- However, there have been no related studies on the number of circRNAs and their overall characteristics including circRNA abundance and expression profiles in peanut, which is one of the most important edible oil seed crops in the world.. - Conclusions: We present the first systematical investigation of the genomic characteristics and expression profiles of circRNAs in peanut. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.. - functions of circRNAs are still largely unknown, their relative abundance, evolutionary conservation, and the fact that they are derived from important gene loci, means that circRNAs are the products of regulated back-splicing rather than by-products of splicing errors.. - Although the pervasiveness of circRNAs has been con- firmed in plants, little is known about the circularization and the biological functions of plant circRNAs at present.. - Different from the biogenesis of circRNAs in animals, the flanking sequences of plant circRNAs do not seem to be enriched for repetitive elements or reverse complementary sequences [5, 6]. - The present study represents the first transcriptome-wide circRNAs identification in peanut, and the results not only prove the existence of circRNA, but also provide clues about the potential function of circRNAs in peanut.. - Seeds of two peanut lines, ‘RIL 8106’ and ‘RIL 8107’, were bred and sown in the field at Henan Agricultural University, Zhengzhou, China. - ipaensis, obtained from the peanut database (https://www.peanutbase.org/) using TopHat (v2.1.0).. - The number of reads spanning the back-splicing junc- tion was used to quantify the expression of circRNAs.. - The circRNA host genes were mapped to terms in the GO database to determine their functions.. - Differential expression analysis of circRNAs was conducted using a two-tailed Student’s t-test and the SPSS Statistics v19.0 software package (IBM, NY, USA). - Validation of circRNAs. - Identification of circRNAs in peanut. - In total candidate back-spliced junction reads were identified in the four samples.. - The number of circRNAs produced from their cor- responding linear mRNAs showed that some parent genes produced more than one circRNA (347 cir- cRNAs from 305 host genes), although most genes (90%, 273 out of 305) produced only one circRNA (Fig. - The largest group consisted of circRNAs that contained two exons, accounting for 30% (103 out of 347), followed by a group con- taining three exons (23%, 78 out of 347). - families in the peanut transcriptome, similar to the two model plants O. - Expression profiles of circRNAs in peanut. - All of the circRNAs identified in the four samples were analyzed together (Fig. - The numbers of circRNAs detected specifically in the four lines were not equally compared, including 38 in C1, and 17 in C2, 10 in T1 and 39 in T2. - The relative expression of circRNAs at 35 DAF was down-regulated compared with 15 DAF (Fig. - We next analyzed the differentially-expressed cir- cRNAs in the different group comparisons (|log 2 fold- change. - We detected and one specific circRNAs that were differentially expressed in the T2 vs. - Among the circRNAs that were differentially expressed in comparisons of 15 DAF and 35 DAF seeds in the same line, we found that more circRNAs were down-regulated than up-regulated (77 down-reg- ulated and 22 up-regulated in T1 vs. - T1, respectively) in the large-seeded. - 1 Identification and characteristics of circRNAs in peanut. - a Genomic origin of circRNAs described in this study. - b Number of circRNAs produced from the corresponding parent gene (347 circRNAs from 305 parent genes). - c The number of circRNAs and back-spliced reads in four samples. - d Distribution of circRNAs on 20 chromosomes. - f The length distribution of circRNAs. - Structural formation of circRNAs in peanut. - 2 Expression profiles of circRNAs in peanut. - a Venn chart of circRNAs detected in each sample. - b Violin plot of relative abundance of circRNAs in four samples. - 3 Visualization of circRNAs generated from the same parent gene in peanut. - The supported unique reads were presented in the parentheses followed the circRNA. - In order to shed light on the potential function of circRNAs in seed development, we performed GO enrichment analyses of the host genes that produced. - To further uncover the possible regulatory functions of circRNAs, we focused on the top GO terms in- volved in seed development, and then screened out the circRNAs that were differentially-expressed be- tween 15 DAF and 35 DAF in the same line (T1 vs. - GO enrichment analysis of the T1 vs. - GO terms in the T2 vs. - We then used GO enrichment analysis to investigate whether circRNAs might regulate seed size in the two peanut lines at 15 and 35 DAF (C2 vs. - The top 20 most significant GO terms in the T2 vs. - c Clustered heat map of 23 parent genes generating 29 circRNAs up-regulated in the T2 vs. - A clustered heatmap of the set of enriched circRNAs revealed that those classified in the same GO terms showed similar expression patterns (Fig. - We found 29 circRNAs that were up-regulated in the T2 vs. - The back-splicing junctions present in the six circRNAs were further validated by Sanger DNA sequencing (Fig. - The results of this experiment indicate that circRNAs identified in the RNA-seq datasets are reliable.. - In this study, we identified 347 circRNAs in the transcriptome of peanut seeds using two algorithms. - Even in the same species, the number of circRNAs identified by different research groups showed obvious difference, for example, Ye et al. - 5 Validation of circRNAs by qRT-PCR and Sanger sequencing. - characterized the expression profiles of circRNAs and speculated their possible functions in regulating gene expression. - The expres- sion patterns of circRNAs derived from the same linear mRNA were diverse between the two peanut lines and in comparisons of two developmental stages. - All of these results suggested the complicated expression of circRNAs in peanut.. - So the role of circRNAs and their associated molecules in gene regula- tion, such as miRNAs or proteins, needs to be established by further experimental identification and characterization in peanut.. - Our study provides the first study of circRNAs generated from two peanut lines with different seed sizes at two developmental stages. - We characterized the genomic structures and expression profiles of circRNAs to gain insight into the features of circRNAs. - Number of circRNAs derived from the same hosting gene. - The amount of circRNA604 was normalized to the value measured in the mock treatment. - https://doi.org/10.1096/fasebj . - https://doi.org/10.1371/. - https://doi.org/10.1038/nature11928.. - https://doi.org/10.1371/journal.pone.0090859.. - https://doi.org/1 0.1261/rna . - https://doi.org/10.1111/nph.13585.. - doi.org/10.1371/journal.pgen.1003777.. - https://doi.org/10.1261/rna . - https://doi.org/10.1016/j.. - 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