K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes
The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationall...
| Main Authors: | , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
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Wiley
2021
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| Online Access: | http://hdl.handle.net/20.500.12123/10882 https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20143 https://doi.org/10.1002/tpg2.20143 |
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| author | Contreras-Moreira, Bruno Filippi, Carla Valeria Naamati, Guy García Girón, Carlos Allen, James E. Flicek, Paul |
| author_browse | Allen, James E. Contreras-Moreira, Bruno Filippi, Carla Valeria Flicek, Paul García Girón, Carlos Naamati, Guy |
| author_facet | Contreras-Moreira, Bruno Filippi, Carla Valeria Naamati, Guy García Girón, Carlos Allen, James E. Flicek, Paul |
| author_sort | Contreras-Moreira, Bruno |
| collection | INTA Digital |
| description | The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts. |
| format | Artículo |
| id | INTA10882 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | INTA108822021-12-10T13:48:21Z K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes Contreras-Moreira, Bruno Filippi, Carla Valeria Naamati, Guy García Girón, Carlos Allen, James E. Flicek, Paul Genomas Fitogenética Genética Genomes Plant Genetics Genetics The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts. Instituto de Biotecnología Fil: Contreras-Moreira, Bruno. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Filippi, Carla Valeria. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: Naamati, Guy. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: García Girón, Carlos. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: Allen, James E. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido Fil: Flicek, Paul. European Bioinformatics Institute. European Molecular Biology Laboratory; Reino Unido 2021-12-10T13:45:33Z 2021-12-10T13:45:33Z 2021-09 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/10882 https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20143 1940-3372 https://doi.org/10.1002/tpg2.20143 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 Wiley The Plant Genome 14 (3) : e20143 (November 2021) |
| spellingShingle | Genomas Fitogenética Genética Genomes Plant Genetics Genetics Contreras-Moreira, Bruno Filippi, Carla Valeria Naamati, Guy García Girón, Carlos Allen, James E. Flicek, Paul K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| title | K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| title_full | K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| title_fullStr | K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| title_full_unstemmed | K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| title_short | K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| title_sort | k mer counting and curated libraries drive efficient annotation of repeats in plant genomes |
| topic | Genomas Fitogenética Genética Genomes Plant Genetics Genetics |
| url | http://hdl.handle.net/20.500.12123/10882 https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20143 https://doi.org/10.1002/tpg2.20143 |
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