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

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

Au Family Short Retroposons Contribute to Transcriptional and Phenotypic Diversity in Tomato (Solanaceae)

Here we report the current gene impact of the Au family of SINEs in tomato. The genome of Solanum lycopersicum ‘Heinz 1706‘ SL3.0 -NCBI annotation release 103- was reference searched and the Au profile was characterized in-depth. Tomato genome comprises ca. 670 Au copies, of entire length -18.5%-or truncated, randomly inserted and eroded, forming three well supported (>80%) super clusters which disperse along the 12 chromosomes mirroring the subtelomeric gene distribution bias of the species. In tomato, the Au clade is largely localized at protein coding genes -69.5% introns, 7.8% 3UTRs, 2.1% 5UTRs, 1.2% CDSs- followed by genomic copies -18.3%-, long non coding RNA genes -1.4%- and pseudogenes -0.8%-. The 419 tomato genes harboring intronic Au are diverse, weakly associated considering biological processes and molecular functions, but include important traits such as stress response, hormone response or phenotype plasticity. Au was found to be transcribed inside circular RNAs derived from 12 genic loci. Exonic Au affect the transcriptional and/or translational profiles of 67 tomato genes, including biological/agronomical important ones, contributing to UTR length and composition, UTR transcript variants, CDS boundary definitions, protein domains and variants. We propose that biased survival of Au in tomato genes is an adaptive feature.Fil: 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; ArgentinaFil: 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; Argentin

Dataset of the first transcriptome assembly of the tree crop “yerba mate” (Ilex paraguariensis) and systematic characterization of protein coding genes

This contribution contains data associated to the research article entitled “Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly” (Debat et al., 2014) [1]. By means of a bioinformatic approach involving extensive NGS data analyses, we provide a resource encompassing the full transcriptome assembly of yerba mate, the first available reference for the Ilex L. genus. This dataset (Supplementary files 1 and 2) consolidates the transcriptome-wide assembled sequences of I. paraguariensis with further comprehensive annotation of the protein coding genes of yerba mate via the integration of Arabidopsis thaliana databases. The generated data is pivotal for the characterization of agronomical relevant genes in the tree crop yerba mate -a non-model species- and related taxa in Ilex. The raw sequencing data dissected here is available at DDBJ/ENA/GenBank (NCBI Resource Coordinators, 2016) [2] Sequence Read Archive (SRA) under the accession SRP043293 and the assembled sequences have been deposited at the Transcriptome Shotgun Assembly Sequence Database (TSA) 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. 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: 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. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentin

An Integrated Physical Map of the Cultivated Hot Chili Pepper, Capsicum baccatum var. Pendulum

Capsicum baccatum var. Pendulum is the most frequently cultivated chili pepper in South America. This taxon is an outstanding source for breeding programs and genetic improvement in the genus, since its traits can be introgressed into C. annuum and related species to generate viable hybrids. In this study, the chromosome complement of C. baccatum var. Pendulum 2n = 24 was deeply characterized through a sequential combination of conventional and molecular cytogenetics approaches comprising Ag-NOR staining, heterochromatic fluorescence C-DAPI and CMA/DA/DAPI bandings and fluorescent in situ hybridization (FISH) of Capsicum-derived 5S and 18S-25S ribosomal genes and spacers probes. The attained markers were systematically integrated into a physical map which allows the identification of each individual chromosome. This is the first integrated physical map of C. baccatum var. Pendulum, which in conjunction with reported genetic linkage maps of Capsicum, would be useful for future high-density genetic mapping and whole-genome studies in C. baccatum and related taxa, as well as in breeding and genetic improvement programs in chili peppersInstituto 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

Cytotaxonomy of Tripogandra diuretica and Tripogandra glandulosa (Commelinaceae) from NE Argentina

Karyotype features and microsporogenesis of Tripogandra diuretica (Mart.) Handlos and Tripogandra glandulosa (Seub.) Rohw. from 15 NE Argentina accessions are analysed via classical cytogenetics, CMA/DA/DAPI and Ag-NOR. The karyotype of T. glandulosa (2n = 2x = 16; 2m + 6sm + 8st) is bimodal (A2 = 0.37; R = 2.65) and asymmetrical (A1 = 0.63; i = 26.06; r > 2 = 0.88) (3B-Stebbins) with a genome size of 33.28 μm; two pairs are satellited, CMA+ and NOR-actives. Another four CMA+ loci and DAPI+ universal centromeric heterochromatin occur. Microsporogenesis is normal (pollen viability short stamens = 97.8%; large = 96.7%), meiotic behaviour is regular and chromosomes pair as 8II. The karyotype of T. diuretica (2n = 8x = 64; 8m + 24sm + 32st) is bimodal (A2 = 0.27; R = 2.54) and asymmetrical (A1 = 0.60; i = 27.32; r > 2 = 0.88) (3B-Stebbins); additionally, two pairs are satellited. Microsporogenesis is normal (short stamens = 77.8%; large = 68.5%), except for micronuclei and low pollen viability in some accessions. Meiotic behaviour is regular with 32II, acting as a cytological diploid, however the arrangement of the haploid karyotype suggests that T. diuretica, which also exhibits a reduction of the genome size (18.58 μm), constitutes an auto-octoploid taxa. Additionally, both species share cytological features common to karyotype orthoselection.Fil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina. Universidad Nacional de Misiones; ArgentinaFil: Honfi, Ana Isabel. Universidad Nacional de Misiones; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Daviña, Julio Rubén. Universidad Nacional de Misiones; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Efficiency of cytogenetic methods in detecting a chromosome rearrangement induced by ionizing radiation in a cultivated chili pepper line (Capsicum baccatum var. pendulum – Solanaceae)

Purpose: To locate transient chromosome aberrations on a selected pepper cultivar and determine the tracing efficiency of different cytogenetic methods. Materials and methods: Seeds from Capsicum baccatum var. pendulum cultivar ‘Cayenne’ were treated with an acute dose of X-rays (300 Gy) and chromosome aberrations were analysed by different cytogenetic methods [Feulgen, silver staining for nucleolus organizer regions (silver positive nucleolus organizing regions or AgNOR), fluorescent banding, fluorescence in situ hybridization (FISH) and meiotic analysis]. Results: A rearranged chromosome carrying two nucleolus organizing regions (NOR) induced by ionizing radiation was detected in the cultivar, with the occurrence of a small reciprocal exchange between a chromosome of pair no. 1 and another chromosome of pair no. 3, both carrying active NOR in short arms and associated chromomycin A positive/diamidino-phenylindole negative (CMA+/DAPI−) heterochromatin. Meiotic analysis showed a quadrivalent configuration, confirming a reciprocal translocation between two chromosomes. Conclusions: The use of X-rays in Capsicum allowed us to develop and identify a pepper line with structural rearrangements between two NOR-carrying chromosomes. We postulate that all the cytological techniques employed in this research were efficient in the search for chromosome aberrations. Particularly, Feulgen and AgNOR were the most suitable in those cases of transient rearrangements, whereas fluorescent banding and FISH were appropriate for intransitive ones.Instituto de Patología VegetalInstituto de GenéticaFil: Scaldaferro, Marisel Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Seijo, Jose Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Nordeste. Instituto de Botánica del Nordeste; ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Romero, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Ducasse, Daniel Adrian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Prina, Alberto Raul. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Genética; ArgentinaFil: Moscone, Eduardo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal; Argentin

Chromosome studies in Orchidaceae from Argentina

Abstract The center of diversity of Argentinean orchids is in the northeast region of the country. Chromosome numbers and karyotype features of 43 species belonging to 28 genera are presented here

Chromosome studies in Orchidaceae from Argentina

The center of diversity of Argentinean orchids is in the northeast region of the country. Chromosome numbers and karyotype features of 43 species belonging to 28 genera are presented here. Five chromosome records are the first ones at the genus level; these taxa are Aspidogyne kuckzinskii (2n = 42), Eurystyles actinosophila (2n = 56), Skeptrostachys paraguayensis (2n = 46), Stigmatosema polyaden (2n = 40) and Zygostates alleniana (2n = 54). In addition, a chromosome number is presented for the first time for 15 species: Corymborkis flava (2n = 56), Cyclopogon callophyllus (2n = 28), C. oliganthus (2n = 64), Cyrtopodium hatschbachii (2n = 46), C. palmifrons (2n = 46), Galeandra beyrichii (2n = 54), Habenaria bractescens (2n = 44), Oncidium edwallii (2n = 42), O. fimbriatum (2n = 56), O. pubes (2n = 84), O. riograndense (2n = 56), Pelexia ekmanii (2n = 46), P. lindmanii (2n = 46) and Warrea warreana (2n = 48). For Oncidium longicornu (2n = 42), O. divaricatum (2n = 56) and Sarcoglottis fasciculata (2n = 46+1B?, 46+3B?), a new cytotype was found. Chromosome data support phylogenetic relationships proposed by previous cytological, morphologic and molecular analyses, and in all the cases cover some gaps in the South American literature on orchid chromosomes

Au SINE element from the cultivated yerba mate tree (Ilex paraguariensis)

SINE2_Ipa. Au SINE element from the cultivated yerba mate tree (Ilex paraguariensis). 1..81 feature=tRNA-related region; 14..24 feature=A box; 57..67 feature=B box; 82..163 feature=tRNA-unrelated region; 164..170 feature=tail. >1 thousand copies in the genome of yerba mate (GCA_905181385.1). It is similar to SINE2-1_JC, SINE2-2_STu, SINE2-1_TAe, SINE-5_Mad and SINE2-1_PD.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: 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; Argentin