Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data
| Autor: | Leandro Quadrana, Vincent Colot, Pierre Baduel |
|---|---|
| Přispěvatelé: | Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Quadrana, Leandro, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Transposable element
[SDV]Life Sciences [q-bio] Sequencing data Arabidopsis Computational biology Genome [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics 03 medical and health sciences 0302 clinical medicine Species level [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BBM] Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] Arabidopsis thaliana [SDV.BV]Life Sciences [q-bio]/Vegetal Biology [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BV] Life Sciences [q-bio]/Vegetal Biology 030304 developmental biology 0303 health sciences Polymorphism Genetic [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] biology TE insertion polymorphism [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] Computational Biology food and beverages [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biology Sequence Analysis DNA Short read biology.organism_classification [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] [SDV] Life Sciences [q-bio] DNA Transposable Elements [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] 030217 neurology & neurosurgery Algorithms Genome Plant |
| Zdroj: | Plant Transposable Elements Plant Transposable Elements, 2250, Springer US, pp.157-169, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1134-0_15⟩ Methods in Molecular Biology ISBN: 9781071611333 |
| Popis: | Transposable elements (TEs) are powerful generators of major-effect mutations, most of which are deleterious at the species level and maintained at very low frequencies within populations. As reference genomes can only capture a minor fraction of such variants, methods were developed to detect TE insertion polymorphisms (TIPs) in non-reference genomes from short-read sequencing data, which are becoming increasingly available. We present here a bioinformatic framework combining an improved version of the SPLITREADER and TEPID pipelines to detect non-reference TE presence and reference TE absence variants, respectively. We benchmark our method on ten non-reference Arabidopsis thaliana genomes and demonstrate its high specificity and sensitivity in the detection of TIPs between genomes. |
| Databáze: | OpenAIRE |
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