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 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 homolog

SUBMITTER: Gonzalez-Garcia LN 

PROVIDER: S-EPMC10439823 | biostudies-literature | 2023 Jul-Aug

REPOSITORIES: biostudies-literature