Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
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Published:2023-09-22
Issue:10
Volume:33
Page:1708-1717
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ISSN:1088-9051
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Container-title:Genome Research
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language:en
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Short-container-title:Genome Res.
Author:
Sproul John S.ORCID,
Hotaling Scott,
Heckenhauer Jacqueline,
Powell Ashlyn,
Marshall Dez,
Larracuente Amanda M.ORCID,
Kelley Joanna L.ORCID,
Pauls Steffen U.ORCID,
Frandsen Paul B.ORCID
Abstract
Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in RE dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE–gene associations in lineages with abundant long interspersed nuclear elements (LINEs). We leveraged this large, empirical data set to quantify impacts of long-read technology on RE detection and investigate fundamental challenges to RE annotation in diverse groups. In long-read assemblies, we detected ∼36% more REs than short-read assemblies, with long terminal repeats (LTRs) showing 162% increased detection, whereas DNA transposons and LINEs showed less respective technology-related bias. In most insect lineages, 25%–85% of repetitive sequences were “unclassified” following automated annotation, compared with only ∼13% inDrosophilaspecies. Although the diversity of available insect genomes has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress toward this goal.
Funder
National Science Foundation
Division of Biological Infrastructure
National Institutes of Health General Medical Sciences
Deutsche Forschungsgemeinschaft
Genomic Basis of Evolutionary Innovations
Hessen State Ministry of Higher Education, Research, and the Arts
Publisher
Cold Spring Harbor Laboratory
Subject
Genetics (clinical),Genetics