Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

Abstract

The wild strawberry (Fragaria vesca) has recently emerged as an excellent model for cultivated strawberry (Fragaria 3 ananassa) as well as other Rosaceae fruit crops due to its short seed-to-fruit cycle, diploidy, and sequenced genome. Deep sequencing and parallel analysis of RNA ends were used to identify F. vesca microRNAs (miRNAs) and their target genes, respectively. Thirtyeight novel and 31 known miRNAs were identified. Many known miRNAs targeted not only conserved mRNA targets but also developed new target genes in F. vesca. Significantly, two new clusters of miRNAs were found to collectively target 94 F-BOX (FBX) genes. One of the miRNAs in the new cluster is 22 nucleotides and triggers phased small interfering RNA production from six FBX genes, which amplifies the silencing to additional FBX genes. Comparative genomics revealed that the main novel miRNA cluster evolved from duplications of FBX genes. Finally, conserved trans-acting siRNA pathways were characterized and confirmed with distinct features. Our work identified novel miRNA-FBX networks in F. vesca and shed light on the evolution of miRNAs/phased small interfering RNA networks that regulate large gene families in higher plants.

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

“…In the Brassicaceae and Cleomaceae (both in the Rosids supergroup of eudictos), miR396 also targets Basic homologs (Debernardi et al, 2012), while in sunflower (Helianthus annus, in the asterid supergroup of eudicots) it has gained a WRKY transcription factor target (Giacomelli et al, 2012). Gains of lineage-specific targets have also been described for the ancient miR156, miR159, miR167, miR398, miR408, and miR482 families Buxdorf et al, 2010;Chorostecki et al, 2012;Brousse et al, 2014;Xia et al, 2015b). These lineage-specific targets frequently have complementarity patterns that include bulged nucleotides, rendering them undetectable by standard plant miRNA target identification software.…”

The evolution of microRNAs in plants

“…During evolution, only a key portion of the hairpin is retained to result in an MIR gene that encodes only one predominant small RNA species - the miRNA (Figure 2A). There are many examples showing sequence homology between MIR genes and target genes, thus supporting this model [26–29]. The original target inverted duplication hypothesis calls for neutral evolution of the sequences other than those of the mature miRNAs and miRNA stars in MIR genes [26].…”

PMS1T , producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

“…PhasiRNAs have been found in a wide range of organisms (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). In animal, a class of phasiRNAs known as Zucchini-dependent piwi-interacting RNAs were required for spermatogenesis (3,4).…”