TE Density: a tool to investigate the biology of transposable elements
Abstract Background Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE’s potential to impact phen...
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Mobile DNA |
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| Online Access: | https://doi.org/10.1186/s13100-022-00264-4 |
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| author | Scott J. Teresi Michael B. Teresi Patrick P. Edger |
| author_facet | Scott J. Teresi Michael B. Teresi Patrick P. Edger |
| author_sort | Scott J. Teresi |
| collection | DOAJ |
| description | Abstract Background Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE’s potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs’ ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly available computational methods that quantify the presence of TEs relative to genes. Results Here, we have developed a tool to more easily quantify TE presence relative to genes through the use of only a gene and TE annotation, yielding a new metric we call TE Density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome. Conclusions Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture, comparative genomics, and the tremendous diversity present of the TE world. TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density . |
| first_indexed | 2024-12-10T03:28:35Z |
| format | Article |
| id | doaj.art-00c6335bed3e4f83b4a787fea5300910 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-10T03:28:35Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-00c6335bed3e4f83b4a787fea53009102022-12-22T02:03:52ZengBMCMobile DNA1759-87532022-04-0113111810.1186/s13100-022-00264-4TE Density: a tool to investigate the biology of transposable elementsScott J. Teresi0Michael B. Teresi1Patrick P. Edger2Department of Horticulture, Michigan State UniversityIndependent ResearcherDepartment of Horticulture, Michigan State UniversityAbstract Background Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE’s potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs’ ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly available computational methods that quantify the presence of TEs relative to genes. Results Here, we have developed a tool to more easily quantify TE presence relative to genes through the use of only a gene and TE annotation, yielding a new metric we call TE Density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome. Conclusions Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture, comparative genomics, and the tremendous diversity present of the TE world. TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density .https://doi.org/10.1186/s13100-022-00264-4Transposable ElementsGenomicsGenome EvolutionBioinformaticsPython |
| spellingShingle | Scott J. Teresi Michael B. Teresi Patrick P. Edger TE Density: a tool to investigate the biology of transposable elements Mobile DNA Transposable Elements Genomics Genome Evolution Bioinformatics Python |
| title | TE Density: a tool to investigate the biology of transposable elements |
| title_full | TE Density: a tool to investigate the biology of transposable elements |
| title_fullStr | TE Density: a tool to investigate the biology of transposable elements |
| title_full_unstemmed | TE Density: a tool to investigate the biology of transposable elements |
| title_short | TE Density: a tool to investigate the biology of transposable elements |
| title_sort | te density a tool to investigate the biology of transposable elements |
| topic | Transposable Elements Genomics Genome Evolution Bioinformatics Python |
| url | https://doi.org/10.1186/s13100-022-00264-4 |
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