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. 2018 Jan 25;9:26. doi: 10.3389/fpls.2018.00026

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Copyright © 2018 Ji, Zhao, Gao, Cao, Mao, Zhou, Fan, Borkovich, Ouyang and Liu.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Prediction of slmiRNA targets and protein domain analysis. (A) Predicted mRNA target sequences and targeting site. Targets of slmiR482 family members were identified using the psRNATarget algorithm (http://plantgrn.noble.org/v1_psRNATarget/). Alignments were made using ClustalW (http://www.ebi.ac.uk/Tools/psa/). The nucleotides shown in red in the mRNA are mismatches with the corresponding miRNA. (B) Prediction of translated protein domains. Domain prediction was performed using Interpro (http://www.ebi.ac.uk/interpro/). CC: Coiled-Coil domain. The miRNA binding site is indicated with a red arrow in the P-loop region. (C) Phylogenetic analysis of Solyc12g099060 and I2 homologs. The Maximum Likelihood method based on the JTT matrix-based model. PAM was used for an amino acid transition matrix. OsGAPDH was used as a root by midpoint method. Evolutionary analyses were conducted in MEGA7. The sequences were including gi| 4689222 (I2), gi| 2258314 (I2C-1), gi| 2258316 (I2C-2), gi| 2258318 (I2C-3), gi| 2318004 (I2C-4), gi| 15553677 (I2C-5), Solyc08g075630, Solyc08g076000, Solyc09g018220, Solyc05g008650, Solyc12g099060 (FRG3) and OsGAPDH.