Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/22/2012
Publication Date: 10/2/2012
Citation: Zabala, G., Campos, E., Varala, K.K., Bloomfield, S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M., Vodkin, L.O. 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. Biomed Central (BMC) Plant Biology. 12:177. Interpretive Summary: When an organism needs to do something, it most often needs to make protein to carry out the task. Proteins are synthesized off of RNA, and RNA molecules are therefore regulated so that an organism only has the RNA presence in a cell that is needed by that cell. Our understanding of how the quantity of RNA is regulated is still not completely known. Within the last decade, a major means of RNA regulation has been identified that uses short RNA sequences to target RNA molecules for degradation, therefore ensuring that synthesis of the protein that is derived off of that RNA is stopped. This study presents a thorough search to identify and characterize small RNA molecules in soybean. The work shows very clearly that small RNA sequences can vary greatly depending on the tissue or organ. This work will be of interest to molecular plant biologists and breeders.
Technical Abstract: Background: Small non-coding RNAs (smRNAs) are known to have major roles in gene regulation in eukaryotes. In plants, knowledge of the biogenesis and mechanisms of action of smRNA classes including microRNAs (miRNAs), short interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs) has been gained mostly through studies with Arabidopsis. In recent years, high throughput sequencing of smRNA populations has enabled extension of knowledge from model systems to plants with larger, more complex genomes. Soybean (Glycine max) now has many genomics resources available including a complete genome sequence and predicted gene models. Relatively little is known, however, about the full complement of its endogenous smRNAs populations and their potentially silenced target genes. Results: Using Illumina sequencing and computational analysis, we characterized eight smRNA populations from multiple tissues and organs of soybean including developing seed and vegetative tissues. A total of 41 million raw sequence reads collapsed into 135,055 unique reads that were mapped to the soybean genome and its predicted cDNA gene models. Bioinformatic analyses were used to distinguish miRNAs and siRNAs and to determine their genomic origins and potentially silenced target genes. In addition, we identified two soybean TAS3 gene homologs, the miRNAs that putatively guide cleavage of their transcripts, and the derived tasiRNAs that target soybean genes annotated as auxin response factors. Tissue-differential expression based on the flux of normalized miRNA and siRNA abundances in the eight smRNA libraries was evident, some of which was confirmed by smRNA blotting. Our global view of these smRNA populations also revealed that the size classes of smRNAs varied amongst different tissues, with the developing seed and seed coat having greater numbers of unique smRNAs of the 24-nt class compared to the vegetative tissues of germinating seedlings. The 24-nt class is known to be derived from repetitive elements including transposons. Detailed analysis of the size classes associated with ribosomal RNAs and transposable element families showed greater diversity of smRNAs in the 22- and 24-nt size classes. Conclusions: The flux of endogenous smRNAs within multiple stages and tissues of seed development was contrasted with vegetative tissues of soybean, one of the dominant sources of protein and oil in world markets. The smRNAs varied in size class, complexity of origins, and possible targets. Sequencing revealed tissue-preferential expression for certain smRNAs and expression differences among closely related miRNA family members.