De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

Transcriptome sequencing of medical herb Salvia Rosmarinus (Rosemary) revealed the phenylpropanoid biosynthesis pathway genes and their phylogenetic relationships

BACKGROUND

The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely.

METHODS AND RESULTS

We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis.

CONCLUSION

The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.

Development of EST-SSR markers in Bergenia ciliata using de novo transcriptome sequencing

Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity (Ho = 0.389, He = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia.

Transcriptome analysis of Lantana camara flower petals reveals candidate anthocyanin biosynthesis genes mediating red flower color development

Flower color plays a crucial role in the appeal and selection of ornamental plants, directly influencing breeding strategies and the broader horticulture industry. Lantana camara, a widely favored flowering shrub, presents a rich palette of flower colors. Yet, the intricate molecular mechanisms governing this color variation in the species have remained largely unidentified. With the aim of filling this gap, this study embarked on a comprehensive de novo transcriptome assembly and differential gene expression analysis across 3 distinct lantana accessions, each showcasing a unique flower color. By harnessing the capabilities of both PacBio and Illumina sequencing platforms, a robust transcriptome assembly, encompassing 123,492 gene clusters and boasting 94.2% BUSCO completeness, was developed. The differential expression analysis unveiled 72,862 unique gene clusters that exhibited varied expression across different flower stages. A pronounced upregulation of 8 candidate core anthocyanin biosynthesis genes in the red-flowered accession was uncovered. This was further complemented by an upregulation of candidate MYB75 (PAP1) and bHLH42 (TT8) transcription factors. A candidate carotenoid cleavage dioxygenase (CCD4a) gene cluster also manifested a marked upregulation in white flowers. The study unveils the molecular groundwork of lantana's flower color variation, offering insights for future research and potential applications in breeding ornamental plants with desired color traits.

Morphological, phytochemical, and transcriptome analyses provide insights into the biosynthesis of monoterpenes in Monarda citriodora

MAIN CONCLUSION

Morphological, phytochemical, and transcriptome analyses revealed candidate genes involved in the biosynthesis of volatile monoterpenes and development of glandular trichomes in Monarda citriodora. Monarda citriodora Cerv. ex Lag. is a valuable aromatic plant due to the presence of monoterpenes as major constituents in its essential oil (EO). Thus, it is of sheer importance to gain knowledge about the site of the biosynthesis of these terpenoid compounds in M. citriodora, as well as the genes involved in their biosynthesis. In this study, we studied different types of trichomes and their relative densities in three different developmental stages of leaves, early stage of leaf development (L1), mid-stage of leaf development (L2), and later stage of leaf development (L3) and the histochemistry of trichomes for the presence of lipid and terpenoid compounds. Further, the phytochemical analysis of this plant through GC-MS indicated a higher content of monoterpenes (thymol, thymoquinone, γ-terpinene, p-cymene, and carvacrol) in the L1 stage with a substantial decrease in the L3 stage of leaf development. This considerable decrease in the content of monoterpenes was attributed to the decrease in the trichome density from L1 to L3. Further, we developed a de novo transcriptome assembly by carrying out RNA sequencing of different plant parts of M. citriodora. The transcriptome data revealed several putative unigenes involved in the biosynthesis of specialized terpenoid compounds, as well as regulatory genes involved in glandular trichome development. The data generated in the present study build a strong foundation for further improvement of M. citriodora, in terms of quantity and quality of its essential oil, through genetic engineering.

Upcoming progress of transcriptomics studies on plants: An overview

Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and developmental stages. RNA-Seq is a significant technique for identifying gene predictions and mining functional analysis that improves gene ontology understanding mechanisms of biological processes, molecular functions, and cellular components, but there is limited information available on this topic. Transcriptomics research on different types of plants can assist researchers to understand functional genes in better ways and regulatory processes to improve breeding selection and cultivation practices. In recent years, several advancements in RNA-Seq technology have been made for the characterization of the transcriptomes of distinct cell types in biological tissues in an efficient manner. RNA-Seq technologies are briefly introduced and examined in terms of their scientific applications. In a nutshell, it introduces all transcriptome sequencing and analysis techniques, as well as their applications in plant biology research. This review will focus on numerous existing and forthcoming strategies for improving transcriptome sequencing technologies for functional gene mining in various plants using RNA- Seq technology, based on the principles, development, and applications.

Differential Gene Expression and Metabolic Pathway Analysis of Cladophora rupestris under Pb Stress Conditions

This study aimed to analyze the transcriptome of C. rupestris under Pb²⁺ stress by using high-throughput sequencing technology, observe the changes of gene expression and metabolic pathway after three and five days under 1.0 and 5.0 mg/L of Pb²⁺ treatment, and analyze the differentially expressed genes (DEGs) and related functional genes after Pb²⁺ treatment. Metabolic pathways were revealed through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Results show that DEGs increased significantly with the increase of Pb²⁺ concentration and stress time. A total of 32 genes were closely related to Pb²⁺ stress response. GO analysis identified two major transporter proteins, namely, ATP-binding transport protein-related (ABC transporters) and zinc finger CCHC domain containing protein (Zfp) in C. rupestris. Pthr19248, pthr19211, Zfp pthr23002, Zfp p48znf pthr12681, Zfp 294 pthr12389, and Zfp pthr23067 played important roles against Pb²⁺ toxicity and its absorption in C. rupestris. KEGG pathway analysis suggested that ABCA1, ATM, and ABCD3 were closely related to Pb²⁺ absorption. Pb²⁺ stress was mainly involved in metallothionein (MT), plant hormone signal transduction, ABC transporters, and glutathione (GSH) metabolism.

Transcriptional Comparison of New Hybrid Progenies and Clone-Cultivars of Tea (Camellia sinensis L.) Associated to Catechins Content

Heterosis or hybrid vigor is the improved performance of a desirable quality in hybrid progeny. Hybridization between high-productive Assam type and high-quality Chinese type clone-cultivar is expected to develop elite tea plant progenies with high quality and productivity. Comparative transcriptomics analyses of leaves from the F1 hybrids and their parental clone-cultivars were conducted to explore molecular mechanisms related to catechin content using a high-throughput next-generation RNA-seq strategy and high-performance liquid chromatography (HPLC). The content of EGCG (epigallocatechin gallate) and C (catechin) was higher in ‘Kiara-8’ × ‘Sukoi’, ‘Tambi-2’ × ‘Suka Ati’, and ‘Tambi-2’ × ‘TRI-2025’ than the other hybrid and clone-cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analysis found that most pathways associated with catechins content were enriched. Significant differentially expressed genes (DEGs) mainly associated with phenylpropanoid, flavonoid, drug metabolism-cytochrome P450, and transcription factor (MYB, bHLH, LOB, and C2H2) pathways appeared to be responsible for the high accumulation of secondary metabolites in ‘Kiara-8’ × ‘Sukoi’, ‘Tambi-2’ × ‘Suka Ati’, and ‘Tambi-2’ × ‘TRI-2025’ as were detected in EGCG and catechin content. Several structural genes related to the above pathways have been obtained, which will be used as candidate genes in the screening of breeding materials.

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.

Research Progress and Future Development Trends in Medicinal Plant Transcriptomics

Transcriptomics is one of the most popular topics in biology in recent times. Transcriptome sequencing (RNA-Seq) is a high-throughput, high-sensitivity, and high-resolution technique that can be used to study model and non-model organisms. Transcriptome sequencing is also an important method for studying the genomes of medicinal plants, a topic on which limited information is available. The study of medicinal plants through transcriptomics can help researchers analyze functional genes and regulatory mechanisms of medicinal plants and improve breeding selection and cultivation techniques. This article analyzes and compares the applications of transcriptome sequencing in medicinal plants over the past decade and briefly introduces the methods of transcriptome sequencing and analysis, their applications in medicinal plant research, and potential development trends. We will focus on the research and application progress of transcriptome sequencing in the following four areas: the mining of functional genes in medicinal plants, development of molecular markers, biosynthetic pathways of secondary metabolites, and developmental mechanisms of medicinal plants. Our review will provide ideas for the mining of functional genes of medicinal plants and breeding new varieties.

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.