FlyBase Reference Report: Crosby et al., 2020-, FlyBase annotation of transposable element insertions in the D. melanogaster reference genome assembly.

Reference

Citation

Crosby, M.A., dos Santos, G., FlyBase Genome Annotators, (2020-). FlyBase annotation of transposable element insertions in the D. melanogaster reference genome assembly.

FlyBase ID

FBrf0261225

Publication Type

FlyBase analysis

Abstract

PubMed ID

PubMed Central ID

DOI

Associated Information

Comments

Transposable element (TE) insertions present in the D. melanogaster reference genome assembly are annotated as FlyBase Insertions of type "transposable_element"; these entities have an "FBti" ID. These annotations are limited to insertions containing both intact ends of the TE. As of FB2025_01, there are 5,753 TE insertions annotated (of which, only 19 have not been mapped to the Release 6 reference genome assembly). Each TE insertion has a FlyBase Insertion report. A search for "transposable_element" or "SO:0000101" in the FlyBase Vocabularies tool allows for retrieval of these entities. TE insertions are displayed in the "Natural TE" JBrowse track (under the "Reference Genome" tracks section). TE insertion sequences and locations are available for download as a FASTA file ("dmel-all-transposon" file in the "Genomes: Annotation and Sequence > "Drosophila melanogaster (Dmel)" > "FASTA" section of the Downloads page).

Over 90% of these annotated TE insertions were identified by Quesneville et al., 2005 (FBrf0186342), which involved analysis of the Release 4 reference genome assembly. In 2008, an analysis of the Release 5 reference genome assembly by DeBaryshe and Parude (FBrf0205582, FBrf0206616) identified 44 new HeT-A, HeT-Tag, TART-A and TART-C elements (corrections were made to another 11 annotations). A more recent analysis of the Release 6 genome assembly by Govindarajan et al., 2021 (FBrf0248425), using a similar algorithm to the Quesneville publication, identified 319 insertions. All TE insertion annotations identified in the Release 4 and Release 5 assemblies have been re-mapped to the current Release 6 genome assembly where possible; see the FBrf0224938 analysis for a list of 18 TE insertions that could not be mapped to the Release 6 assembly. Only 26 annotated TE insertions were not identified in the four aforementioned publications (listed below):

1360{}680 (FBti0019922)

1360{}700 (FBti0019937)

Bari2{}1203 (FBti0020303)

Bari2{}506 (FBti0019843)

GATE{}721 (FBti0019951)

Rt1b{}599 (FBti0019889)

Rt1b{}601 (FBti0019890)

Stalker2{}660 (FBti0019915)

Stalker{}1135 (FBti0020246)

Stalker{}1141 (FBti0020252)

Xanthias{}6297 (FBti0131273)

X{}1173 (FBti0020284)