Abstract
Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100 Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.
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Claims 13
Claim · model-written summary
A novel DNA transposon was discovered in the genome of Selaginella lepidophylla.
- Taxon
- Selaginella lepidophylla
Selaginella lepidophyllae1 - Outcome
- novel DNA transposone1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
Claim · model-written summary
The GingerRoot element appears restricted to bryophytes and lycophytes among plants.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e2“this element appears restricted to Bryophytes and Lycophytes in plants”
Claim · model-written summary
The GingerRoot transposon has a 6 bp target site duplication.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- target site duplicatione3
- Value
- 6 bpe3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e3“This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats”
Claim · model-written summary
The GingerRoot transposon has 100-150 bp terminal inverted repeats.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- terminal inverted repeatse3
- Value
- 100-150 bpe3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e3“This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats”
Claim · model-written summary
The transposase of GingerRoot has a DDE motif similar to the integrase of Gypsy-like long terminal repeat retrotransposons.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- the DDE motife4
- Comparator
- the integrase of Gypsy-like long terminal repeat retrotransposonse4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e4“Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons”
Claim · model-written summary
A total of 77 intact and several hundred truncated copies of GingerRoot were identified in S. lepidophylla.
- Taxon
- S. lepidophyllaSelaginella lepidophyllae5
- Outcome
- copies of GingerRoot elementse5
- Value
- 77 intact and several hundred truncatede5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla”
Claim · model-written summary
GingerRoot elements show a lack of insertion preference near genes.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- insertion preference near genese6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e6“Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes”
Claim · model-written summary
A considerable portion of GingerRoot elements carry gene fragments.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- carry gene fragmentse7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e7“a considerable portion of GingerRoot elements was found to carry gene fragments”
Claim · model-written summary
Elements carrying gene fragments are less methylated than those without gene fragments.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- methylatede2
- Direction
- less methylatede2
- Comparator
- those without gene fragmentse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e2“Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments”
Claim · model-written summary
Elements carrying gene fragments are more diverged than those without gene fragments.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- divergede2
- Direction
- more divergede2
- Comparator
- those without gene fragmentse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e2“Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments”
Claim · model-written summary
Elements carrying gene fragments are more distal to genes than those without gene fragments.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- distal to genese2
- Direction
- more distale2
- Comparator
- those without gene fragmentse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e2“Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments”
Claim · model-written summary
GingerRoot is the first plant DNA transposon with an integrase-related transposase.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- the first plant DNA transposon with an integrase-related transposasee2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e2“This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase”
Claim · model-written summary
De novo formation of Gypsy-like elements in plants is possible, as suggested by GingerRoot.
- Taxon
- Selaginella lepidophyllaSelaginella lepidophyllae1
- Outcome
- de novo formation of Gypsy-like elementse2
- Qualifier
- possibilitye2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla”
e2“suggesting the possibility of de novo formation of Gypsy-like elements in plants”