Towards the high-quality, de novo annotation of transposable elements in eukaryotes

Abstract

Sequencing technology and assembly algorithms have matured to the point that contiguous de novo assembly is possible for large, repetitive genomes. Numerous methods exist for annotation of varying types of TEs, but their relative performances are often suboptimal. Moreover, diverse TE landscapes of eukaryotic genomes challenge each pipeline to produce high-quality TE annotations. We benchmark existing programs based on carefully curated TE annotations of model species. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces annotation of structurally intact and fragmented transposing. As an evolving program, we continuously improve existing pipelines and incorporate them into EDTA for more robust and scalable TE annotations in genomes with diverse TE landscapes. The resulting TE annotations have promoted a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels.

About the speaker

区树俊，美国俄亥俄州立大学分子遗传系计算生物学Assistant Professor。2018 年博士毕业于密西根州立大学，植物遗传与进化专业。随后分别在爱荷华州立大学和约翰斯·霍普金斯大学从事博士后2023年在俄亥俄州立大学组建实验室，任独立PI。区树俊教授长期致力于研究转座子(Transposable element,TE)的进化及其活动对生物功能 (抗逆、环境适应以及物种形成)的贡献。其开发一系列广泛使用的 TE 注释和分析工具，推动了高质量基因组时代转座子研究的革新，包括灵敏和准确的注释LTR 反转录转座子的LTR retriever; 用于de novo注释全基因组转座子的 EDTA; 用于评估转座子组装质量的 LAI 等。区教授在植物基因组组装算法和进化生物学方面也具有很深造诣，迄今为止，在包括Nature、Science、Cell、NatureGenetics、Nature Communications、Genome Biology等权威期刊上发表近50篇高水平研究论文，被引用7200余次。