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

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Title Identification and co-evolution pattern of stem cell regulator miR394s and their targets among diverse plant species
 
Creator Kumar, Ashutosh
Gautam, Vibhav
Kumar, Pramod
Mukherjee, Shalini
Verma, Swati
Sarkar, Ananda K.
 
Subject miR394
LCR
Small RNA
Phylogenetic analysis
miRNA evolution
 
Description Accepted date: 5 February 2019
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.
AK, SM, and SV thank the Department of Science and Technology - Science
and Engineering Research Board (DST-SERB) for National-Post Doctoral Fellowship (N-PDF). VG and PK thank the Council for Scientific and Industrial Research (CSIR), India and National Institute of Plant Genome Research (NIPGR),
New Delhi, India for funding and grants. AKS thanks NIPGR for core grants. This study was funded by Science and Engineering Research Board (SERB),
Department of Science and Technology (DST), Govt. of India, for National-Post
Doctoral Fellowship (NPDF) to AKS (NPDF/2015/000232).
 
Date 2019-02-19T06:19:35Z
2019-02-19T06:19:35Z
2019
 
Type Article
 
Identifier BMC Evolutionary Biology, 19(1): 55
1471-2148
http://223.31.159.10:8080/jspui/handle/123456789/920
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1382-7
https://doi.org/10.1186/s12862-019-1382-7
 
Language en_US
 
Format application/pdf
 
Publisher BioMed Central Ltd