ArticleGigaScience2019
RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 41 citations in OpenAlex.
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- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- The evolution history of an allotetraploid mangrove tree analysed with a new tool Allo4D.Plant biotechnology journal · 2024Article
- PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution.Molecular biology and evolution · 2024Article
- Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.Scientific data · 2024Article
- High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae).BMC genomics · 2023Article
- Integrating gene annotation with orthology inference at scale.Science (New York, N.Y.) · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposons and other repetitive sequences make up a large part of complex genomes. Repetitive sequences can be co-opted into a variety of functions and thus provide a source for evolutionary novelty. However, comprehensively detecting ancestral repeats that align between species is difficult because considering all repeat-overlapping seeds in alignment methods that rely on the seed-and-extend heuristic results in prohibitively high runtimes.
resultsHere, we show that ignoring repeat-overlapping alignment seeds when aligning entire genomes misses numerous alignments between repetitive elements. We present a tool, RepeatFiller, that improves genome alignments by incorporating previously undetected local alignments between repetitive sequences. By applying RepeatFiller to genome alignments between human and 20 other representative mammals, we uncover between 22 and 84 Mb of previously undetected alignments that mostly overlap transposable elements. We further show that the increased alignment coverage improves the annotation of conserved non-exonic elements, both by discovering numerous novel transposon-derived elements that evolve under constraint and by removing thousands of elements that are not under constraint in placental mammals.
conclusionsRepeatFiller contributes to comprehensively aligning repetitive genomic regions, which facilitates studying transposon co-option and genome evolution. Source code: https://github.com/hillerlab/GenomeAlignmentTools.
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