BED files containing Transposable Element (TE) annotations for 47 Drosophila melanogaster genomes
We annotated TE copies only in the euchromatic regions of the genome since heterochromatic regions are gene-poor (Smith et al. 2007) and their assembly and annotation usually require specific methods and extensive curation (Chakraborty et al. 2019; Khost et al. 2017). In this work, we considered as...
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| Tipo de recurso: | conjunto de datos |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/242513 |
| Acceso en línea: | http://hdl.handle.net/10261/242513 |
| Access Level: | acceso abierto |
| Palabra clave: | Drosophila melanogaster Transposable elements Bed Annotation Transposable Elements Drosophila Melanogaster Rech 2021 |
| Sumario: | We annotated TE copies only in the euchromatic regions of the genome since heterochromatic regions are gene-poor (Smith et al. 2007) and their assembly and annotation usually require specific methods and extensive curation (Chakraborty et al. 2019; Khost et al. 2017). In this work, we considered as euchromatic those genomic regions determined by the recombination rate calculator (RRC) (Fiston-Lavier et al. 2010) available at http://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl. Such coordinates were originally calculated based on release 5 of D. melanogaster genome, so we converted them to release 6 coordinates using the coord_converter.pl script from FlyBase (Gramates et al. 2017), resulting in the following regions: 2L:530,000..18,870,000; 2R:5,982,495..24,972,477; 3L:750,000..19,026,900; 3R:6,754,278..31,614,278; X:1,325,967..21,338,973. In order to determine the coordinates of the euchromatic regions in each scaffolded genome, we mapped scaffolds to the euchromatic region of the ISO-1 genome using MUMmer (v3.0) (Kurtz et al. 2004). We then determined the coordinates in the scaffolded genomes by parsing MUMmer´s output and extracting the coordinates mapping at the boundaries of the euchromatic region of the ISO-1 genome. After running the TEannot pipeline over the euchromatic regions of each genome, we performed a post-annotation filtering step consisting in the removal of TE copies <100bp. To identify orthologous TEs, we first transferred the TE coordinates from each strain to the ISO-1 reference genome. Briefly, we used a similarity and synteny approach based on minimap2 (v.2.9) (Li 2018) mapping of the TE sequence and its flanking regions to the ISO-1 genome and the coordinates of genes as anchored synteny sequences. To transfer the TEs, we took into account whether its flanking region mapped unequivocally or not, whether it mapped completely or partially, whether it was a tandem or nested TE, among others. Then, based on the information of the alignment and characteristics of the transfer, we defined each of the TEs as either reliable or unreliable (which were discarded from the transfer). Finally, once all the reliable TEs of each strain were transferred to the reference, the orthologous TEs were defined. To avoid false positives, we only used those TEs for which more than half of the orthologous TEs were larger than 120bp. All scripts used for the TE transfer are available at www.github.com/sradiouy/deNovoTEsDmel. Details on the BED files: DeNovoCoordinates: Columns 1-3: Chr, Start, End: Coordinates for the TE annotation in the strain’s genome. Column 4: TE Name: encoded as the name of the strain, a number and the family (e.g.: A1_1_Bari1). Column 5: length of the TE insertion. Column 6: strand. ReferenceCoordinates: Columns 1-3: Chr, Start, End: Coordinates for the TE annotation considering the reference genome coordinates (ISO-1). If the insertion is not present in the reference genome, the coordinate will then represent the insertion breakpoint, spanning a few bp. Column 4: TE Name: can be encoded in three ways (1) “FBti” followed by a seven-digit number (e.g.: FBti0019386), which identifies TEs annotated in the D. melanogaster reference genome available also at FlyBase, (2) “ISO-1” followed by a digit and the TE family (e.g.: ISO1_36_INE-1) identifies TEs that have been discovered de novo in the reference genome; and (3), a coordinate, indicating the region where the TE was discovered, and the TE family name (e.g.: 2R_14873922_14873929_roo), which identifies TE insertions discovered de novo in non-reference genomes. Column 5: empty (.) Column 6: empty (.) Column 7: TE family DeNovoCoordinatesTransferred: Columns 1-3: Chr, Start, End: Coordinates for the TE annotation in the strain’s genome. Column 4: TE Name: encoded as in ReferenceCoordinates BED files. Column 5: length of the TE insertion. Column 6: strand. Column 7: TE family. Important: the coordinates in these bed files are 1-based, not 0-based. |
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