Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s

Abstract

BackgroundmicroRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood.ResultsWe identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity.ConclusionThis study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or under abiotic stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-0983-9) contains supplementary material, which is available to authorized users.

The Polycistronic miR166k-166h Positively Regulates Rice Immunity via Post-transcriptional Control of EIN2

“…These observations support conservation of the miR166k-166h polycistron in the Oryza genus ( Baldrich et al, 2016 ). miR166 clusters have been identified in the genome of several plant species (e.g., M. truncatula , soybean and Physcomitrella patens ) but, in most cases, the polycistronic nature of these miR166 clusters has not been demonstrated ( Boualem et al, 2008 ; Zhang et al, 2009 ; Barik et al, 2014 ; Li et al, 2017 ).…”

“…In line with this, miR166b has been reported to target rice RDD1 ( rice Dof daily fluctuations 1 ), a non- HD-ZIP III transcription factor involved in nutrient uptake and accumulation ( Iwamoto and Tagiri, 2016 ). Very recently, miR166-guided cleavage of ATHB14-LIKE transcripts encoding a homeobox-leucine zipper protein has been described in soybean ( Li et al, 2017 ). In M. truncatula , a miR166 polycistron containing two copies of miR166a targeting HD-ZIP III transcripts was found to control root architecture and nodule development after infection by Sinorhizobium meliloti ( Boualem et al, 2008 ).…”

Comparative analysis of miRNA expression profiles in transgenic and non-transgenic rice using miRNA-Seq

“…Among these miRNAs, some have been shown to play roles in plant stress resistance and seed development. The miR166 target ATHB14-LIKE transcript was experimentally validated by RACE PCR 36 . The expression patterns of the miR166s and 12 target genes were examined during seed development and in response to abiotic stresses.…”

Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

“…Expression of a miR160resistant version of ARF17 in plants causes dramatic developmental defects, and overexpression of miR160 results in fewer starch granules and disorganized root tips [52,53]. Analysis of the conservation and diversification of the miR166 family in plants showed that miR166 members play a wide and important regulatory role in seed development [54]. Therefore, these data suggest that these miRNAs have multiple regulatory functions in grain filling.…”