Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca

Abstract

Conifers’ exceptionally large genome (20–30 Gb) is scattered with 60% retrotransposon (RT) components and we have little knowledge on their origin and evolutionary implications. RTs may impede the expression of flanking genes and provide sources of the formation of novel small RNA (sRNAs) populations to constrain events of transposon (TE) proliferation/transposition. Here we show a declining expression of 24-nt-long sRNAs and low expression levels of their key processing gene, pgRTL2 (RNASE THREE LIKE 2) at seed set in Picea glauca. The sRNAs in 24-nt size class are significantly less enriched in type and read number than 21-nt sRNAs and have not been documented in other species. The architecture of MIR loci generating highly expressed 24-/21-nt sRNAs is featured by long terminal repeat—retrotransposons (LTR-RTs) in families of Ty3/Gypsy and Ty1/Copia elements. This implies that the production of sRNAs may be predominantly originated from TE fragments on chromosomes. Furthermore, a large proportion of highly expressed 24-nt sRNAs does not have predictable targets against unique genes in Picea, suggestive of their potential pathway in DNA methylation modifications on, for instance, TEs. Additionally, the classification of computationally predicted sRNAs suggests that 24-nt sRNA targets may bear particular functions in metabolic processes while 21-nt sRNAs target genes involved in many different biological processes. This study, therefore, directs our attention to a possible extrapolation that lacking of 24-nt sRNAs at the late conifer seed developmental phase may result in less constraints in TE activities, thus contributing to the massive expansion of genome size.

Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories

“…The other aspect aims to investigate whether MIRNA s originate from TEs and undergo evolution coupled in time with genome evolution between species within spermatophyte and how the environment contributes to adaptive variation at molecular levels (e.g., epigenetic imprinting, genetic variants, etc.). This conception is emanated from our results concerning MIRNA s for abundant sRNAs in Arabidopsis (i.e., conserved miRNAs) containing more DNA repeat modules than those for enriched ones in P. glauca (Figure S8 ; also see Liu and El-Kassaby, 2017b ). This may be linked to their giga-genome evolution, in the sense that genetic divergence is suppressed in conifers, thus leading to few WGDs.…”

Identification of microRNAs involved in lipid biosynthesis and seed size in developing sea buckthorn seeds using high-throughput sequencing

“…3c,d ). The 20–22 nts plant sRNA mediate target gene cleavage or inhibition of protein translation, while the 24 nt sRNA class affects chromatin modelling of target genes 38 .…”

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

“…Since all land plants and green algae possess the small RNA-generating RNAi machinery ( You et al, 2017 ), it is conceivable that gymnosperms, ferns and club mosses can potentially accumulate siRNAs derived from endogenous caulimovirids and/or their extant not-yet-identified episomal counterparts. Likewise, genomes of all land plants contain long terminal repeat (LTR) retrotransposons of the families Metaviridae (Ty3/Gypsy) and Pseudoviridae (Ty1/Copia) which can give rise to siRNAs as has been reported for the angiosperms A. thaliana ( Creasey et al, 2014 ; Masuta et al, 2017 ), strawberry ( Šurbanovski et al, 2016 ), mangrove ( Wang Y. et al, 2018 ), maize ( Alejandri-Ramírez et al, 2018 ) and wheat ( Sun et al, 2013 ); transposon-derived small RNAs were also reported for gymnosperms such as Picea glauca ( Liu and El-Kassaby, 2017 ) and Cryptomeria japonica ( Ujino-Ihara et al, 2018 ).…”