Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat
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 t...
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doaj-7b57e60f2e4940b190820defccb584c52020-11-25T02:28:10ZengPensoft PublishersComparative Cytogenetics1993-07711993-078X2018-12-0112449351310.3897/CompCytogen.v12i4.3101531015Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeatIlya Kirov0Marina Gilyok1Andrey Knyazev2Igor Fesenko3Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryShemyakin and Ovchinnikov Institute of Bioorganic ChemistryShemyakin and Ovchinnikov Institute of Bioorganic ChemistryShemyakin and Ovchinnikov Institute of Bioorganic Chemistry 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, Physcomitrella patens (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. https://compcytogen.pensoft.net/article/31015/ |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ilya Kirov Marina Gilyok Andrey Knyazev Igor Fesenko |
spellingShingle |
Ilya Kirov Marina Gilyok Andrey Knyazev Igor Fesenko Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat Comparative Cytogenetics |
author_facet |
Ilya Kirov Marina Gilyok Andrey Knyazev Igor Fesenko |
author_sort |
Ilya Kirov |
title |
Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat |
title_short |
Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat |
title_full |
Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat |
title_fullStr |
Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat |
title_full_unstemmed |
Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat |
title_sort |
pilot satellitome analysis of the model plant, physcomitrella patens, revealed a transcribed and high-copy igs related tandem repeat |
publisher |
Pensoft Publishers |
series |
Comparative Cytogenetics |
issn |
1993-0771 1993-078X |
publishDate |
2018-12-01 |
description |
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, Physcomitrella patens (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.
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url |
https://compcytogen.pensoft.net/article/31015/ |
work_keys_str_mv |
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