ArticleApplications in plant sciences
Efficient homology-based annotation of transposable elements using minimizers.
Article in Applications in plant sciences. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Genome-wide association study of cassava brown streak disease resistance in cassava germplasm conserved in South America.Scientific reports · 2024Article
- A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families.Scientific reports · 2024Article
- Efficient homology-based annotation of transposable elements using minimizers.Applications in plant sciencesArticle
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5 authors.
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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 Conclusions: NGSEP allows rapid analysis of TEs, especially in very large and TE-rich plant genomes.
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