Open Access
Plants, volume 9, issue 12, pages 1794
Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development
Kirov Ilya
1, 2
,
Dudnikov Maxim
1, 2
,
Merkulov Pavel
1
,
Shingaliev Andrey
1
,
Omarov Murad
1, 3
,
Kolganova Elizaveta
1
,
Sigaeva Alexandra
1
,
Soloviev Alexander
1
2
Publication type: Journal Article
Publication date: 2020-12-17
PubMed ID:
33348863
Plant Science
Ecology, Evolution, Behavior and Systematics
Ecology
Abstract
The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered “junk”, DNA as they are frequently associated with repeat-rich regions of the genome. The latter makes the annotations of these loci and the assembly of the corresponding transcripts using short RNAseq reads particularly challenging. Here, using long-read Nanopore direct RNA sequencing, we aimed to identify these “junk” RNA molecules, including long non-coding RNAs (lncRNAs) and transposon-derived transcripts expressed during early stages (10 days post anthesis) of seed development of triticale (AABBRR, 2n = 6x = 42), an interspecific hybrid between wheat and rye. Altogether, we found 796 lncRNAs and 20 LTR retrotransposon-related transcripts (RTE-RNAs) expressed at this stage, with most of them being previously unannotated and located in the intergenic as well as intronic regions. Sequence analysis of the lncRNAs provide evidence for the frequent exonization of Class I (retrotransposons) and class II (DNA transposons) transposon sequences and suggest direct influence of “junk” DNA on the structure and origin of lncRNAs. We show that the expression patterns of lncRNAs and RTE-related transcripts have high stage specificity. In turn, almost half of the lncRNAs located in Genomes A and B have the highest expression levels at 10–30 days post anthesis in wheat. Detailed analysis of the protein-coding potential of the RTE-RNAs showed that 75% of them carry open reading frames (ORFs) for a diverse set of GAG proteins, the main component of virus-like particles of LTR retrotransposons. We further experimentally demonstrated that some RTE-RNAs originate from autonomous LTR retrotransposons with ongoing transposition activity during early stages of triticale seed development. Overall, our results provide a framework for further exploration of the newly discovered lncRNAs and RTE-RNAs in functional and genome-wide association studies in triticale and wheat. Our study also demonstrates that Nanopore direct RNA sequencing is an indispensable tool for the elucidation of lncRNA and retrotransposon transcripts.
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1
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Kirov I. et al. Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development // Plants. 2020. Vol. 9. No. 12. p. 1794.
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Kirov I., Dudnikov M., Merkulov P., Shingaliev A., Omarov M., Kolganova E., Sigaeva A., Karlov G. I., Soloviev A. Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development // Plants. 2020. Vol. 9. No. 12. p. 1794.
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TY - JOUR
DO - 10.3390/plants9121794
UR - https://doi.org/10.3390%2Fplants9121794
TI - Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development
T2 - Plants
AU - Dudnikov, Maxim
AU - Shingaliev, Andrey
AU - Omarov, Murad
AU - Kolganova, Elizaveta
AU - Soloviev, Alexander
AU - Kirov, Ilya
AU - Merkulov, Pavel
AU - Sigaeva, Alexandra
AU - Karlov, Gennady I.
PY - 2020
DA - 2020/12/17 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 1794
IS - 12
VL - 9
PMID - 33348863
SN - 2223-7747
ER -
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@article{2020_Kirov,
author = {Maxim Dudnikov and Andrey Shingaliev and Murad Omarov and Elizaveta Kolganova and Alexander Soloviev and Ilya Kirov and Pavel Merkulov and Alexandra Sigaeva and Gennady I. Karlov},
title = {Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development},
journal = {Plants},
year = {2020},
volume = {9},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {dec},
url = {https://doi.org/10.3390%2Fplants9121794},
number = {12},
pages = {1794},
doi = {10.3390/plants9121794}
}
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MLA
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Kirov, Ilya, et al. “Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development.” Plants, vol. 9, no. 12, Dec. 2020, p. 1794. https://doi.org/10.3390%2Fplants9121794.
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