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, 20 (1), 997

Tissue-specific Transposon-Associated Small RNAs in the Gymnosperm Tree, Norway Spruce

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Tissue-specific Transposon-Associated Small RNAs in the Gymnosperm Tree, Norway Spruce

Miyuki Nakamura et al. BMC Genomics.

Abstract

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.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Size distribution of sRNA in different organs, a sRNA size distribution of total read counts in needles and pollen samples after removing transfer RNA (tRNA)-, ribosomal RNA (rRNA)-, small nucleolar RNA (snoRNA)-, and small nuclear (snRNA) RNA-derived sequences. b sRNA size distribution of non-duplicated read counts after removing t/r/sn(o)RNA. c–f sRNA size distribution; (c) in genes, and (d) in TEs of Arabidopsis and P.abies vegetative tissues. (e) in genes, and (f) in TEs of Arabidopsis and P.abies pollen. At: Arabidopsis thaliana, Pa: Picea abies. Error bars indicate standard error of the mean
Fig. 2
Fig. 2
Differences in 24-nt producing loci between pollen and somatic embryonic callus, a Total sRNA size distribution of somatic embryonic callus treated at different temperatures. b Non-redundant sRNA size distribution in the same samples. c–d sRNA size distribution in each genomic features; c in genes and d in TEs. Error bars indicate standard error of the mean. e Correlation of 24-nt sRNA counts associated with TE sequences between samples. Each dot indicates a different TE subfamily. r indicates correlation coefficiency. f Proportions of sRNA derived from each genomic feature producing putative phased RNAs. SEC: somatic embryonic callus
Fig. 3
Fig. 3
TE-derived 21-nt and 24-nt sRNAs correlate, a–b Correlation between 21-nt and 24-nt sRNA mapped to each TE subfamily in pollen (a) and in somatic embryonic callus at 22 °C (b). TE families that had a limited number of sRNAs were omitted. c sRNA colored by size at sRNA clustered regions in pollen. d Read density of 21-nt and 24-nt sRNA are shown as histograms at representative loci

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