Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat

Abstract

Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In the last decade, it has been shown that satDNA is not an inert part of the genome and its function extends beyond the nuclear membrane. However, the number of model plant species suitable for studying the novel horizons of satDNA functionality is low. Here, we explored the satellitome of the model “basal” plant, Physcomitrellapatens (Hedwig, 1801) Bruch & Schimper, 1849 (moss), which has a number of advantages for deep functional and evolutionary research. Using a newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) coupled with fluorescence in situ hybridization (FISH), we identified five high copy number tandem repeats (TRs) occupying a long DNA array in the moss genome. The nuclear organization study revealed that two TRs had distinct locations in the moss genome, concentrating in the heterochromatin and knob-rDNA like chromatin bodies. Further genomic, epigenetic and transcriptomic analysis showed that one TR, named PpNATR76, was located in the intergenic spacer (IGS) region and transcribed into long non-coding RNAs (lncRNAs). Several specific features of PpNATR76 lncRNAs make them very similar with the recently discovered human lncRNAs, raising a number of questions for future studies. This work provides new resources for functional studies of satellitome in plants using the model organism P.patens, and describes a list of tandem repeats for further analysis.

Large vs small genomes inPassiflora: the influence of the mobilome and the satellitome

“…rDNA. There are several examples where satDNA originated from the IGS or rDNA coding genes (Garrido-Ramos 2015; Plohl 2012; Kirov et al 2018) for example, the satDNA jumper, in the Phaseolus genus, derives from the NTS of the 5S rDNA (Ribeiro et al 2017), showing that this phenomenon is quite common, even in plants in low proportions of satDNA and TEs increased genomes.…”

Unique Epigenetic Features of Ribosomal RNA Genes (rDNA) in Early Diverging Plants (Bryophytes)

“…This is in line with a comparative whole genomic methylation analysis of M. polymorpha that showed reduced 35S rDNA methylation compared with other repeats (Schmid et al, 2018). In P. patens , a contig carrying several rDNA copies seemed to be almost devoid of DNA methylation (Kirov et al, 2018). The authors suggested that the contig may derive from an active part of the array and that inactive condensed rDNA arrays may have different methylation patterns.…”

“…However, it is also possible that the rDNA chromatin condensation in bryophytes relies on other epigenetic mechanisms, such as noncoding RNAs. In this context, transcripts derived from IGS subrepeats were identified in P. patens (Kirov et al, 2018). In any case, it is likely that silencing and accurate nuclear position of rDNA may function without significant cytosine methylation of units in some bryophyte species at least.…”

“…Despite high copy numbers, the intragenomic diversity is low in coding regions, at least (Liu et al, 2013; Rosato et al, 2016), indicating efficient concerted evolution (Nieto Feliner and Rossello, 2012). Cytogenetic observations indicate that the number of 35S-5S rDNA loci is also low, typically 1–2 sites per haploid chromosomal set (Nakayama et al, 2001; Orzechowska et al, 2010; Garcia et al, 2012b; Kirov et al, 2018; Orzechowska et al, 2018, Goffová et al, 2019). The rDNA units are GC-rich (Orzechowska et al, 2018) and appear to be highly condensed in interphase (Rosato et al, 2016; Orzechowska et al, 2018).…”

“…The subtelomeric positions that frequently accumulated rDNA repeats (Garcia et al, 2017) were shown to be heavily methylated in Marchantia paleacea (Takio et al, 1999). Recently, a contig containing several rDNA units derived from the major P. patens rDNA locus was reported to be largely euchromatic without significant cytosine methylation and heterochromatic marks, suggesting that it derived from an active part of the array (Kirov et al, 2018). We aimed to fill a gap in our knowledge of bryophyte epigenetic landscape by focusing on methylation of their rDNA.…”