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Background  Micro RNAs (miRNAs), a class of small non-coding RNAs, have been implicated in various aspects of plant development. miR394 is required for shoot apical meristem organization, stem cell maintenance and abiotic stress responses in  Arabidopsis,  where it functions by negatively regulating the transcript level of target  LEAF CURLING RESPONSIVENESS  ( LCR ), which is an  F-box  protein-coding gene. The evolutionary conservation of stem cell regulatory miR394- LCR  module among plants remains elusive.    Results  Our study has identified 79 miR394 and 43 target sequences across 40 plant species using various homology based search tools and databases, and analysed their co-evolution pattern. We customised an annotation workflow which computationally validates 20 novel miR394s from 14 plant species. Independent phylogenetic trees were reconstructed with precursor  MIR394s , mature miR394s, and their target sequences along with complementary miR394 binding sites. The phylogeny revealed that mature sequences of miR394s as well as their targets belonging to the  F-box  protein encoding gene families, were highly conserved. Though, miR394–3p were complementary to miR394s/miR394–5p, they clustered separately.    Conclusion  The existence and separate clustering of miR394–3p and miR394s/miR394–5p indicate their independent regulation. The phylogeny also suggests that miR394s had evolved at the beginning of gymnosperm-angiosperm divergence. Despite strong conservation, some level of sequence variation in miR394s and the complementary binding sites of their targets suggests possible functional diversification of miR394- LCR  mediated stem cell regulation in plants.    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1382-7) contains supplementary material, which is available to authorized users.

Identification and co-evolution pattern of stem cell regulator miR394s and their targets among diverse plant species