Phylogenetic Analysis and Molecular Evolution Patterns in the MIR482-MIR1448 Polycistron of Populus L

Abstract

The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the “duplicated MIR482” evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the “frameshift targeted mechanism” to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

The poplar pangenome provides insights into the evolutionary history of the genus

“…Large differences in the mapping rate (lowest: 59.34%, highest: 81.04%) were observed among the 10 sequenced species, where the species in the section Leuce had the lowest mapping rate followed by the species of the section Turanga, and the species of the other three sections had the highest mapping rates (Supplementary Table 2). Studies based on morphological traits and molecular phylogenetic analyses showed that species in the sections Turanga and Leuce were older than those in the sections Tacamahaca, Aigeiros, and Leucoides in Populus relative to a species from section Tacamahaca 1,2,5,6 . Therefore, the distinct mapping rate of the 10 species was most likely caused by the genetic divergence of each species from the reference.…”

“…Of the five original sections, species in the sections Tacamahaca, Aigeiros, and Leucoides are thought to be modern poplars, whereas species in the sections Turanga and Leuce are thought to be older 1,2,5,6 . However, the oldest species remain disputed; some researchers have suggested that species in the section Leuce are the oldest 2,5 , whereas others have shown species in the section Turanga to be the oldest 1,6 . Synonymous substitutions (Ks) are neutral mutations that can be used to estimate the time since divergence of two species 44 .…”

Identification of MicroRNAs in Response to Different Day Lengths in Soybean Using High-Throughput Sequencing and qRT-PCR

“…Few reports of species-specific, non-conserved microRNAs of soybean exist, except for miR5371 and miR5368 (involved in abiotic and biotic stresses) [ 28 ] and miR4412 and miR4998 (involved in the shoot apical meristem of soybean) [ 31 ]. In addition, the results of the present study revealed conserved miRNAs detected in other plants, such as miR166 (regulating shoot apical meristem and floral development in Arabidopsis) [ 63 , 64 ], miR482 (in resistance to disease or abiotic stress via NBS-LRR proteins) [ 65 ], miR319 (affecting organ development and the processes of phase change in Arabidopsis) [ 46 ], miR160 (responses to the plant hormone auxin) [ 66 ], miR167 (involved in the floral organ formation) [ 27 ], miR390 (influence not only vegetative developmental transitions but also organ polarity in flowering plants) [ 67 , 68 ], miR395 (regulating sulfate accumulation and allocation) [ 69 ], and miR408 (influenced through a variety of environmental conditions) [ 70 , 71 ]. These molecules have not been previously reported, but confirmed to respond to the day length changes in the present study.…”

Analysis of phytoplasma-responsive sRNAs provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease

“…MicroRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are two main categories of small regulatory RNAs which globally regulate plant immunity by inhibiting target gene expression at transcriptional or post-transcriptional level9. Increasing evidence indicated that miRNAs serve as one important mechanism for mediating gene expression in plant-microorganism interactions1011121314. As for the phytoplasma-responsive miRNAs, only one study has explored in Mexican lime ( Citrus aurantifolia L.) infected by ‘ Candidatus Phytoplasma aurantifolia ’15.…”