Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization

Abstract

Angelica sinensis is a “low-temperature and long-day” perennial plant that produces bioactive compounds such as phthalides, organic acids, and polysaccharides for various types of clinical agents, including those with cardio-cerebrovascular, hepatoprotective, and immunomodulatory effects. To date, the regulatory mechanism of flowering under the photoperiod has been revealed, while the regulatory network of flowering genes during vernalization, especially in the role of lncRNAs, has yet to be identified. Here, lncRNAs associated with flowering were identified based on the full-length transcriptomic analysis of A. sinensis at vernalization and freezing temperatures, and the coexpressed mRNAs of lncRNAs were validated by qRT-PCR. We obtained a total of 2327 lncRNAs after assessing the protein-coding potential of coexpressed mRNAs, with 607 lncRNAs aligned against the TAIR database of model plant Arabidopsis, 345 lncRNAs identified, and 272 lncRNAs characterized on the SwissProt database. Based on the biological functions of coexpressed mRNAs, the 272 lncRNAs were divided into six categories: (1) chromatin, DNA/RNA and protein modification; (2) flowering; (3) stress response; (4) metabolism; (5) bio-signaling; and (6) energy and transport. The differential expression levels of representatively coexpressed mRNAs were almost consistent with the flowering of A. sinensis. It can be concluded that the flowering of A. sinensis is positively or negatively regulated by lncRNAs, which provides new insights into the regulation mechanism of the flowering of A. sinensis.

Full-Length Transcriptome and the Identification of lncRNAs Involved in Salicylic Acid-Induced Flowering in Duckweed (Lemna gibba)

“…In this study, a total of 474 lncRNAs were systematically identified in L. gibba during SA-induced flowering. The lncRNA number was approximately 1.5-fold greater than that identified in L. sativa [48] but was less than that reported in A. sinensis, P. sibirica, and chickpea [17,18,20]. To some extent, these findings demonstrate impact of the species, sequenced depth, and used criteria on the identification of lncRNAs.…”

“…The lncRNAs also showed co-expression with genes relevant to photosynthesis, tetrapyrrole synthesis, jasmonate metabolism, signaling, and transport (Figure 2B), indicating similar roles of lncRNAs in L. gibba during SA-induced flowering. LncRNAs have been evidenced to play comparable roles in the flowering of other species: in A. sinensis, Liu et al [18] found the co-expression of lncRNAs with genes related to carbohydrate metabolism, biosignaling, energy, and transport during vernalization; in P. sibirica, Xu et al [20] revealed that lncRNAs participated in secondary metabolism, hormone signaling, and starch and sucrose metabolism during flowering; in L. sativa and chickpea, lncRNAs were reported to participate in flowering based on their co-expression with protein-coding genes related to photoperiodism, transport, and hormone signaling [17,48]. Most importantly, fifteen lncRNAs were co-expressed with flowering-related genes (including LHY, CCA1a, PI, and SVP) (Figure 4), providing us with excellent hints to further characterize the function of lncRNAs by examining their interactions [4,10].…”

“…In chickpea, 1414 lncRNAs were identified by RNA-seq profiling, and 37 could bind to flowering-related genes to maintain inflorescence development [17]. In Angelica sinensis, 2327 lncRNAs were identified during vernalization, and 36 were characterized as participants in flowering [18]. In Chinese cabbage, 3382 lncRNAs were identified in response to plumule vernalization, and a few of them were involved in promoting flowering [19].…”

The Dynamic Accumulation Rules of Chemical Components during the Medicine Formation Period of Angelica sinensis and Chemometric Classifying Analysis for Different Bolting Times Using ATR-FTIR

“…In addition, autumn bolting (AB) will also happen in the cultivation process in September. Transcriptomics and metabolomics have been employed to investigate the regulatory mechanisms underlying bolting, as well as the reduction in the accumulation of bioactive metabolites and the identification of genes involved in the biosynthesis of ferulic acid, flavonoids, and lignin in A. sinensis, which are associated with the shikimic acid and phenylpropanoid pathways [18][19][20][21]. The AB root is often mistaken for the AS root due to its similar morphological characteristics.…”