Article

Genome organization and characteristics of soybean microRNAs

BMC Genomics (Impact Factor: 3.99). 05/2012; 13(1):169. DOI: 10.1186/1471-2164-13-169
Source: PubMed

ABSTRACT

Background
microRNAs (miRNAs) are key regulators of gene expression and play important roles in many aspects of plant biology. The role(s) of miRNAs in nitrogen-fixing root nodules of leguminous plants such as soybean is not well understood. We examined a library of small RNAs from Bradyrhizobium japonicum-inoculated soybean roots and identified novel miRNAs. In order to enhance our understanding of miRNA evolution, diversification and function, we classified all known soybean miRNAs based on their phylogenetic conservation (conserved, legume- and soybean-specific miRNAs) and examined their genome organization, family characteristics and target diversity. We predicted targets of these miRNAs and experimentally validated several of them. We also examined organ-specific expression of selected miRNAs and their targets.

Results
We identified 120 previously unknown miRNA genes from soybean including 5 novel miRNA families. In the soybean genome, genes encoding miRNAs are primarily intergenic and a small percentage were intragenic or less than 1000 bp from a protein-coding gene, suggesting potential co-regulation between the miRNA and its parent gene. Difference in number and orientation of tandemly duplicated miRNA genes between orthologous genomic loci indicated continuous evolution and diversification. Conserved miRNA families are often larger in size and produce less diverse mature miRNAs than legume- and soybean-specific families. In addition, the majority of conserved and legume-specific miRNA families produce 21 nt long mature miRNAs with distinct nucleotide distribution and regulate a more conserved set of target mRNAs compared to soybean-specific families. A set of nodule-specific target mRNAs and their cognate regulatory miRNAs had inverse expression between root and nodule tissues suggesting that spatial restriction of target gene transcripts by miRNAs might govern nodule-specific gene expression in soybean.

Conclusions
Genome organization of soybean miRNAs suggests that they are actively evolving. Distinct family characteristics of soybean miRNAs suggest continuous diversification of function. Inverse organ-specific expression between selected miRNAs and their targets in the roots and nodules, suggested a potential role for these miRNAs in regulating nodule development.

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Available from: Senthil Subramanian
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    • "Since soybean (Glycine max) is one of the most economically important agricultural crops around the world, and one of the main global sources of protein and oil, both for food and for livestock feed, the interest in clarify the gene regulation network is crescent in this species. As miRNAs play important regulatory roles in a wide variety of developmental and metabolic processes in plants, they are being the focus of several researches in soybean (Zhang et al., 2008; Wang et al., 2009; Joshi et al. , 2010 ; Kulcheski et al. , 2011 ; Song et al., 2011 ; Turner et al. , 2012 ; Zeng et al., 2012 ; Fang et al., 2013 ; Wang et al. , 2013 ; Yan et al . , 2013 ; Yin et al . "
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    ABSTRACT: MicroRNAs (miRNAs) correspond to a class of endogenous small non-coding RNAs (19-24 nt) that regulates the gene expression, through mRNA target cleavage or translation inhibition. In plants, miRNAs have been shown to play pivotal roles in a wide variety of metabolic and biological processes like plant growth, development, and response to biotic and abiotic stress. Soybean is one of the most important crops worldwide, due to the production of oil and its high protein content. The reproductive phase is considered the most important for soybean yield, which is mainly intended to produce the grains. The identification of miRNAs is not yet saturated in soybean, and there are no studies linking them to the different floral organs. In this study, three different mature soybean floral whorls were used in the construction of sRNA libraries. The sequencing of petal, carpel and stamen libraries generated a total of 10,165,661 sequences. Subsequent analyses identified 200 miRNAs sequences, among which, 41 were novel miRNAs, 80 were conserved soybean miRNAs, 31 were new antisense conserved soybean miRNAs and 46 were soybean miRNAs isoforms. We also found a new miRNA conserved in other plant species, and finally one miRNA-sibling of a soybean conserved miRNA. Conserved and novel miRNAs were evaluated by RT-qPCR. We observed a differential expression across the three whorls for six miRNAs. Computational predicted targets for miRNAs analyzed by RT-qPCR were identified and present functions related to reproductive process in plants. In summary, the increased accumulation of specific and novel miRNAs in different whorls indicates that miRNAs are an important part of the regulatory network in soybean flower. Copyright © 2015. Published by Elsevier B.V.
    Full-text · Article · Sep 2015 · Gene
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    • "Expression levels of these miRNAs were quantified, and a subset of miRNAs was found to be differentially regulated during the early phases of nodulation (Subramanian et al., 2008). More recently, with the aid of the complete soybean genome sequence, reanalysis of these small RNA data resulted in the identification of 120 novel miRNAs (Turner et al., 2012). In a separate study of small RNAs from a variety of soybean tissues, including nitrogen-fixing nodules collected 7, 14 and 21 days after B. japonicium inoculation , 129 miRNAs, including 87 novel miRNA, were identified (Joshi et al., 2010). "
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    ABSTRACT: Three soybean [Glycine max (L) Merr.] small RNA libraries were generated and sequenced using the Illumina platform to examine the role of miRNAs during soybean nodulation. The small RNA libraries were derived from root hairs inoculated with Bradyrhizobium japonicum (In_RH) or mock-inoculated with water (Un_RH), as well as from the comparable inoculated stripped root samples (i.e. inoculated roots with the root hairs removed). Sequencing of these libraries identified a total of 114 miRNAs, including 22 novel miRNAs. A comparison of miRNA abundance among the 114 miRNAs identified 66 miRNAs that were differentially expressed between root hairs and stripped roots, and 48 miRNAs that were differentially regulated in infected root hairs in response to B. japonicum when compared to uninfected root hairs (P ≤ 0.05). A parallel analysis of RNA ends (PARE) library was constructed and sequenced to reveal a total of 405 soybean miRNA targets, with most predicted to encode transcription factors or proteins involved in protein modification, protein degradation and hormone pathways. The roles of gma-miR4416 and gma-miR2606b during nodulation were further analysed. Ectopic expression of these two miRNAs in soybean roots resulted in significant changes in nodule numbers. miRNA target information suggested that gma-miR2606b regulates a Mannosyloligosaccharide 1, 2-alpha-mannosidase gene, while gma-miR4416 regulates the expression of a rhizobium-induced peroxidase 1 (RIP1)-like peroxidase gene, GmRIP1, during nodulation.
    Full-text · Article · May 2015 · Plant Biotechnology Journal
    • "Expression levels of these miRNAs were quantified, and a subset of miRNAs was found to be differentially regulated during the early phases of nodulation (Subramanian et al., 2008). More recently, with the aid of the complete soybean genome sequence, reanalysis of these small RNA data resulted in the identification of 120 novel miRNAs (Turner et al., 2012). In a separate study of small RNAs from a variety of soybean tissues, including nitrogen-fixing nodules collected 7, 14 and 21 days after B. japonicium inoculation , 129 miRNAs, including 87 novel miRNA, were identified (Joshi et al., 2010). "
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