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

Table S1. Tomato genes with SINE_Au at intronic regions

Table S1. Tomato genes with SINE_Au at intronic regions. This table contains the names of genes of Solanum lycopersicum 'Heinz 1706' SL3.0 -NCBI annotation release 103- inhabited by Au SINE members at intronic regions. This table is supplementary material to the contribution in BABT "Au Family Short Retroposons Contribute to Transcriptional and Phenotypic Diversity in Tomato (Solanaceae)" by Grabiele & Aguilera.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Data for: Molecular characterization of the 5S rDNA non transcribed spacer and reconstruction of phylogenetic relationships in Capsicum

This contribution contains data associated to the research article entitled “Molecular characterization of the 5S rDNA non transcribed spacer and reconstruction of phylogenetic relationships in Capsicum” [1]. By means of molecular and computational biology approaches involving extensive data analyses, we provide a resource encompassing the full characterization and annotation of the 5S ribosomal (rDNA) non transcribed spacer (NTS) of chili peppers and overall related sequences in Solanaceae at DDBJ/ENA/GenBank [2]. The generated data is pivotal for upcoming characterization and reference annotation of comparable repetitive regions throughout the family and related taxa, from small to genomic scale projects, and become an essential resource for germplasm characterization and evolutionary studies in Solanaceae. The fully annotated sequencing data of chili peppers presented here is available at the Nucleotide database of the DDBJ/ENA/GenBank under the accessions MK650892-1009 and JF773766

FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae)

ABSTRACT We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus

Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly.

Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop