title: Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages.
abstract: Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; fromPHASloci), 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, 50PHASloci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41PHASloci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistantTIR-NB-LRRgenes constitute a very large family ofPHASloci. 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 thePHAS-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.
authors.affiliation: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. yzsun@hku.hk.
authors.forename: Yuzhe
authors.initials: Y
authors.lastname: Sun
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. zeta.mui@gmail.com.|Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. zeta.mui@gmail.com.
authors.forename: Zeta
authors.initials: Z
authors.lastname: Mui
authors.affiliation: Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China. liuxuan@connect.hku.hk.
authors.forename: Xuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. aldrinlaurent@gmail.com.|Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. aldrinlaurent@gmail.com.
authors.forename: Aldrin Kay-Yuen
authors.initials: AK
authors.lastname: Yim
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. qinhao13@gmail.com.
authors.forename: Hao
authors.initials: H
authors.lastname: Qin
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. wongfl@gmail.com.|Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. wongfl@gmail.com.
authors.forename: Fuk-Ling
authors.initials: FL
authors.lastname: Wong
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. tf.chan@cuhk.edu.hk.|Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. tf.chan@cuhk.edu.hk.
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
authors.affiliation: Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong, China. smyiu@cs.hku.hk.
authors.forename: Siu-Ming
authors.initials: SM
authors.lastname: Yiu
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. honming@cuhk.edu.hk.|Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. honming@cuhk.edu.hk.
authors.forename: Hon-Ming
authors.initials: HM
authors.lastname: Lam
authors.affiliation: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. bllim@hku.hk.|Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. bllim@hku.hk.
authors.forename: Boon Leong
authors.initials: BL
authors.lastname: Lim
mesh_terms: D007887:Fabaceae / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering; D013025:Glycine max / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: Glycine max; Glycine soja; PHAS loci; PHAS-phasiRNA pathway; miRNA; phasiRNA; sliding window analysis