TEs along a region of the genome:
We reconstruct the history of TEs nesting into each other. For example, the blue TE on the left inserted first, and then was disrupted by the insertion of green and yellow TEs.
We have reconstructed this history of transposition, using methods described in Jiao et al., 2017, Anderson et al., 2019, and Stitzer et al., 2021.
The linked files provide updated TIR, soloLTR, and LINE searches, which better identify matched target site duplications (TSDs) and terminal inverted repeats (where applicable).
We suggest using a version of the annotation that fits your needs, either the full-length TE or disjoined TE versions.
The full-length TE gff3 version is useful for counting the number of TEs in the genome, or for assessing the presence/absence of a copy based on split read and read pair approaches. Each bar here is represented as a separate gff3 line.
B73: B73.structuralTEv2.fulllength.gff3.gz
W22: W22.structuralTEv2.fulllength.gff3.gz
PH207: PH207.structuralTEv2.fulllength.gff3.gz
Mo17: Mo17.structuralTEv2.fulllength.gff3.gz
The disjoined TE gff3 version is useful for mapping reads and assigning each to a TE. Each base pair in the genome is assigned to only one TE copy, that which brought the sequence into the genome. Fragments of individual copies can be reunited by their shared TE identifier (see below).
B73: B73.structuralTEv2.disjoined.gff3.gz
W22: W22.structuralTEv2.disjoined.gff3.gz
PH207: PH207.structuralTEv2.disjoined.gff3.gz
Mo17: Mo17.structuralTEv2.disjoined.gff3.gz
DTA00001Zm00001d00001
DTA : Superfamily, codes from Wicker et al., 2007
00001: Family number (For TIR elements, these match numbers assigned in MTEC of v1 of the maize genome, see Legacy Annotations below)
DTA00001: Together, these then define the family name
Zm00001d: Assembly version code for the reference genome, as assigned by the Maize Genetics Nomenclature Committee, see Complete table here
00001: Copy ID number, unique to this copy in the genome. For disjoined copies, each line in the gff3 file contains this ID
Complementary Annotations
Anderson et al., 2019 further filters these annotations, and identifies shared and non-shared TE copies across B73, W22, Mo17, and PH207.
Annotations are available here, for example, a non-redundant TE set that identifies copies shared and non-shared with B73:
non-redundant_TEs_4genomes_1Feb19.txt.gz.
Legacy Annotations
Original TE annotations from the publications of B73 (Jiao et al., 2017) and W22 (Springer et al., 2018) can be found here:
B73: B73v4.TE.filtered.gff3.gz
W22: W22.allTE.withSolo_10Jan18.gff3.gz
Consensus and exemplar TEs from the Maize TE Consortium (MTEC) as published in Schnable et al., 2009 and Baucom et al., 2009, previously available at maizetedb.org (link broken as of September 2018) are available here: