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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #374785
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Author
item OU, SHUJUN - Iowa State University
item SU, WEIJA - Iowa State University
item LIAO, YI - University Of California
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item AGDA, JIREH - University Of Guelph
item HELLINGA, ADAM - University Of Guelph
item LUGO, CARLOS SANTIAGO - University Of Guelph
item ELLIOTT, TYLER - University Of Guelph
item Ware, Doreen
item PETERSON, THOMAS - Iowa State University
item JIANG, NING - Michigan State University
item HIRSCH, CANDICE - University Of Minnesota
item HUFFORD, MATTHEW - Iowa State University

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/28/2019
Publication Date: 12/16/2019
Citation: Ou, S., Su, W., Liao, Y., Chougule, K.M., Agda, J.R., Hellinga, A.J., Lugo, C., Elliott, T.A., Ware, D., Peterson, T., Jiang, N., Hirsch, C.N., Hufford, M.B. 2019. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20(1):275. https://doi.org/10.1186/s13059-019-1905-y.
DOI: https://doi.org/10.1186/s13059-019-1905-y

Interpretive Summary: Genome sequences often consist of functional regions that are represented by genes as well as repetitive regions called Transposable Elements (TE) that have the ability to make copies and integrate in the genome. In plant genomes, especially in large plant genomes, they represent a very large fraction of the genomes. TEs play a functional or gene regulatory role in the genome architecture and their characterization is essential to the understanding of plant function and evolution. However, their repetitive nature makes it challenging to characterize them. This benchmarking study offers a comprehensive approach in the characterization and annotation of TEs for reference genomes.

Technical Abstract: Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations.