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Results: 5

1.
Figure 1

Figure 1. From: Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.

Maximum likelihood analysis ofA. vaga Penelopenucleotide sequences. Branch support is indicated at the nodes. Penelope insertions localized in collinear allelic pairs are shaded. Intact copies are boxed. Brackets designated N1-N4 denote the presence of different N-rich inserts in each group of elements, as described in the text. Scale bar, nucleotide substitutions per site.

Irina R Arkhipova, et al. Mob DNA. 2013;4:19-19.
2.
Figure 5

Figure 5. From: Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.

Phylogenetic relationships of EN-containing and EN-deficient PLEs. Clade markers are as follows: Perere in flatworms and A. vaga, magenta diamonds; Penelope/Poseidon, cyan triangles; Neptune, blue circles; Nematis, gray triangles; EN-deficient Athena, green squares; EN-deficient protist and fungal PLEs, brown squares. Most taxon designations are from datasets in [10,20]; Bman, Brachionus manjavacas; Bcal, Brachionus calyciflorus; EN, endonuclease; PLEs, Penelope-like elements. Branch support values over 60% are shown. Scale bar, amino acid substitutions per site.

Irina R Arkhipova, et al. Mob DNA. 2013;4:19-19.
3.
Figure 4

Figure 4. From: Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.

Penelope-mediated mobilization of an intron-containing NRPS gene. Shown are the two scaffolds which constitute an allelic pair containing glucose-6-phosphate isomerase (G6PI) and RXR-like retinoic acid receptor (RXR) coding sequences. Scaffold 385 harbors a NRPS insertion flanked by Pen3a pLTRs (see Figure 2i) and by an 8-bp target site duplication (GAATTAAT), which is present only once on scaffold 561. Introns are denoted by V-shaped lines; other features are as in Figure 2. Scale bar, 1 kb.

Irina R Arkhipova, et al. Mob DNA. 2013;4:19-19.
4.
Figure 2

Figure 2. From: Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.

Structural features of selectedA. vaga Peneloperetrotransposons. ORFs are represented by colored boxes with arrows. RT, reverse transcriptase; EN, endonuclease. Thin arrows denote pLTRs, and small colored rectangles - its optional short extension (“tail”). Panels (a-i) correspond to different families. Thicker arrows represent repeats derived from sequences other than pLTRs. N1 to N3 denote different N-rich inserts within ORFs, shown by darker colors. Palindromes are shown by double lines; frameshifts or stop codons, by vertical lines; deletions, by dashed lines; gaps, by dotted lines. Numbers above small yellow boxes indicate the length of target site duplications in bp. Scale bar, 1 kb.

Irina R Arkhipova, et al. Mob DNA. 2013;4:19-19.
5.
Figure 3

Figure 3. From: Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families.

Transcription and RNA-mediated silencing ofA. vaga Penelopefamilies. (a) RNA-seq counts per family. Numbers on the Y axis represent RNA-seq counts per kb, and the moderately transcribed A. vaga Dicer-like genes [14] are used for comparison. Transcripts originating from the N2-related segment on scaffold 412 (see text) could not be accommodated using the same scale. (b-e) Small RNA coverage plots along selected full-length Penelope copies shown in Figure 2. X axis, element length in bp; Y axis, small RNA counts per window of indicated size; red, sense reads; blue, antisense reads. (f) Coverage plot for scaffold 412; Pen3A pLTR is in the opposite orientation to the transcribed N2-related segment.

Irina R Arkhipova, et al. Mob DNA. 2013;4:19-19.

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