Figure 7 - uploaded by Richard Dixon
Content may be subject to copyright.
Lignin biosynthesis pathway and lignin-related gene expression in the early stage seeds and stems. (A) A simplified lignin biosynthesis pathway. (B) The expression levels of PAL, 4CL, CCR, CAD, C4H and CCoAOMT were represented as RPKM values in the light and dark pod tissues, seeds at 6, 8 and 10 weeks, and in stems. Each color represents one contig annotated as the corresponding class of lignin-related gene.
Source publication
Background
Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier stages, the developing seeds within the pod synthesize a novel lignin polymer, catechyl (C) lignin, in their coats. Genomic re...
Contexts in source publication
Context 1
... lignin is naturally synthesized from the unusual mono- lignol caffeyl alcohol, whereas lignin in the vegetative tissues of V. planifolia is of the normal guaiacyl/syringyl (G/S) type [5]. To address potential pathways of C-lignin biosynthesis, we used annotated lignin pathway genes in Arabidopsis as query sequences (Figure 7A [28,29]), and caffeoyl-CoA O- methyltransferase-like (named as OMT-4 and OMT-5; 8 contigs; characterized in [30]), cinnamyl alcohol dehydro- genase (CAD; 23 contigs), caffeoyl shikimate esterase (CSE; 64 contigs) [31]. ...
Context 2
... of the predicted lignin-related genes shared similar expression patterns in pod tissues, with highest expres- sion in seeds at 10 weeks post-pollination, and with lowest expression in the dark and light mesocarp tis- sues ( Figure 7B). This pattern was observed for most of the contigs representing each gene. ...
Citations
... gov/tools/primer-blast/; accessed on 12 July 2023). Vanilla actin 1 gene was used as an internal control for normalization between samples [21]. Relative transcript levels were calculated using the 2 −∆∆CT method. ...
Vanilla (Vanilla planifolia Andrews) is a valuable orchid spice cultivated for its highly priced beans. Vanilla has been planted in Hainan province of China via cutting propagation for about 40 years. The yield has been decreasing annually for the past ten years due to pod numbers declining significantly even though it seems to grow normally without disease symptoms, while the reason is still unknown. In this study, we found that Cymbidium mosaic virus (CymMV), one of the most devastating viruses causing losses in the vanilla industry, massively presented within the pods and leaves of vanilla plants, so the virus infecting the vanilla seems to be a highly probable hypothesis of the main contributions to low yield via decreasing the number of pods. This represents the first speculation of CymMV possibly affecting the yield of vanilla in China, indicating the important role of virus elimination in restoring high yield in vanilla. This research can also serve as a warning to important economic crops that rely on cuttings for propagation, demonstrating that regular virus elimination is very important for these economically propagated crops through cuttings.
... Furthermore, Mint (Mentha) transcriptome analysis reveals trichomes development, and secondary metabolite accumulation (Mishra et al., 2021), monoterpene synthesis and light-induced impact on biosynthesis (Qi et al., 2018;Yu et al., 2021;An et al., 2023), salicylic acid induced enhanced antioxidant potential (Figueroa-Pérez et al., 2019), and biosynthesis of peltate-glandular trichomes (Jin et al., 2014). Moreover, in depth-transcriptome of vanilla suggests orchid pod growth, and Fusarium infection suggest translational control during the early stage of infection (Rao et al., 2014;Adame--García et al., 2019). In the case of cayenne peppers (Capsicum annuum), transcriptomic studies are reported highlighting genes involved in pepper gold mosaic virus (PepGMV) infection (Gongora-Castillo et al., 2012a), biosynthesis of capsaicinoids (Liu et al., 2013), marker discovery (SNPs and SSRs), >24 K candidate gene models (Ashrafi et al., 2012), cold injury processes (Ge et al., 2019), and different storage temperatures (Tang et al., 2019). ...
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25–30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
... RNA-Seq data (accession numbers SRP043630 and SRP214274) were obtained from the Sequence Read Archive (SRA) database to investigate the expression patterns of VpGLR genes in different tissues and biotic stress processes after infection with F. oxysporum. The details of growth conditions and treatment conditions were as described by Rao et al. 35 and Solano-De et al. 20 respectively. The expression pattern of different tissues was obtained at the age of six months: leaf, stem, mesocarp, placental laminae, hair cells, and seeds. ...
Glutamate receptor-like genes (GLRs) are essential for plant growth and development and for coping with environmental (biological and non-biological) stresses. In this study, 13 GLR members were identified in the Vanilla planifolia genome and attributed to two subgroups (Clade I and Clade III) based on their physical relationships. Cis-acting element analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated the GLR gene regulation’s complexity and their functional diversity. Expression analysis revealed a relatively higher and more general expression pattern of Clade III members compared to the Clade I subgroup in tissues. Most GLRs showed significant differences in expression during Fusarium oxysporum infection. This suggested that GLRs play a critical role in the response of V. planifolia to pathogenic infection. These results provide helpful information for further functional research and crop improvement of VpGLRs.
... Among all plants capable of accumulating C-lignin in the seed coats, the seed coats of Vanilla and Cactaceae contained only Clignin, while those of Euphorbiaceae, Cleomaceae, the orchid families N. veratrifolia and C. formosanum contained C-lignin and conventional G/S-type lignin. 14,19 In the seed coat of these crops where C-lignin and G/S-type lignin coexist, the synthesis of C-lignin and the synthesis of conventional lignin units are temporally independent of each other. For example, in Cleome hassleriana, G-lignin is synthesized in the seed coat shortly aer pollination and stopped around 14 days aer pollination. ...
... Aerward, the formation of C-lignin begins. 13,19 The biosynthesis of monolignols begins with phenylalanine, which is converted to p-coumaroyl-CoA via the general phenylpropane pathway with the catalysis of L-phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), and 4coumarate-CoA ligase (4CL) (Fig. 2) converted to caffeoyl shikimate with the help of catalysis by shikimate/quinate hydroxycinnamoyl transferase (HCT) and coumaroyl shikimate 3 ′ -hydroxylase (C3 ′ H). This biosynthetic pathway presumably leads to the introduction of the 3-hydroxyl group of the caffeoyl portion of C-lignin. ...
... For example, vanilla seed coats contain C-lignin in high purity because they almost do not contain CCoAOMT transcript that could convert caffeoyl to feruloyl by methylation of hydroxyl groups to methoxy. 13,19 Wagner and colleagues also reported that the silencing of the CCoAOMT gene resulted in the accumulation of C-lignin in Pinus radiata. 21 It was found that in Pinus radiata, cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) were able to convert caffeoyl-CoA to caffealdehyde and caffeyl alcohol. ...
Lignin is the dominant aromatic renewable polymer on earth. Generally, its complex and heterogeneous structure hinders its high-value utilization. Catechyl lignin (C-lignin), a novel lignin discovered in the seed coats of vanilla and several members of Cactaceae, has received increasing attention due to its unique homogeneous linear structure. Obtaining substantial amounts of C-lignin either by gene regulation or effective isolation is essential to advance C-lignin's valorization. Through a fundamental understanding of the biosynthesis process, genetic engineering to promote the accumulation of C-lignin in certain plants was developed to facilitate C-lignin valorization. Various isolation methods were also developed to isolate C-lignin, among which deep eutectic solvents (DESs) treatment is one of the most promising approaches to fractionate C-lignin from biomass materials. Since C-lignin is composed of homogeneous catechyl units, depolymerization to produce catechol monomers demonstrates a promising way for value-added utilization of C-lignin. Reductive catalytic fractionation (RCF) represents another emerging technology for effective depolymerizing C-lignin, leading to a narrow distribution of lignin-derived aromatic products (e.g., propyl and propenyl catechol). Meanwhile, the linear molecular structure predisposes C-lignin as a potential promising feedstock for preparing carbon fiber materials. In this review, the biosynthesis of this unique C-lignin in plants is summarized. C-lignin isolation from plants and various depolymerization approaches to obtaining aromatic products are overviewed with highlights on RCF process. Exploring new application areas based on C-lignin's unique homogeneous linear structure is also discussed with its potential for high-value utilization in the future.
... For each sample, RNA-seq raw reads were trimmed and filtered using in-house perl scrips as described previously (44). Clean reads were mapped to the A. thaliana genome sequence and the reference-annotated genes (TAIR10) using Bowtie v2.3.2.0 (45) and TopHat v2.1.1 (46) with default parameters. ...
Altering the content or composition of the cell wall polymer lignin is a favored approach to valorize lignin toward biomaterial and chemical production in the biorefinery. However, modifying lignin or cellulose in transgenic plants can induce expression of defense responses and negatively affect growth. Through genetic screening for suppressors of defense gene induction in the low lignin ccr1-3 mutant of Arabidopsis thaliana, we found that loss of function of the receptor-like kinase FERONIA, although not restoring growth, affected cell wall remodeling and blocked release of elicitor-active pectic polysaccharides as a result of the ccr1-3 mutation. Loss of function of multiple wall-associated kinases prevented perception of these elicitors. The elicitors are likely heterogeneous, with tri-galacturonic acid the smallest but not necessarily the most active component. Engineering of plant cell walls will require development of ways to bypass endogenous pectin signaling pathways.
... However, most research to date has employed homogenized tissue samples, thereby ignoring spatial variations in transcripts, some of which information is either obscured or missing entirely (Kudapa et al. 2018;Shinozaki et al. 2018). With the development of methods for preservation of RNA integrity, massively high throughput sequencing and meticulous tissue separation, plant gene expression can be studied at higher spatial resolution (Matas et al. 2012;Motomu et al. 2014;Rao et al. 2014Rao et al. , 2016Shinozaki et al. 2018). For example, in transcript expression profiles of dissected tomato (Solanum lycopersicum) fruit, genes with expression previously diluted in homogenized organs were identified, and differences and synergies in spatial regulatory networks were revealed (Matas et al. 2012;Shinozaki et al. 2018). ...
Main conclusion
Transcriptomics of manually dissected leaf layers from Medicago truncatula identifies genes with preferential expression in upper and/or lower epidermis. The promoters of these genes confer epidermal-specific expression of transgenes.
Abstract
Improving the quality and quantity of proanthocyanidins (PAs) in forage legumes has potential to improve the nitrogen nutrition of ruminant animals and protect them from the risk of pasture bloat, as well as parasites. However, ectopic constitutive accumulation of PAs in plants by genetic engineering can significantly inhibit growth. We selected the leaf epidermis as a candidate tissue for targeted engineering of PAs or other pathways. To identify gene promoters selectively expressed in epidermal tissues, we performed comparative transcriptomic analyses in the model legume Medicago truncatula, using five tissue samples representing upper epidermis, lower epidermis, whole leaf without upper epidermis, whole leaf without lower epidermis, and whole leaf. We identified 52 transcripts preferentially expressed in upper epidermis, most of which encode genes involved in flavonoid biosynthesis, and 53 transcripts from lower epidermis, with the most enriched category being anatomical structure formation. Promoters of the preferentially expressed genes were cloned from the M. truncatula genome and shown to direct tissue-selective promoter activities in transient assays. Expression of the PA pathway transcription factor TaMYB14 under control of several of the promoters in transgenic alfalfa resulted in only modest MYB14 transcript accumulation and low levels of PA production. Activity of a subset of promoters was confirmed by transcript analysis in field-grown alfalfa plants throughout the growing season, and revealed variable but consistent expression, which was generally highest 3–4 weeks after cutting. We conclude that, although the selected promoters show acceptable tissue-specificity, they may not drive high enough transcription factor expression to activate the PA pathway.
... Expression of PlCHS, PlCHI, and PlFLS was upregulated in white petals but colored petals had higher expression of PlF3'H, PlDFR, and PlANS in Pleione limprichtii (Zhang et al., 2020b). PAL, 4CL, and C4H were upregulated in 8 and 10 weeks old seeds of Vanilla planifolia (Rao et al., 2014). Expression of trans-resveratrol-di-O-methyltransferase-like (ROMT) encoding gene, responsible for resveratrol biosynthesis, was high in tubers of Dactylorhiza hatagirea (Dhiman et al., 2019). ...
Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.
... To elucidate the fine mechanism of C-lignin formation, transcriptomic studies have been conducted on plant species known to accumulate this type of lignin in seed coats. As expected, downregulation of COMT and/or CCoAOMT genes was observed in tissues that produce C-lignin in species like Vanilla orchid, Cleome hassleriana, and Paphiopedilum armeniacum (Fang et al., 2020;Rao et al., 2014;Zhuo et al., 2019). In addition, the requirement of a laccase with activity toward caffeyl alcohol has been recently demonstrated in C. hassleriana . ...
Lignin is considered to represent the second most abundant terrestrial biopolymer next to cellulose. Although quite variable across vascular plants, its content can account for up to 30% of total biomass in certain woody species. Lignin plays important roles in plants, but often represents hurdles to the utilization of cellulosic biomass in different sectors such as pulp industry, forage digestibility, and bioenergy. Certain natural or mutagenesis-induced lignin mutants, which are notorious for exhibiting brown midribs in grasses or red-brown wood in trees, have long been recognized to produce biomass more amenable to animal digestion, biological conversion, and other agro-industrial processes. Advances in molecular biology techniques for DNA sequencing and manipulation have facilitated the identification of genes involved in lignin biosynthesis and enabled the modification of their expression. The first reports on plants modified in lignin via genetic engineering techniques trace back to the mid 90’s. Since then, with the emergence of genome sequencing capabilities and the deployment of large-scale transcriptomic, proteomic, and metabolomic approaches, our understanding on lignin metabolism and regulation has expanded. Correspondingly, substantial efforts have been made in tailoring lignin biosynthesis. In this chapter, we cover several bioengineering strategies that leverage recent knowledge obtained on the mechanistic understanding of lignin formation and chemical composition. Modification of lignin content and/or monomeric composition can be achieved not only by tailoring gene expression, but also by exploiting enzyme post-translational modifications, altering enzyme cofactors and co-substrates, and rerouting lignin metabolic precursors.
... As described [82], each RNA-library was prepared from 1 μg of total RNA isolated from one sample each of Kudzu Kingdom (P. phaseoloides) and Oklahoma (P.m. lobata) roots using TruSeq RNA Sample Prep Kits v2 (Illumina Inc., San Diego, CA), according to the manufacturer's instructions, at the Genomics Core Facility at the Noble Foundation. ...
... Processing of the 100 bp paired-end Illumina reads began by interleaving the read mates for each sample into a single file and trimming bases with quality scores of 20 or less from the end of each read. Reads less than 40 bp long after trimming were discarded along with their mates [82]. Each of the Pueraria root Illumina libraries was assembled separately using a combination of Velvet 1.2.10 [18] and Oases 0.2.08 [19]. ...
Background
Kudzu is a term used generically to describe members of the genus Pueraria. Kudzu roots have been used for centuries in traditional Chinese medicine in view of their high levels of beneficial isoflavones including the unique 8-C-glycoside of daidzein, puerarin. In the US, kudzu is seen as a noxious weed causing ecological and economic damage. However, not all kudzu species make puerarin or are equally invasive. Kudzu remains difficult to identify due to its diverse morphology and inconsistent nomenclature.
Results
We have generated sequences for the internal transcribed spacer 2 (ITS2) and maturase K (matK) regions of Pueraria montana lobata, P. montana montana, and P. phaseoloides, and identified two accessions previously used for differential analysis of puerarin biosynthesis as P. lobata and P. phaseoloides. Additionally, we have generated root transcriptomes for the puerarin-producing P. m. lobata and the non-puerarin producing P. phaseoloides. Within the transcriptomes, microsatellites were identified to aid in species identification as well as population diversity.
Conclusions
The barcode sequences generated will aid in fast and efficient identification of the three kudzu species. Additionally, the microsatellites identified from the transcriptomes will aid in genetic analysis. The root transcriptomes also provide a molecular toolkit for comparative gene expression analysis towards elucidation of the biosynthesis of kudzu phytochemicals.
... Seed dormancy is a common problem in many orchid species which affects their germination. Mature orchid seeds have adopted seed dormancy which impart brown colour to the seeds on maturation; however, immature orchid seeds are not dormant and are usually white in colour (Yamazaki and Miyoshi, 2006;Barsberg et al., 2013;Rao et al., 2014). Final stage of seed maturation leads to the lignin synthesis and its deposition on integument (Barsberg et al., 2013;Rao et al., 2014;Yang and Lee, 2014;Pierce et al., 2019). ...
... Mature orchid seeds have adopted seed dormancy which impart brown colour to the seeds on maturation; however, immature orchid seeds are not dormant and are usually white in colour (Yamazaki and Miyoshi, 2006;Barsberg et al., 2013;Rao et al., 2014). Final stage of seed maturation leads to the lignin synthesis and its deposition on integument (Barsberg et al., 2013;Rao et al., 2014;Yang and Lee, 2014;Pierce et al., 2019). The outer integument of seeds is lignified which helps the seeds to remain viable for longer-time (Rasmussen, 1992;Baskin and Baskin, 1998). ...
