Abstract
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3′ and 5′ ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.
Highlights
Circular RNAs are a novel type of endogenous noncoding RNAs characterized by the presence of a covalent bond linking the 3′and 5′ ends[1]
After rRNA deleption and RNase R treatment, the remaining RNAs were used for library constructions, and sequencing of the libraries were performed with an Illumina Hiseq 2500 analyzer
The circRNAs identified in soybean was less than that in Oryza sativa (12,037) and Arabidopsis thaliana (6,012)[22]
Summary
Circular RNAs (circRNAs) are a novel type of endogenous noncoding RNAs characterized by the presence of a covalent bond linking the 3′and 5′ ends[1]. The different isoforms of circRNAs were results of alternative back-spliced circularization, and circRNA-host genes with alternative circularization preferentially contained more exons than those genes with non-alternative circularization in soybean (Supplementary Fig. S3). To explore whether circRNAs were conserved in different plant species, we further compared the circRNAs derived from the orthologous genes of Arabidopsis thaliana, Oryza sativa and soybean.
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