Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Abstract

Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.

Longer Duration of Active Oil Biosynthesis during Seed Development Is Crucial for High Oil Yield—Lessons from Genome-Wide In Silico Mining and RNA-Seq Validation in Sesame

“…SAD desaturates stearoyl-ACP (18:0) to form oleic acid (18:1), and FAD2 catalyzes synthesis of linoleic acid (18:2) from oleic acid (18:1) [ 24 ]. The expression pattern of SAD and FAD2 corresponds with oleic acid (18:1) and linoleic acid (18:2) at the early and middle stages of developing seeds of sesame [ 126 ]. The oleosins have been linked to lipids’ biosynthesis/metabolism and the size of seed oil bodies [ 127 , 128 ].…”

Comprehensive analysis of sesame LRR-RLKs: structure, evolution and dynamic expression profiles under Macrophomina phaseolina stress

“…For in silico expression analysis of sesame seed development, RNA-seq data of variety S. indicum var. ‘Wanzhi No.2’ during seed development comprising 7 days after flowering (7 DAF, S1), 14 DAF (S2), 21 DAF (S3) and full maturity (28 DAF, S4) were used (PRJNA739094) ( Zhang et al., 2021 ). For in silico expression analysis, the RNA-seq data of the disease-resistant variety S. indicum var.…”

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

“…Zhang et al [ 77 ] identified 351 known miRNAs and 91 novel miRNAs from 18 sesame libraries, and 116 miRNAs were found to be involved in the salt-stress response through the comparison between the salt-treated group and the control group. Subsequently, Zhang et al [ 92 ] sequenced a total of 220 miRNAs in seed development and constructed a regulatory co-expression network through transcriptomics, small RNAs and degradome. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were observed for regulating the accumulation of unsaturated fatty acid biosynthesis.…”

“…In terms of organ development, seeds, leaves, carpels, roots, fertile and sterile buds are introduced [ 41 , 55 , 86 , 87 , 88 , 89 , 90 ]. It also introduces several non-coding RNAs, such as tRNAs, rRNAs, miRNAs, lncRNAs [ 77 , 91 , 92 , 93 ].…”