A role for MIR828 in pineapple fruit development

Abstract

Chen et al. ( Nature Genet. 51: 1549-1558; Oct. 2019) sequenced Ananas comosus var. bracteatus accession CB5, cultivated for its bright pink-to-red colored fruit, and yellow-fleshed A. comosus accession F153, reporting an improved F153 reference assembly while annotating MICRORNA (MIRNA) loci and gene family expressions relevant to lignin and anthocyanin biosynthesis. An independent article (Xiong et al.Sci. Rep. 8: 1947; 2018) reported var. bracteatus MIRNAs but not MIR828, a negative regulator of anthocyanin and polyphenolics biosynthesis by targeting MYB transcription factors associated with UV light- and sugar-signaling in dicots. MIR828 has been reported in gymnosperms, Amborella (sister to flowering plants), and basal monocot orders Liliales, Asparagales, Zingiberales, Arecales, but not in the Poales, a sister order comprising grasses and ~3,000 species of bromeliads including pineapple. Here I show MIR828 exists in pineapple and directs post-transcriptional gene silencing of mRNAs encoding MYB family members with inferred function to regulate the conspicuous red fruit trait in var. bracteatus. MIR828 plesiomorphy (an ancient basal trait) may shed light on monocot apomorphic fruit development, postulated for 21 monocot families with fleshy fruits as due to homoplasy/convergence driven by tropical climate and/or enticements to vertebrate endozoic seed dispersers.

Keywords: RNA interference; anthocyanins; evolution; fruit development; microRNAs.

Figure 1.. Pseudo-degradome (from sRNA libraries) T plots of 5’ ends of sRNA alignments show post-transcriptional gene silencing of miR828 MYB targets in MD-2 leaf sRNA libraries .

Concatenated sRNA libraries were used as pseudo-degradome on grounds sliced mRNAs subject to production of amplified diced dsRNAs are manifest in sRNA libraries ^{, ,} . Slicing is at nt10 from 5' end of miR828 (arrow, inset; same target sequence for Aco020986.1 at mRNA nt 115). Y axis is numbers of reads in sRNA libraries mapped to cDNAs; red dot is the documented miR828 sliced sRNA species that sets the register for 3’ phasiRNA production.

Figure 2.. Evidence for relatively different expressions of pri-MIR828 and target MYB Aco017254.1, Aco020986.1 mRNAs in yellow-fleshed F153 (A, B) versus (C) red-fleshed CB5 reproductive tissues .

A) Inverse relationship of pri-MIR828 (high; see Extended data: Table S1, rows 23–36) to target MYB Aco017254.1 (low Extended data: Table S2, rows 406–470) anthocyanin effector expressions in F153 ovules. Error bars are s.e.m., n=3 biological replicates. B) Down regulation of miR828-targeted MYB anthocyanin effectors during MD2 yellow-fleshed fruit development (n=1 per stage Extended data: Table S2, rows 134–405)). Asterisk (*) denotes stage 1 significantly different across Aco017254.1 and Aco020986.1 than stages 2-8, p = 0.02 (Student’s two-sided paired t-test, equal variance assumed). Stage 1 error bars show the 95% confidence interval for significance. C) Apparent maintenance of positive anthocyanin effector MYB Aco017254.1 expression at “ripe” two-month stage of CB5 red-fleshed fruit development, concordant with trend of lower pri-MIR828 expression (see Extended data: Table S1, rows 37–52; Table S2, rows 471–883). Error bars are s.e.m., n=5 biological replicates.