High-throughput sequencing reveals the change of microRNA expression caused by allopolyploidization in Cucumis

Abstract

Allopolyploidy is long recognized as an essential driving force in plant evolution. Recent studies have demonstrated that small RNAs, including microRNAs (miRNAs), play important roles in the process of allopolyploidy. However, the question that how the distinct parent-of-origin miRNAs are maintained in allopolyploids and how these small RNAs affect gene expression and phenotype remain to be answered. Therefore, we investigated the miRNA expression profiles of a synthesized allotetraploid, Cucumis ×hytivus and its parents. The different developmental stages of leaves of C.×hytivus showing contrasting leaf colour were compared as well. Following high-throughput sequencing, 546 conserved d 287 novel miRNAs were identified. The expressions of nine miRNAs obtained by real-time quantitative PCR were consistent with the sequencing results. We detected that 15 miRNAs were divergently expressed between the parent species, and 23 miRNAs were differentially expressed in C. ×hytivus compared to either of its parents or both, which suggests the significant effect of allopolyploidization on miRNAs accumulation. Additionally, 26 conserved and 13 novel miRNAs differed in expression between the young and mature leaves of C. ×hytivus, indicating an essential role of miRNA-mediated regulation of leaf development following allopolyploidization. This study enriches the context of allopolyploidy effect on miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in phenotypic variation in allopolyploids.

Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis

“…C. hytivus has become one of the most important resources for introgression of needed traits from wild relatives into cucumber ( Cucumis hystrix Chakr., 2n = 2x = 24) [ 62 , 63 , 64 , 65 ]. Taking advantage of its small genome size and clear genetic background, the newly synthesized allotetraploid has been examined as a model for many studies of allopolyploidization, such as genomic changes [ 66 , 67 , 68 , 69 , 70 , 71 ], gene expression patterns [ 39 , 72 ], epigenetic modification [ 73 ], chromosomal behavior [ 67 , 74 ], and miRNA regulation [ 75 ]. Like miRNAs, long non-coding RNA (lncRNAs) are crucial “regulatory” ncRNAs in the post-transcriptional and transcriptional regulation in eukaryotes [ 76 ].…”