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.
Highlights
MicroRNA166 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
Identification of novel miR166s in soybean To identify novel miR166s in soybean, pre-miR165/166 sequences from soybean, Arabidopsis and rice were used as queries to conduct BLAST search against the soybean genomic database
The matched genomic sequences were analyzed following a series of screening criteria for encoding miRNA sequence, and five novel pre-miR166s were identified in soybean
Summary
MicroRNA166 (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. MicroRNA166 (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. The evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. MiRNAs range from 20 to 24 nt in length and regulate the expression of target genes mainly at post-transcriptional levels [1]. A MIR gene is transcribed by Polymerase II into a capped and polyadenylated primary miRNA (pri-miRNA) [5, 6]. DCL protein carries out the cleavage of pri-miRNA into the stemloop precursor (pre-miRNA), which is further processed by DCL1 to generate mature miRNA and miRNA*. Mature miRNA is loaded into an Argonaute protein to form the miRNA-induced silencing complex (miRISC)
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