerba mate

LAReferencia - Red Federada de Repositorios Institucionales de Publicaciones Científicas Latinoamericanas

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

Patricia M. Aguilera

Humberto J. Debat

Mauro Grabiele

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https://ri.conicet.gov.ar/bitstream/11336/46345/2/CONICET_Digital_Nro.800d03be-f5df-4bd0-a2af-3e606273aac6_A.pdf

Dataset of the transcribed 45S ribosomal RNA sequence of the tree crop yerba mate

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