MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
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 e...
| Main Authors: | , , , |
|---|---|
| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
| Published: |
BioMed Central
2018
|
| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.12123/3607 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y https://doi.org/10.1186/s12859-018-2376-y |
| _version_ | 1855035171812671488 |
|---|---|
| author | Crescente, Juan Manuel Zavallo, Diego Helguera, Marcelo Vanzetti, Leonardo Sebastian |
| author_browse | Crescente, Juan Manuel Helguera, Marcelo Vanzetti, Leonardo Sebastian Zavallo, Diego |
| author_facet | Crescente, Juan Manuel Zavallo, Diego Helguera, Marcelo Vanzetti, Leonardo Sebastian |
| author_sort | Crescente, Juan Manuel |
| collection | INTA Digital |
| description | 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA3607 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | BioMed Central |
| publisherStr | BioMed Central |
| record_format | dspace |
| spelling | INTA36072018-10-17T13:00:37Z MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes Crescente, Juan Manuel Zavallo, Diego Helguera, Marcelo Vanzetti, Leonardo Sebastian Arroz Trigo Triticum Aestivum Oryza Sativa Genomas Transposones Rice Wheat Genomes Transposons Transposable Element MITE Miniature Inverted-repeat Transposable Elements 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 Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina Fil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina 2018-10-17T12:33:16Z 2018-10-17T12:33:16Z 2018 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/3607 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y 1471-2105 https://doi.org/10.1186/s12859-018-2376-y eng info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) application/pdf BioMed Central BMC bioinformatics 19 : 348. (2018) |
| spellingShingle | Arroz Trigo Triticum Aestivum Oryza Sativa Genomas Transposones Rice Wheat Genomes Transposons Transposable Element MITE Miniature Inverted-repeat Transposable Elements Crescente, Juan Manuel Zavallo, Diego Helguera, Marcelo Vanzetti, Leonardo Sebastian MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes |
| title | MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes |
| title_full | MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes |
| title_fullStr | MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes |
| title_full_unstemmed | MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes |
| title_short | MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes |
| title_sort | mite tracker an accurate approach to identify miniature inverted repeat transposable elements in large genomes |
| topic | Arroz Trigo Triticum Aestivum Oryza Sativa Genomas Transposones Rice Wheat Genomes Transposons Transposable Element MITE Miniature Inverted-repeat Transposable Elements |
| url | http://hdl.handle.net/20.500.12123/3607 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y https://doi.org/10.1186/s12859-018-2376-y |
| work_keys_str_mv | AT crescentejuanmanuel mitetrackeranaccurateapproachtoidentifyminiatureinvertedrepeattransposableelementsinlargegenomes AT zavallodiego mitetrackeranaccurateapproachtoidentifyminiatureinvertedrepeattransposableelementsinlargegenomes AT helgueramarcelo mitetrackeranaccurateapproachtoidentifyminiatureinvertedrepeattransposableelementsinlargegenomes AT vanzettileonardosebastian mitetrackeranaccurateapproachtoidentifyminiatureinvertedrepeattransposableelementsinlargegenomes |