Gonzalez-García Laura Natalia, Lozano-Arce Daniela, Londoño Juan Pablo, Guyot Romain, Duitama Jorge
Systems and Computing Engineering Department Universidad de los Andes Bogotá Colombia.
UMR DIADE, Institut de Recherche pour le Développement Université de Montpellier, CIRAD 34394 Montpellier France.
Appl Plant Sci. 2023 May 11;11(4):e11520. doi: 10.1002/aps3.11520. eCollection 2023 Jul-Aug.
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.
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 , , and (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 genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95.
NGSEP allows rapid analysis of TEs, especially in very large and TE-rich plant genomes.
转座元件（TEs）在复杂植物物种的基因组中所占比例超过一半，并且可以调节邻近基因的表达，从而产生与农艺相关性状的显著变异性。长读长测序技术的出现使得构建具有大而复杂基因组的植物物种的基因组组装成为可能。不幸的是，目前TE注释是基因组组装注释中的一个瓶颈。
我们展示了新一代测序体验平台（NGSEP）的一项新功能，用于高效地基于同源性进行TE注释。参考文库中的序列被视为长读长，并映射到输入的基因组组装上。然后使用参考文库的注释通过同源性进行分层注释。我们在不同植物物种的基因组组装上测试了我们算法的性能，包括普通小麦、硬粒小麦和面包小麦。我们的算法在速度上比传统的基于同源性的注释工具快3到20倍，将面包小麦基因组的注释时间从数月缩短到数小时，并以高达0.95的精度找回了高达80%用RepeatMasker注释的TEs。
NGSEP允许对TEs进行快速分析，特别是在非常大且富含TE的植物基因组中。
