RNA-Seq and Iso-Seq Reveal the Important Role of COMT and CCoAOMT Genes in Accumulation of Scopoletin in Noni (Morinda citrifolia)

Abstract

Scopoletin, the main component of clinical drugs and the functional component of health products, is highly abundant in noni fruit (Morinda citrifolia). Multiple enzyme genes regulate scopoletin accumulation. In the present study, differentially expressed genes of noni were analyzed by RNA sequencing (RNA-Seq) and the full-length genes by isoform-sequencing (Iso-Seq) to find the critical genes in the scopoletin accumulation mechanism pathway. A total of 32,682 full-length nonchimeric reads (FLNC) were obtained, out of which 16,620 non-redundant transcripts were validated. Based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation and differential expression analysis, two differentially expressed genes, caffeic acid 3-O-methyltransferase (COMT) and caffeoyl-CoA O-methyltransferase (CCoAOMT), were found in the scopoletin accumulation pathway of noni. Real-time quantitative polymerase chain reaction (q-PCR), phylogenetic tree analysis, gene expression analysis, and the change in scopoletin content confirmed that these two proteins are important in this pathway. Based on these results, the current study supposed that COMT and CCoAOMT play a significant role in the accumulation of scopoletin in noni fruit, and COMT (gene number: gene 7446, gene 8422, and gene 6794) and CCoAOMT (gene number: gene 12,084) were more significant. These results provide the importance of COMT and CCoAOMT and a basis for further understanding the accumulation mechanism of scopoletin in noni.

Using Isoform Sequencing for De Novo Transcriptome Sequencing and the Identification of Genes Related to Drought Tolerance and Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb.)

“…Next-generation sequencing has generated short, incomplete transcriptome assemblies and provided limited genomic information for this species [26][27][28][29][30]. Recently, isoform sequencing (Iso-Seq) technology developed by Pacific Biosciences has been used to analyze full-length transcriptomes in multiple plant species, such as Triticum aestivum, Morinda citrifolia, Salvia miltiorrhiza, Zea mays, Panax ginseng, and Astragalus membranaceus [31][32][33][34][35][36][37]. Unlike other methods, Iso-Seq produces full-length transcripts without assembly and is a much better system for genome annotation, the identification of novel genes and isoforms, the discovery of long non-coding RNA (lncRNA) sequences, and the detection of alternative splicing (AS) events.…”

Deciphering the roles of unknown/uncharacterized genes in plant development and stress responses

“…U/U genes are always identified by RNA-seq, but their assembled sequences are not always accurate. Therefore, transcriptome sequencing techniques such as Iso-seq that yield full-length reference sequences are recommended in studies examining U/U function (Yuan et al, 2015;Yuan et al, 2016;Jia et al, 2022). Iso-seq can directly obtain complete transcripts without disrupting splicing, in order to accurately analyze structural information such as variable splicing and fusion genes of reference genome species.…”

“…Iso-seq can directly obtain complete transcripts without disrupting splicing, in order to accurately analyze structural information such as variable splicing and fusion genes of reference genome species. This technology can also promote the optimization of genome annotation and quantification of transcriptome abundance, providing opportunities for the discovery of new genes (Rhoads and Au, 2015;Li et al, 2017;Beiki et al, 2019;Jia et al, 2022).…”

Enhanced Bioactivity of Botanical Acaricidal Compound-Scopoletin Encapsulated by Polydopamine and Cellulose Nanocrystals Against Carmine Spider Mite

“…12 Therefore, mite population control represents a great challenge. 13 Scopoletin (7-hydroxy-6-methoxychromen-2-one, abbreviated as Sco), an important coumarin phytoalexin, has been found in numerous herbaceous plants, including Nicotiana tabacum, 9 Morinda citrifolia, 14,15 Argyreia speciosa, 16 and Arabidopsis thaliana. 17 It exhibits various pharmacological bioactivities, such as anticholinesterasic, 18 anti-inflammatory, and antitumorigenesis effects.…”