The evolution of microRNAs in plants

Cui, Jie; You, Chenjiang; Chen, Xuemei

doi:10.1016/j.pbi.2016.11.006

Cited by 124 publications

(90 citation statements)

References 49 publications

(57 reference statements)

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“…One strand of the duplex is associated with a member of the Argonaute (AGO) family. The resulting miRNA-AGO complex is the miRNA-induced silencing complex, which interacts with the complementary site of target mRNA transcript, thereby repressing the expression of the target transcripts at the post-transcriptional level [2]. …”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

et al. 2017

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BackgroundmicroRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sites) can alter miRNA targets in animal and human. Whether these single nucleotide polymorphisms (SNPs) in plant are functional have not yet been determined.ResultsIn this study, we constructed leaf, root, and stem-derived small libraries of cucumber (Cucumis sativus) line 9930 (cultivated China-group cucumber) and C. sativus var. hardwickii (wild India group cucumber). A total of 22 conserved miRNA families, nine less-conserved miRNA families, and 49 cucumber-specific miRNAs were identified in both line 9930 and hardwickii. We employed cucumber resequencing data to perform a genome-wide scan for SNPs in cucumber miRNA-target interaction sites, including miRNA mature sequences and miRNA-target binding sites. As a result, we identified a total of 19 SNPs in mature miRNA sequences and 113 SNPs in miRNA-target binding sites with the potential to affect miRNA-target interactions. Furthermore, we experimentally confirmed that these SNPs produced 14 9930-unique targets mRNAs and 15 hardwickii-unique targets mRNA for cucumber miRNAs. This is the first experimental validation of SNPs in miRNA-target interaction sites affecting miRNA-target binding in plants.ConclusionsOur results indicate that SNPs can alter miRNA function and produce unique miRNA targets in cultivated and wild cucumbers. Therefore, miRNA-related SNPs may have played important in events that led to the agronomic differences between domestic and wild cucumber.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3665-y) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

et al. 2017

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“…As proposed in a number of organisms 2, 20, 32, 47, 52 , low level transcription of inverted repeats or mutationally engendered hairpin structures could give rise to a diversity of RNAs recognized as substrates by the sRNA biogenesis machinery. However, most young miRNAs would likely be neutral 32, 47, 48, 52 , either by not being expressed at a high enough level or by not having enough sequence identity to regulate any meaningful target.…”

Section: Discussionmentioning

confidence: 99%

miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation

Voshall

Kim

et al. 2017

Sci Rep

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The unicellular alga Chlamydomonas reinhardtii contains many types of small RNAs (sRNAs) but the biological role(s) of bona fide microRNAs (miRNAs) remains unclear. To address their possible function(s) in responses to nutrient availability, we examined miRNA expression in cells cultured under different trophic conditions (mixotrophic in the presence of acetate or photoautotrophic in the presence or absence of nitrogen). We also reanalyzed miRNA expression data in Chlamydomonas subject to sulfur or phosphate deprivation. Several miRNAs were differentially expressed under the various trophic conditions. However, in transcriptome analyses, the majority of their predicted targets did not show expected changes in transcript abundance, suggesting that they are not subject to miRNA-mediated RNA degradation. Mutant strains, defective in sRNAs or in ARGONAUTE3 (a key component of sRNA-mediated gene silencing), did not display major phenotypic defects when grown under multiple nutritional regimes. Additionally, Chlamydomonas miRNAs were not conserved, even in algae of the closely related Volvocaceae family, and many showed features resembling those of recently evolved, species-specific miRNAs in the genus Arabidopsis. Our results suggest that, in C. reinhardtii, miRNAs might be subject to relatively fast evolution and have only a minor, largely modulatory role in gene regulation under diverse trophic states.

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“…The 3' adapter was trimmed using perfect string matching on the first 7 nucleotides of the adapter (TGGAATT); the HD signatures, 4 assigned nucleotides at the 3' and 5' end of the insert (10, 16) were also trimmed. Next, the files were converted from redundant to non-redundant format (17,18) and the results were summarized into redundant and nonredundant size class distributions.…”

Section: Smallrnasmentioning

confidence: 99%

“…The abundances of the reads were normalized using the reads per total method (22)(23)(24). The replicate to replicate differential expression was called on offset fold change, offset = 20 (empirically determined) (18,25) calculated on the proximal ends of maximal confidence intervals built on the available replicates. The differential expression on loci (regions on the genome) was conducted using a simplified form of CoLIde (26) applicable on 2 samples, with 2 replicates each.…”

Section: Smallrnasmentioning

confidence: 99%

Evolution of flower color pattern through selection on regulatory small RNAs

Bradley

Mohorianu

et al. 2017

Science

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One Sentence Summary:Selection acting on an inverted duplication that generates small RNAs leads to evolution of regulatory interactions and phenotypic change. LENGTH Main Text:A convenient system for studying selection in natural populations is afforded by hybrid zones, where closely-related species or populations come into contact (1). Such a hybrid zone has been described for two subspecies of Antirrhinum majus (snapdragon), that 4 differ in flower color (2), a trait involved in pollinator attraction (3-7). Both subspecies are pollinated by bees but have alternate patterns for guiding flower entry:A.m.pseudomajus flowers are magenta, with a patch of yellow highlighting the bee entry point (Fig. 1A), whereas A.m.striatum flowers are yellow with magenta veins at the entry point (Fig. 1B). The magenta and yellow flower color intensities show sharp clines at a hybrid zone (2) where the subspecies come into contact. Production of magenta is regulated by ROSEA (ROS) and ELUTA (EL) (8-10). ROS encodes a MYB-like transcription factor that promotes anthocyanin biosynthetic gene expression in A.m.pseudomajus and exhibits a steep cline in allele frequencies at the hybrid zone (2, 9).Distribution of yellow pigment is regulated by SULF (Fig. 1B, C), which represses production of the yellow flavonoid aurone in A.m.pseudomajus ( Fig. 1D) (2, 9, 10). Here we study the molecular nature of SULF.To isolate SULF we first mapped it to an interval of ~3Mb on chromosome 4 by sequencing pools of sulf and SULF phenotypes from a segregating population ( fig. S1).In parallel, we carried out a transposon mutagenesis experiment in A. majus (SULF) and isolated a mutant, sulf-660, that was both somatically and genetically unstable ( fig. S2A and Methods). Comparing the genome sequence of sulf-660 and its revertants revealed a single insertion site, within the mapped region of SULF, specific to sulf-660. Three independent revertants had different excision footprints at this site, confirming that the transposon was responsible for the sulf phenotype ( fig. S2B). 5BLAST searches of the sequence flanking the transposon insertion site revealed regions of 74-88% nucleotide sequence identity to A.majus chalcone 4'-O-gluosyltransferase (Am4'CGT), which encodes an enzyme involved in synthesis of the yellow pigment aurone ( Fig. 2A and table S1) (11). The regions of Am4'CGT homology were organized as an inverted duplication in the A. majus SULF genome. Both the left and right arms of the duplication carried deletions relative to intact Am4'CGT, suggesting they had independently degenerated from a more complete precursor. A contiguous region of inverted homology between the left and right arms spanned a ~590 bp region (red arrows, Fig. 2A), separated by a ~600 bp spacer region, which contained the transposon insertion site of sulf-660. Phylogenetic analysis indicated that the SULF inverted repeats were likely generated from Am4'CGT recently in the evolution of the Antirrhinum lineage ( Fig. 2B and fig. S3).To determine whether the inverted duplicatio...

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The evolution of microRNAs in plants

Cited by 124 publications

References 49 publications

Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation

Evolution of flower color pattern through selection on regulatory small RNAs

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