Publication Date: 2018.
Language: English.
Abstract:
Background: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
EEA Marcos Juárez
Author affiliation: Crescente, Juan Manuel. INTA. Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Zavallo, Diego. INTA. Instituto de Biotecnología; Argentina
Author affiliation: Helguera, Marcelo. INTA. Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina
Author affiliation: Vanzetti, Leonardo Sebastian. INTA. Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Repository: INTA Digital (INTA). Instituto Nacional de Tecnología Agropecuaria
Authors: De Haro, Luis Alejandro; Dumon, Analia Delina; Mattio, Maria Fernanda; Arguello Caro, Evangelina Beatriz; Llauger, Gabriela; Zavallo, Diego; Blanc, Hervé; Mongelli, Vanesa Claudia; Truol, Graciela Ana Maria; Saleh, María-Carla; Asurmendi, Sebastian; Del Vas, Mariana
Publication Date: 2017.
Language: English.
Abstract:
Plant reoviruses are able to multiply in gramineae plants and delphacid vectors encountering different defense strategies with unique features. This study aims to comparatively assess alterations of small RNA (sRNA) populations in both hosts upon virus infection. For this purpose, we characterized the sRNA profiles of wheat and planthopper vectors infected by Mal de Río Cuarto virus (MRCV, Fijivirus, Reoviridae) and quantified virus genome segments by quantitative reverse transcription PCR We provide evidence that plant and insect silencing machineries differentially recognize the viral genome, thus giving rise to distinct profiles of virus-derived small interfering RNAs (vsiRNAs). In plants, most of the virus genome segments were targeted preferentially within their upstream sequences and vsiRNAs mapped with higher density to the smaller genome segments than to the medium or larger ones. This tendency, however, was not observed in insects. In both hosts, vsiRNAs were equally derived from sense and antisense RNA strands and the differences in vsiRNAs accumulation did not correlate with mRNAs accumulation. We also established that the piwi-interacting RNA (piRNA) pathway was active in the delphacid vector but, contrary to what is observed in virus infected mosquitoes, virus-specific piRNAs were not detected. This work contributes to the understanding of the silencing response in insect and plant hosts.
Inst. de Biotecnología
Author affiliation: De Haro, Luis Alejandro. INTA. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Dumon, Analia Delina. INTA. Instituto de Patología Vegetal; Argentina
Author affiliation: Mattio, Maria Fernanda. INTA. Instituto de Patología Vegetal; Argentina
Author affiliation: Arguello Caro, Evangelina Beatriz. INTA. Instituto de Patología Vegetal; Argentina
Author affiliation: Llauger, Gabriela. INTA. Instituto de Biotecnología; Argentina
Author affiliation: Zavallo, Diego. INTA. Instituto de Biotecnología; Argentina
Author affiliation: Blanc, Hervé. Centre National de la Recherche Scientifique. Institut Pasteur, Viruses and RNA Interference Unit; Francia
Author affiliation: Truol, Graciela Ana Maria. INTA. Instituto de Patología Vegetal; Argentina
Author affiliation: Mongelli, Vanesa Claudia. Centre National de la Recherche Scientifique. Institut Pasteur, Viruses and RNA Interference Unit; Francia
Author affiliation: Saleh, María-Carla. Centre National de la Recherche Scientifique. Institut Pasteur, Viruses and RNA Interference Unit; Francia
Author affiliation: Asurmendi, Sebastian. INTA. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Del Vas, Mariana. INTA. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Keywords: ARN; Virus de las Plantas; Trigo; Fulgoroidea; Plant Viruses; Wheat; RNA; Virus del Mal de Río Cuarto; Fijivirus.
Repository: INTA Digital (INTA). Instituto Nacional de Tecnología Agropecuaria
Authors: de Haro, Luis Alejandro; Dumón, Analía Delina; Mattio, Maria Fernanda; Argüello Caro, Evangelina Beatriz; Llauger, Gabriela; Zavallo, Diego; Blanc, Hervé; Mongelli, Vanesa Claudia; Truol, Graciela Ana; Saleh, María Carla; Asurmendi, Sebastian; del Vas, Mariana
Publication Date: 2017.
Language: English.
Abstract:
Plant reoviruses are able to multiply in gramineae plants and delphacid vectors encountering different defense strategies with unique features. This study aims to comparatively assess alterations of small RNA (sRNA) populations in both hosts upon virus infection. For this purpose, we characterized the sRNA profiles of wheat and planthopper vectors infected by Mal de Río Cuarto virus (MRCV, Fijivirus, Reoviridae) and quantified virus genome segments by quantitative reverse transcription PCR We provide evidence that plant and insect silencing machineries differentially recognize the viral genome, thus giving rise to distinct profiles of virus-derived small interfering RNAs (vsiRNAs). In plants, most of the virus genome segments were targeted preferentially within their upstream sequences and vsiRNAs mapped with higher density to the smaller genome segments than to the medium or larger ones. This tendency, however, was not observed in insects. In both hosts, vsiRNAs were equally derived from sense and antisense RNA strands and the differences in vsiRNAs accumulation did not correlate with mRNAs accumulation. We also established that the piwi-interacting RNA (piRNA) pathway was active in the delphacid vector but, contrary to what is observed in virus-infected mosquitoes, virus-specific piRNAs were not detected. This work contributes to the understanding of the silencing response in insect and plant hosts.
Author affiliation: de Haro, Luis Alejandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Dumón, Analía Delina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Mattio, Maria Fernanda. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Argüello Caro, Evangelina Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Llauger, Gabriela. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Blanc, Hervé. Instituto Pasteur; Francia
Author affiliation: Mongelli, Vanesa Claudia. Instituto Pasteur; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Truol, Graciela Ana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina
Author affiliation: Saleh, María Carla. Instituto Pasteur; Francia
Author affiliation: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: del Vas, Mariana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: de Haro, Luis Alejandro; Dumón, Analía Delina; Mattio, Maria Fernanda; Argüello Caro, Evangelina Beatriz; Llauger, Gabriela; Zavallo, Diego; Blanc, Hervé; Mongelli, Vanesa Claudia; Truol, Graciela Ana; Saleh, María Carla; Asurmendi, Sebastian; del Vas, Mariana
Publication Date: 2017.
Language: English.
Abstract:
Plant reoviruses are able to multiply in gramineae plants and delphacid vectors encountering different defense strategies with unique features. This study aims to comparatively assess alterations of small RNA (sRNA) populations in both hosts upon virus infection. For this purpose, we characterized the sRNA profiles of wheat and planthopper vectors infected by Mal de Río Cuarto virus (MRCV, Fijivirus, Reoviridae) and quantified virus genome segments by quantitative reverse transcription PCR We provide evidence that plant and insect silencing machineries differentially recognize the viral genome, thus giving rise to distinct profiles of virus-derived small interfering RNAs (vsiRNAs). In plants, most of the virus genome segments were targeted preferentially within their upstream sequences and vsiRNAs mapped with higher density to the smaller genome segments than to the medium or larger ones. This tendency, however, was not observed in insects. In both hosts, vsiRNAs were equally derived from sense and antisense RNA strands and the differences in vsiRNAs accumulation did not correlate with mRNAs accumulation. We also established that the piwi-interacting RNA (piRNA) pathway was active in the delphacid vector but, contrary to what is observed in virus-infected mosquitoes, virus-specific piRNAs were not detected. This work contributes to the understanding of the silencing response in insect and plant hosts.
Author affiliation: de Haro, Luis Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Author affiliation: Dumón, Analía Delina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Author affiliation: Mattio, Maria Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Author affiliation: Argüello Caro, Evangelina Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Author affiliation: Llauger, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Author affiliation: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Author affiliation: Blanc, Hervé. Instituto Pasteur; Francia
Author affiliation: Mongelli, Vanesa Claudia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Pasteur; Francia
Author affiliation: Truol, Graciela Ana. Instituto Nacional de Tecnología Agropecuaria; Argentina
Author affiliation: Saleh, María Carla. Instituto Pasteur; Francia
Author affiliation: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Author affiliation: del Vas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina
Keywords: FIJIVIRUS; MRCV; PIRNAS; PLANTHOPPER; RNA SILENCING; SRNAS; VSIRNAS; WHEAT; Virología; Ciencias Biológicas; CIENCIAS NATURALES Y EXACTAS.
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas