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Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons

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Soybean cotyledons have evolved as a sink organ to synthesize and deposit the storage protein and oil reserve over seed maturation. MicroRNAs represent a class of key components in gene regulatory networks underlying diverse biological processes. However, our understanding of the microRNAs in soybean cotyledon over seed maturation remains limited. In the study, we generated 292 million small RNA reads by sequencing 18 small RNA libraries from soybean cotyledon at six different stages of maturation. 129 novel cotyledon microRNAs and 93 novel miRNA families were identified. A total of 1193 cotyledon miRNA family-target transcript interaction were predicted. The targeted genes encode proteins with diverse biological functions, but preferentially encode proteins in pathways related to RNA metabolism, RNA transcription and protein degradation. Twenty-six of the transcripts are likely to be targeted by multiple miRNAs. Cotyledon miRNAs are preferentially transcribed in a coordinate orientation with their overlapping mRNA transcripts. Unlike the other plant miRNAs, a high percentage of soybean cotyledon miRNAs are intronic. Some of them are located in introns that are subjected to alternative splicing. The miRNA loci in duplicated genome segments from the recent Glycine whole genome replication have much higher loss/gain rate than the protein coding genes. The conserved miRNAs have lower loss/gain rate than non-conserved miRNAs.
Wolfgang Goettel , Zongrang Liu , Jing Xia , Weixiong Zhang , Patrick X. Zhao , Yong-Qiang An
Glycine max , RNA libraries , alternative splicing , cotyledons , loci , messenger RNA , metabolism , microRNA , protein degradation , proteins , regulator genes , seed maturation , soybeans
Plos One 2014 1 27 v.9 no.1
Journal Articles, USDA Authors, Peer-Reviewed
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