000			02315 am a22002653u 4500
042			_adc
100	1	0	_aContreras-Moreira, Bruno _eauthor
700	1	0	_aFilippi, Carla V _eauthor _93003
700	1	0	_aNaamati, Guy _eauthor
700	1	0	_aGirón, Carlos García _eauthor _93005
700	1	0	_aAllen, James E _eauthor
700	1	0	_aFlicek, Paul _eauthor
245	0	0	_aK-mer counting and curated libraries drive efficient annotation of repeats in plant genomes
260			_c2021-11-01.
500			_a/pmc/articles/PMC7614178/
500			_a/pubmed/34562304
520			_aThe annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.
540			_a
540			_ahttps://creativecommons.org/licenses/by/4.0/This work is licensed under a CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) International license.
546			_aen
690			_aArticle
655	7		_aText _2local
786	0		_nPlant Genome
856	4	1	_uhttp://dx.doi.org/10.1002/tpg2.20143 _zConnect to this object online.
999			_c989 _d989