Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Aug 19:11:1274.
doi: 10.3389/fpls.2020.01274. eCollection 2020.

Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens

Pol Vendrell-Mir  1 , Mauricio López-Obando  2 , Fabien Nogué  3 , Josep M Casacuberta  1
Affiliations

Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium (Physcomitrella) patens

Pol Vendrell-Mir et al. Front Plant Sci. .

Abstract

Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. We have already shown that RLG1, the most abundant TE in P. patens, is expressed in non-stressed protonema tissue. Here we present a non-targeted analysis of the TE expression based on RNA-Seq data and confirmed by qRT-PCR analyses that shows that, at least four LTR-RTs (RLG1, RLG2, RLC4 and tRLC5) and one DNA transposon (PpTc2) are expressed in P. patens. These TEs are expressed during development or under stresses that P. patens frequently faces, such as dehydratation/rehydratation stresses, suggesting that TEs have ample possibilities to transpose during P. patens life cycle. Indeed, an analysis of the TE polymorphisms among four different P. patens accessions shows that different TE families have recently transposed in this species and have generated genetic variability that may have phenotypic consequences, as a fraction of the TE polymorphisms are within or close to genes. Among the transcribed and mobile TEs, tRLC5 is particularly interesting as it concentrates in a single position per chromosome that could coincide with the centromere, and its expression is specifically induced in young sporophyte, where meiosis takes place.

Keywords: Physcomitrium (Physcomitrella) patens; centromere; genetic variability; transcription; transposable element.

PubMed Disclaimer

Figures

Figure 1
Figure 1
TE content of the P. patens, rice, and melon genomes. Genome coverage of class 1 and class 2 TEs is shown as red and blue boxes respectively.
Figure 2
Figure 2
Phylogenetic analysis of the transposases potentially encoded by PpTc1 (A) and PpTc2 (B) with those potentially encoded by plant, fungal, animals and bacterial Mariner-like elements. P. patens sequences are shown in dark green, plant sequences in light green, fungal sequences in brown, animal sequences in blue and bacterial sequences in red.
Figure 3
Figure 3
Developmental expression of P. patens TEs. Normalized TE expression (see methods) in different developmental conditions selected from the P. patens Gene Atlas library (Perroud et al., 2018).
Figure 4
Figure 4
P. patens TE expression under stress conditions. Normalized TE expression (see methods) under different stress conditions selected from the P. patens Gene Atlas library (Perroud et al., 2018).
Figure 5
Figure 5
Relative age of expressed TEs. Kimura-2-parameter distance between the two LTRs of all elements (white bars) or of elements similar to the corresponding RNA assembly, and therefore potentially expressed (black bars) belonging to the RLG1 (A), RLG2 (B) and tRLC5 (C) families.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. 10.1016/S0022-2836(05)80360-2 - DOI - PubMed
    1. Anderson S. N., Stitzer M. C., Zhou P., Ross-Ibarra J., Hirsch C. D., Springer N. M. (2019). Dynamic patterns of transcript abundance of transposable element families in maize. G3 Genes Genomes Genet. 9, 3673–3682. 10.1534/g3.119.400431 - DOI - PMC - PubMed
    1. Bennetzen J. L., Park M. (2018). Distinguishing friends, foes, and freeloaders in giant genomes. Curr. Opin. Genet. Dev. 49, 49–55. 10.1016/j.gde.2018.02.013 - DOI - PubMed
    1. Blanc G., Agarkova I., Grimwood J., Kuo A., Brueggeman A., Dunigan D. D., et al. (2012). The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol. 13. 10.1186/gb-2012-13-5-r39 - DOI - PMC - PubMed
    1. Bowen N. J., McDonald J. F. (2001). Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 11, 1527–1540. 10.1101/gr.164201 - DOI - PMC - PubMed