Identifying Terpenoid Biosynthesis Genes in Euphorbia maculata via Full-Length cDNA Sequencing

Diosgenin biosynthesis investigation in medicinal herb (Tribulus terrestris) by transcriptome analysis

Next-generation sequencing (NGS) has revolutionized the analysis of specific genes, pathways, and their regulation in various species. Tribulus terrestris L., an annual medicinal herb of Zygophyllaceae family, has gained significant attention due to its diverse medicinal properties, including anti-inflammatory, antimicrobial, and anti-cancer effects. Diosgenin, a steroidal saponin, is the major bioactive compound responsible for the medicinal importance of T. terrestris. However, there is a paucity of information regarding the genes involved in the diosgenin biosynthetic pathway in T. terrestris. To address this gap, this study aimed to identify candidate genes associated with diosgenin biosynthesis through whole transcriptome profiling. A total of ∼7.9 GB of data, comprising 482 million reads, was obtained and assembled into 148,871 unigenes. Subsequently, functional annotations were assigned to 50 % of the unigenes using sequence similarity searches against the NCBI non-redundant (NR), Uniprot, KEGG, Pfam, GO, and COG databases, primarily based on Gene Ontology and KEGG-KAAS pathways. The majority of unigenes associated with the biosynthesis of the steroidal diosgenin backbone exhibited up-regulation in the fruit, leaf, and root tissues, except the SQE gene in root. The differential expression of selected genes was further validated through quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, the study identified 21,026 unigenes related to transcription factors and 15,551 unigenes containing simple sequence repeats (SSR). Notably, di-nucleotide SSR motifs exhibited a high repeat frequency. These findings greatly enhance our understanding of the diosgenin biosynthesis pathway and provide a basis for future research in molecular investigation and metabolic engineering, specifically for boosting diosgenin content.

Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review

The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.

Fully sequencing the cassava full-length cDNA library reveals unannotated transcript structures and alternative splicing events in regions with a high density of single nucleotide variations, insertions-deletions, and heterozygous sequences

The primary transcript structure provides critical insights into protein diversity, transcriptional modification, and functions. Cassava transcript structures are highly diverse because of alternative splicing (AS) events and high heterozygosity. To precisely determine and characterize transcript structures, fully sequencing cloned transcripts is the most reliable method. However, cassava annotations were mainly determined according to fragmentation-based sequencing analyses (e.g., EST and short-read RNA-seq). In this study, we sequenced the cassava full-length cDNA library, which included rare transcripts. We obtained 8,628 non-redundant fully sequenced transcripts and detected 615 unannotated AS events and 421 unannotated loci. The different protein sequences resulting from the unannotated AS events tended to have diverse functional domains, implying that unannotated AS contributes to the truncation of functional domains. The unannotated loci tended to be derived from orphan genes, implying that the loci may be associated with cassava-specific traits. Unexpectedly, individual cassava transcripts were more likely to have multiple AS events than Arabidopsis transcripts, suggestive of the regulated interactions between cassava splicing-related complexes. We also observed that the unannotated loci and/or AS events were commonly in regions with abundant single nucleotide variations, insertions-deletions, and heterozygous sequences. These findings reflect the utility of completely sequenced FLcDNA clones for overcoming cassava-specific annotation-related problems to elucidate transcript structures. Our work provides researchers with transcript structural details that are useful for annotating highly diverse and unique transcripts and alternative splicing events.