Efficient homology‐based annotation of transposable elements using minimizers
Abstract Premise Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the build...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-07-01
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| Series: | Applications in Plant Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/aps3.11520 |
| _version_ | 1828716870001229824 |
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| author | Laura Natalia Gonzalez‐García Daniela Lozano‐Arce Juan Pablo Londoño Romain Guyot Jorge Duitama |
| author_facet | Laura Natalia Gonzalez‐García Daniela Lozano‐Arce Juan Pablo Londoño Romain Guyot Jorge Duitama |
| author_sort | Laura Natalia Gonzalez‐García |
| collection | DOAJ |
| description | Abstract Premise Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies. Methods and Results We present a new functionality of the Next‐Generation Sequencing Experience Platform (NGSEP) to perform efficient homology‐based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology‐based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95. Conclusions NGSEP allows rapid analysis of TEs, especially in very large and TE‐rich plant genomes. |
| first_indexed | 2024-03-12T14:19:45Z |
| format | Article |
| id | doaj.art-a5b30d69609746548a62e37e8dc9c756 |
| institution | Directory Open Access Journal |
| issn | 2168-0450 |
| language | English |
| last_indexed | 2024-03-12T14:19:45Z |
| publishDate | 2023-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Applications in Plant Sciences |
| spelling | doaj.art-a5b30d69609746548a62e37e8dc9c7562023-08-19T21:30:40ZengWileyApplications in Plant Sciences2168-04502023-07-01114n/an/a10.1002/aps3.11520Efficient homology‐based annotation of transposable elements using minimizersLaura Natalia Gonzalez‐García0Daniela Lozano‐Arce1Juan Pablo Londoño2Romain Guyot3Jorge Duitama4Systems and Computing Engineering Department Universidad de los Andes Bogotá ColombiaSystems and Computing Engineering Department Universidad de los Andes Bogotá ColombiaDepartment of Biological Sciences Universidad de los Andes Bogotá ColombiaUMR DIADE, Institut de Recherche pour le Développement Université de Montpellier, CIRAD 34394 Montpellier FranceSystems and Computing Engineering Department Universidad de los Andes Bogotá ColombiaAbstract Premise Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies. Methods and Results We present a new functionality of the Next‐Generation Sequencing Experience Platform (NGSEP) to perform efficient homology‐based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology‐based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95. Conclusions NGSEP allows rapid analysis of TEs, especially in very large and TE‐rich plant genomes.https://doi.org/10.1002/aps3.11520bioinformaticsgenomicssoftwaretransposable elements |
| spellingShingle | Laura Natalia Gonzalez‐García Daniela Lozano‐Arce Juan Pablo Londoño Romain Guyot Jorge Duitama Efficient homology‐based annotation of transposable elements using minimizers Applications in Plant Sciences bioinformatics genomics software transposable elements |
| title | Efficient homology‐based annotation of transposable elements using minimizers |
| title_full | Efficient homology‐based annotation of transposable elements using minimizers |
| title_fullStr | Efficient homology‐based annotation of transposable elements using minimizers |
| title_full_unstemmed | Efficient homology‐based annotation of transposable elements using minimizers |
| title_short | Efficient homology‐based annotation of transposable elements using minimizers |
| title_sort | efficient homology based annotation of transposable elements using minimizers |
| topic | bioinformatics genomics software transposable elements |
| url | https://doi.org/10.1002/aps3.11520 |
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