Abstract
Long non-coding RNAs (lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position. Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants.
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Acknowledgements
This work was supported by Zhejiang Provincial Natural Science Foundation of China (LR16C060001), the National Key Program on Transgenic Research and the Fundamental Research Funds for the Central Universities (2016QNA6014).
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Figure S1
Distribution of distance from lncRNAs to the nearest gene.
Figure S2
Conservation of acceptor and donor splicing signals in plants.
Table S1
The detail information of lncRNA pairs showed orthologous relationship
Table S2
List of lncRNA pairs showed positional conservation
Table S3
Detailed list of lncRNAs correlated with the expression of adjacent protein-coding genes in rice
Table S4
List of high-abundance lncRNAs co-expressed with protein-coding genes in rice
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Deng, P., Liu, S., Nie, X. et al. Conservation analysis of long non-coding RNAs in plants. Sci. China Life Sci. 61, 190–198 (2018). https://doi.org/10.1007/s11427-017-9174-9
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DOI: https://doi.org/10.1007/s11427-017-9174-9