Whole-Genome Doubling Affects Pre-miRNA Expression in Plants.

Salvatore Esposito,Pasquale Tripodi,Riccardo Aversano,Domenico Carputo

doi:10.3390/plants10051004

Abstract

Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.

Highlights

Polyploidy is the term used to denote the presence of more than two complete chromosome sets in somatic cells, tissues, or individuals
Since small RNAseq data on 2x vs. 4x were not available in the literature, we used a total of 600M already available RNAseq reads belonging to 2x and synthetic 4x genotypes of A. thaliana L., I. indigotica Fort., B. rapa L., S. commersonii Dun., and M. alba L
Exploiting the comparative data generated, we attempted to bridge the gap of knowl7 of 14 edge between whole-genome doubling (WGD) and transcriptomic and metabolomic changes experienced by synthetic Solanum autotetraploids [32]

Summary

Introduction

Polyploidy is the term used to denote the presence of more than two complete chromosome sets in somatic cells, tissues, or individuals. It is quite rare in animals, whereas it is widespread in angiosperms [1]. Polyploid plants are traditionally distinguished as autopolyploids and allopolyploids. The former designate individuals formed from within one species by the doubling of structurally similar, homologous chromosome complements; the latter combine genomes from more than one species via hybridization and the subsequent doubling of differentiated, nonhomologous (homoeologous) chromosomes. Many aspects of the advantages of being polyploid have been elucidated over the last decades, the significance of whole-genome doubling (WGD)

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Conclusion