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Science China Life Sciences

, Volume 61, Issue 2, pp 190–198 | Cite as

Conservation analysis of long non-coding RNAs in plants

  • Pingchuan Deng
  • Shu Liu
  • Xiaojun Nie
  • Song Weining
  • Liang Wu
Research Paper

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.

Keywords

lncRNA conservation monocots dicots rice 

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Notes

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).

Supplementary material

11427_2017_9174_MOESM1_ESM.jpg (96 kb)
Figure S1 Distribution of distance from lncRNAs to the nearest gene.
11427_2017_9174_MOESM2_ESM.jpg (116 kb)
Figure S2 Conservation of acceptor and donor splicing signals in plants.
11427_2017_9174_MOESM3_ESM.xlsx (22 kb)
Table S1 The detail information of lncRNA pairs showed orthologous relationship
11427_2017_9174_MOESM4_ESM.xlsx (32 kb)
Table S2 List of lncRNA pairs showed positional conservation
11427_2017_9174_MOESM5_ESM.xls (23 kb)
Table S3 Detailed list of lncRNAs correlated with the expression of adjacent protein-coding genes in rice
11427_2017_9174_MOESM6_ESM.xls (20 kb)
Table S4 List of high-abundance lncRNAs co-expressed with protein-coding genes in rice

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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Pingchuan Deng
    • 1
  • Shu Liu
    • 1
  • Xiaojun Nie
    • 2
  • Song Weining
    • 2
  • Liang Wu
    • 1
  1. 1.State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
  2. 2.State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingChina

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