Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

BMC Genomics. 2019 Dec 19;20(1):997. doi: 10.1186/s12864-019-6385-7.


Background: Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms.

Results: Here, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture.

Conclusion: Our data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.

Keywords: Gymnosperm; Male gametophyte; Norway spruce; Small RNA; Transposable elements.

MeSH terms

  • Genetic Loci
  • Interspersed Repetitive Sequences*
  • Picea / embryology
  • Picea / genetics*
  • Picea / metabolism
  • Pollen / genetics
  • Pollen / metabolism
  • RNA, Plant / metabolism*
  • RNA, Plant / physiology
  • RNA, Small Untranslated / metabolism*
  • RNA, Small Untranslated / physiology


  • RNA, Plant
  • RNA, Small Untranslated