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Int. J. Mol. Sci. 2016, 17(12), 2043; doi:10.3390/ijms17122043

Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages

1
School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
2
School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
3
Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
4
Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China
The authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Marcello Iriti
Received: 28 October 2016 / Revised: 24 November 2016 / Accepted: 29 November 2016 / Published: 6 December 2016
(This article belongs to the Special Issue Pulses)
View Full-Text   |   Download PDF [2049 KB, uploaded 6 December 2016]   |  

Abstract

Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions. Based on a sliding window analysis workflow that we developed, 50 PHAS loci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41 PHAS loci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistant TIR-NB-LRR genes constitute a very large family of PHAS loci. PhasiRNAs were also generated from several loci that encode for NAC transcription factors, Dicer-like 2 (DCL2), Pentatricopeptide Repeat (PPR), and Auxin Signaling F-box 3 (AFB3) proteins. To investigate the possible involvement of miRNAs in initiating the PHAS-phasiRNA pathway, miRNA target predictions were performed and 17 C08 miRNAs and 15 W05 miRNAs were predicted to trigger phasiRNAs biogenesis. In summary, we provide a comprehensive description of the sRNA profiles of wild versus cultivated soybeans, and discuss the possible roles of sRNAs during soybean germination. View Full-Text
Keywords: miRNA; phasiRNA; Glycine max; Glycine soja; sliding window analysis; PHAS loci; PHAS-phasiRNA pathway miRNA; phasiRNA; Glycine max; Glycine soja; sliding window analysis; PHAS loci; PHAS-phasiRNA pathway
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Sun, Y.; Mui, Z.; Liu, X.; Yim, A.K.-Y.; Qin, H.; Wong, F.-L.; Chan, T.-F.; Yiu, S.-M.; Lam, H.-M.; Lim, B.L. Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages. Int. J. Mol. Sci. 2016, 17, 2043.

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