Metatranscriptomic analysis of larvae guts from field-collected and laboratory-reared Spodoptera frugiperda from the South American subtropical region

This is the first study to report a high-throughput approach integrating gene expression data from Spodoptera frugiperda guts and their associated metatranscriptomes. Our datasets provide information on the potential effects of environmental conditions on the expression profile of S. frugiperda larval guts, their associated metatranscriptome, and putative interactions between them.Fil: Mccarthy, Cristina Beryl. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cabrera, Natalia Alina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Virla, Eduardo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentin

Inside the gut: Revelations of metatranscriptomic and transcriptomic analyses of Spodoptera frugiperda larvae from an organic maize plantation at 2283 meters above sea level (Tafí del Valle, Tucumán)

Spodoptera frugiperda is a noctuid moth that devastates various crops, including corn, and is found in most of the American continent. Transgenic crops that produce insecticidal proteins from Bacillus thuringiensis are currently the most successful biotechnological pest management application, but S. frugiperda has developed field-evolved resistance. In this regard, insect gut microbiota conform a complex community that establishes symbiotic relationships with its host, contributing to its viability. For this reason, metatranscriptomic and transcriptomic analyses of insect guts in their natural environment are invaluable to better comprehend their biology and to identify genes as targets for pest control. We previously captured S. frugiperda specimens from different environments, altitudes and food sources in the province of Tucumán (Argentina). For all samples, total RNA extracted from fifth instar larval guts was submitted to a one-step reverse transcription and PCR sequence independent amplification procedure, and then pyrosequenced. In this study we analysed one of these samples, namely, larvae that were captured in an organic maize field in Tafí del Valle (26°55´40.75´´S, 65°45´19.90´´W; Tucumán province) at 2283 meters above sea level. Sequence reads were trimmed and assembled. Homology searches were performed against various NCBI databases. Taxonomic and functional contents were analysed with MEGAN. The metatranscriptome, in which we identified sequences from archaea, bacteria, fungi, nematodes and plants, revealed potential biocontrol candidates for this pest, and others related with host metabolism and digestion. Furthermore, the host transcriptome showed that most transcripts were associated with the digestive tract structure and development, among others. Some of these genes could be possible targets for pest control via RNA interference (RNAi). In summary, this study has shown the potential effects of this particular food source (i.e., organic maize) and of the environmental conditions (altitude, among others), on the expression profile of S. frugiperda larval guts, their associated metatranscriptome, and putative interactions between them. Future studies will test the potential biocontrol candidates that we identified.Fil: Rozadilla, Gastón. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cabrera, Natalia Alina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Virla, Eduardo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Mccarthy, Cristina Beryl. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaX Congreso Argentino de EntomologíaMendozaArgentinaSociedad Argentina de EntomologíaUniversidad Nacional de Cuyo. Facultad de Ciencias AgrariasUniversidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas ÁridasInstituto Nacional de Tecnología Agropecuari

Metatranscriptomic and transcriptomic databases (DB4S) of Spodoptera frugiperda larvae guts from Northern Argentina (Tucumán province)

Spodoptera frugiperda is a noctuid moth that devastates various crops including corn, rice and cotton, and is found in most of the American continent. The purpose of this study was to integrate gene expression data from S. frugiperda guts and their associated metatranscriptomes, under natural and controlled conditions. For this, four S. frugiperda samples from the province of Tucumán (Argentina; subtropical region) were analysed. Specimens were obtained from different environments, altitudes and food sources, namely: 1) a transgenic maize (Zea mays) field at 495 m.a.s.l. where insecticides and fertilisers were applied (named MM; 26o49’50”S; 65o16’59.4”W); 2) Sorghum halepense at 495 m.a.s.l. (MS; 26o49’50”S; 65o16’59.4”W); 3) a maize field at 2283 m.a.s.l. where no insecticides or fertilisers were used (TV; 26o55’40.75”S; 65o45’19.90”W) ; and 4) a colony established from larvae originally collected from the same transgenic maize field as Sf_MM, reared for 9 generations under controlled conditions on an artificial diet adapted from [8], without the addition of antibiotics (BT). For all samples, total RNA extracted from fifth instar larvae guts (two digestive tracts per sample), was submitted to a modified one-step reverse transcription and polymerase chain reaction sequence-independent amplification procedure, as described previously. High-throughput pyrosequencing of the samples was performed using a Roche GS FLX (Macrogen Inc., Korea), yielding ~1Gb of metatranscriptomic reads with lengths of 50 to 1600 bases (nt) (652 nt average). Raw sequence reads were trimmed to remove nucleotides derived from the amplification primers using a custom application. Below follows an outline of the main steps we followed to create the uploaded databases: I.Sequences were compared locally to a combined nucleotide database (nt16SLep = “Non-redundant” nucleotide sequence (nt) database + 16S rRNA gene (16S) database + Lepidopteran whole genome shotgun (Lep) projects completed at the time of the analysis) using BLASTN (Altschul et al., 1990) with a 1e-50 cutoff E-value, and to the protein database (nr = non-redundant protein sequence) using Diamond (Buchfink et al., 2014) with a 1e-17 cutoff E-value. II.The homology search results were then processed as follows: Step A: The output files from both homology searches were processed with MEGAN, a software which performs taxonomic binning and assigns sequences to taxa using the Lowest Common Ancestor (LCA)-assignment algorithm (Huson et al., 2007). Taxonomic and functional assignments performed by MEGAN for each sequence were then exported using a MEGAN functionality. Note: MEGAN computes a “species profile” by finding the lowest node in the NCBI taxonomy that encompasses the set of hit taxa and assigns the sequence to the taxon represented by that lowest node. With this approach, every sequence is assigned to some taxon; if the sequence aligns very specifically only to a single taxon, then it is assigned to that taxon; the less specifically a sequence hits taxa, the higher up in the taxonomy it is placed. Step B: The output files from both homology searches were also processed with a custom bash script. This script parses the homology search output files and generates two files (one for each homology search) containing the name of each sequence, its best hit (or no hit) and the corresponding E-value. III. Create local database (Step C): All this information (from the exported MEGAN files and from the bash script output files) was then used to create a local SQLite database which included all the available information for each sequence (from both homology searches).Fil: Rozadilla, Gastón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Mccarthy, Cristina Beryl. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentin

Soil metagenomes from different pristine environments of northwest Argentina

This is the first study to use a high-throughput metagenomic shotgun approach to explore the biosynthetic potential of soil metagenomes from different pristine environments of northwest Argentina. Our data sets characterize these metagenomes and provide information on the possible effect these ecosystems have on their diversity and biosynthetic potential.Fil: Mccarthy, Cristina Beryl. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Escuela de Ciencias Agrarias, Naturales y Ambientales; ArgentinaFil: Colman, Déborah Inés. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Escuela de Ciencias Agrarias, Naturales y Ambientales; Argentin

Bicodon bias can determine the role of synonymous SNPs in human diseases

Background: For a long time synonymous single nucleotide polymorphisms were considered as silent mutations. However, nowadays it is well known that they can affect protein conformation and function, leading to altered disease susceptibilities, differential prognosis and/or drug responses, among other clinically relevant genetic traits. This occurs through different mechanisms: by disrupting the splicing signals of precursor mRNAs, affecting regulatory binding-sites of transcription factors and miRNAs, or by modifying the secondary structure of mRNAs. Results: In this paper we considered 22 human genetic diseases or traits, linked to 35 synonymous single nucleotide polymorphisms in 27 different genes. We performed a local sequence context analysis in terms of the ribosomal pause propensity affected by synonymous single nucleotide polymorphisms. We found that synonymous mutations related to the above mentioned mechanisms presented small pause propensity changes, whereas synonymous mutations that were not related to those mechanisms presented large pause propensity changes. On the other hand, we did not observe large variations in the codon usage of codons associated with these mutations. Furthermore, we showed that the changes in the pause propensity associated with benign sSNPs are significantly lower than the pause propensity changes related to sSNPs associated to diseases. Conclusions: These results suggest that the genetic diseases or traits related to synonymous mutations with large pause propensity changes, could be the consequence of another mechanism underlying non-silent synonymous mutations. Namely, alternative protein configuration related, in turn, to alterations in the ribosome-mediated translational attenuation program encoded by pairs of consecutive codons, not codons. These findings shed light on the latter mechanism based on the perturbation of the co-translational folding process.Fil: Mccarthy, Cristina Beryl. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Carrea, Alejandra. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Diambra, Luis Anibal. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets

Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy. When using taxonomy-dependent alignment-based methods to classify and label reads, the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX. Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show inconsistencies, which can be notorious when working with RNA-seq. Moreover, and to the best of our knowledge, existing tools do not criss-cross and integrate information from the different homology searches, but provide the results of each analysis separately. We developed the HoSeIn workflow to intersect the information from these homology searches, and then determine the taxonomic and functional profile of the sample using this integrated information. The workflow is based on the assumption that the sequences that correspond to a certain taxon are composed of:1)sequences that were assigned to the same taxon by both homology searches;2)sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one.Fil: Rozadilla, Gastón. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Moreiras Clemente, Jorgelina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Mccarthy, Cristina Beryl. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Departamento de Informática y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentin

Caracterización independiente de la composición de la comunidad del bacterioplancton en un embalse mesotrófico (Embalse Río III, Argentina)

Este estudio constituye el primer análisis de la estructura de la comunidad del bacterioplancton en un reservorio de agua dulce de Argentina utilizando amplificación completa del gen ADNr 16S. Incluye las relaciones filogenéticas y una descripción del bacterioplacton de las zonas fótica y afótica del Embalse Río III, Córdoba, Argentina. El análisis ecológico clásico indicó que la zona fótica tenía mayor diversidad, mientras que la afótica tenía mayor abundancia y una distribución más uniforme de especies. Sin embargo, cuando se utilizó la información filogenética para comparar las comunidades microbianas de ambas zonas, este análisis indicó que ambos ambientes eran similares y que en ninguno predominaba algún linaje en particular. Los phyla identificados en el Embalse del Río III fueron Acidobacteria, Actinobacteria y Proteobacteria. Las especies dominantes en ambas zonas fueron “Candidatus Planktophila sp.” (clase Actinobacteria) y Polynucleobacter sp. (clase Betaproteobacteria).This study represents the first analysis of the bacterioplankton community structure from an Argentine freshwater reservoir using amplification of the entire 16S rDNA gene. It includes the description and the phylogenetic relationships of the bacterioplankton community from the photic and aphotic layers of the Río III Reservoir in Córdoba, Argentina. The classical ecological approach indicated that the photic layer showed greater diversity and the aphotic layer a more even distribution of species and higher biomass. Nevertheless, when the microbial communities in both layers were compared using phylogenetic information, this analysis indicated that both environments were similar and that neither was enriched for any particular lineage. The phyla present in the Río III reservoir were Acidobacteria, Actinobacteria and Proteobacteria and the two dominant species in both layers were Candidatus Planktophila sp. (class Actinobacteria) and Polynucleobacter sp. (class Betaproteobacteria).Fil: Polverino, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Mariñelarena, Alejandro Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Mccarthy, Cristina Beryl. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Rivera Pomar, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentin

Polymerase chain reaction-based assay for the detection and identification of sand fly gregarines in Lutzomyia longipalpis, vector of visceral leishmaniasis

Gregarines that parasitise phlebotomine sand flies belong to the genus Psychodiella and, even though they are highly host-specific, only five species have been described to date. Their most outstanding features include the unique localisation of the oocysts in the accessory glands of the female host, which ensures contamination of the egg surface during oviposition, and the fact that they naturally parasitise the vectors of Leishmania, causal agent of leishmaniasis. The type species, Ps. chagasi, was first described in Lutzomyia longipalpis, vector of visceral leishmaniasis (VL), from Brazil. We recently reported Ps. chagasi sequences in Lu. longipalpis from Posadas (Misiones, Argentina), an endemic VL location where this gregarine had not been previously recorded. In order to analyse the incidence of Ps. chagasi infections in Lu. longipalpis from this location, the aim of this study was to develop a diagnostic assay for sand fly gregarine parasites in Lu. longipalpis. For this, we designed primers using the Ps. chagasi sequences we previously identified and performed an in vitro validation by PCR amplification of the original sand fly samples. Their specificity and sensitivity as diagnostic primers were subsequently confirmed by PCR reactions using total DNA extracted from naturally infected Lu. longipalpis from the same location (Posadas, Argentina).Fil: Caligiuri, Lorena Gisel. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; ArgentinaFil: Acardi, Soraya Alejandra. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Santini, Maria Soledad. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Centro Nacional de Diagnóstico e Investigaciones Endemo-epidémicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Salomón, Oscar Daniel. Ministerio de Salud. Instituto Nacional de Medicina Tropical; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Mccarthy, Cristina Beryl. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin