Transcriptome profiling unveils the mechanism of phenylpropane biosynthesis in rhizome development of Caucasian clover

Caucasian clover is the only perennial herb of the genus Leguminous clover with underground rhizomes. However, we know very little about its development process and mechanism. Transcriptome studies were conducted on the roots of Caucasian clover without a rhizome (NR) at the young seedling stage and the fully developed rhizome, including the root neck (R1), main root (R2), horizontal root (R3), and rhizome bud (R4), of the tissues in the mature phase. Compared with the rhizome in the mature phase, NR had 893 upregulated differentially expressed genes (DEGs), most of which were enriched in ‘phenylpropanoid biosynthesis’, ‘phenylalanine metabolism’, ‘DNA replication’ and ‘biosynthesis of amino acids’. A higher number of transcription factors (AP2/ERF, C2H2 and FAR1) were found in NR. There were highly expressed genes for R4, such as auxin response factor SAUR, galacturonosyltransferase (GAUT), and sucrose synthase (SUS). Phenylpropanoids are very important for the entire process of rhizome development. We drew a cluster heat map of genes related to the phenylpropanoid biosynthesis pathway, in which the largest number of genes belonged to COMT, and most of them were upregulated in R4.

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Garlic Volatile Diallyl Disulfide Induced Cucumber Resistance to Downy Mildew

International Journal of Molecular Sciences ◽

10.3390/ijms222212328 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12328

Author(s):

Fan Yang ◽

Hui Wang ◽

Chengchen Zhi ◽

Birong Chen ◽

Yujie Zheng ◽

...

Keyword(s):

Downy Mildew ◽

Resistance Mechanism ◽

Transcriptome Profiling ◽

Defense Responses ◽

Mapk Signaling ◽

Diallyl Disulfide ◽

Modern Agriculture ◽

Phenylpropanoid Biosynthesis ◽

Phenylalanine Metabolism ◽

Insight Into

Allicin compositions in garlic are used widely as fungicides in modern agriculture, in which diallyl disulfide (DADS) is a major compound. Downy mildew, caused by Pseudoperonospora cubensis (P. cubensis), is one of the most destructive diseases and causes severe yield losses in cucumbers. To explore the potential mechanism of DADS-induced cucumber resistance to downy mildew, cucumber seedlings were treated with DADS and then inoculated with P. cubensis at a 10-day interval. Symptom observation showed that DADS significantly induced cucumber resistance to downy mildew. Furthermore, both lignin and H2O2 were significantly increased by DADS treatment to responding P. cubensis infection. Simultaneously, the enzyme activities of peroxidase (POD) in DADS-treated seedlings were significantly promoted. Meanwhile, both the auxin (IAA) and salicylic acid (SA) contents were increased, and their related differentially expressed genes (DEGs) were up-regulated when treated with DADS. Transcriptome profiling showed that many DEGs were involved in the biological processes of defense responses, in which DEGs on the pathways of ‘phenylpropanoid biosynthesis’, ‘phenylalanine metabolism’, ‘MAPK signaling’, and ‘plant hormone signal transduction’ were significantly up-regulated in DADS-treated cucumbers uninoculated with the pathogen. Based on the results of several physiological indices and transcriptomes, a potential molecular mechanism of DADS-induced cucumber resistance to downy mildew was proposed and discussed. The results of this study might give new insight into the exploration of the induced resistance mechanism of cucumber to downy mildew and provide useful information for the subsequent mining of resistance genes in cucumber.

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Transcriptome and mebabolomic profiling: the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings

10.21203/rs.3.rs-26873/v1 ◽

2020 ◽

Author(s):

Dejin Xie ◽

Lingyan Chen ◽

Chengcheng Zhou ◽

Muhammad Waqqas Khan Tarin ◽

Deming Yang ◽

...

Keyword(s):

Leaf Area ◽

Molecular Mechanism ◽

Red Light ◽

Chinese Herb ◽

Leaf Tissue ◽

Transcriptome Profiling ◽

Accumulation Pattern ◽

Phenylpropanoid Biosynthesis ◽

Myb Proteins ◽

Almost All

Abstract Background Sarcandra glabra is an evergreen and traditional Chinese herb, having medicinal significance as anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor. Recently, China has initiated to establish cultivation of this plant in greenhouse under artificial light-emitting diodes (LED). However, little is known regarding the effects of the different LED lights on plant growth, accumulation pattern of secondary metabolites, and the molecular mechanism of Sarcandra glabra. Results Compared to white light (WL), the red light (RL) increased the height and decreased the stem diameter and leaf area, while blue light (BL) suppressed the height and leaf area. According to our transcriptome profiling, some differentially expressed genes (DEGs) were enriched in the phenylpropanoid biosynthesis. We identified 46 unigenes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, while the expression level of RNA-seq and qPCR were largely consistent. Meanwhile, we found 53 unigenes encoding R2R3-MYB proteins and 53 unigenes encoding bHLH proteins that several of them were related to flavonoids biosynthesis. Based on metabolomic profiling, a total of 454 metabolites were detected and the distribution of chemicals varied significantly. While flavonoids, phenolic acids, and tannins were mainly located in leaves; Organic acids, lignans and coumarins, and terpenoids were much more abundant in WG (root tissue under WL). Meanwhile, the yields of most flavonoids from BY (leaf tissue under BL) and the synthesis of primarily targeted compounds was lower than in WY (leaf tissue under WL) and RY (leaf tissue under RL). Instead, the leaves grown under RL exhibited a greater production of bioactive phytochemicals such as esculetin, fraxetin, esculin, and scopoletin. Conclusion These results provide further insight into the molecular mechanism of metabolites accumulation patterns in S. glabra under different light conditions, enabling the development of optimum breeding conditions for this plant.

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Characterization of lncRNAs and mRNAs involved in powdery mildew resistance in cucumber

Phytopathology ◽

10.1094/phyto-11-20-0521-r ◽

2021 ◽

Author(s):

Jingtao Nie ◽

Huazen Wang ◽

Wanlu Zhang ◽

Xue Teng ◽

Chao Yu ◽

...

Keyword(s):

Powdery Mildew ◽

Powdery Mildew Resistance ◽

Severe Disease ◽

Mature Mirnas ◽

Marker Assisted Breeding ◽

Resistant Varieties ◽

Mirna Sequencing ◽

Phenylpropanoid Biosynthesis ◽

Phenylalanine Metabolism

Powdery mildew (PM) is a severe fungal disease of cucumber worldwide. Identification of genetic factors resistant to PM is of great importance for marker-assisted breeding to ensure cucumber production. Long noncoding RNAs (lncRNAs) and miRNAs have been shown to play important roles in plant development and immunity; however, whether they have a role in PM response in cucurbit crops remains unknown. Here, we performed strand-specific RNA sequencing and miRNA sequencing using RNA from cucumber leaves of two near-isogenic lines (NILs) S1003 and NIL (Pm5.1) infected with PM, and systematically characterized the profiles of cucumber lncRNAs and mRNAs responsive to PM. In total, we identified 12903 lncRNAs and 25598 mRNAs responsive to powdery mildew. Differential expression (DE) analysis showed that 119 lncRNAs and 136 mRNAs correlated with PM resistance. Functional analysis of these DE lncRNAs and DE mRNAs revealed that they are significantly associated with phenylpropanoid biosynthesis, phenylalanine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and endocytosis. Particularly, two lncRNAs, LNC_006805 and LNC_012667, might play important roles in PM resistance. In addition, we also predicted mature miRNAs and ceRNA(competing endogenouse RNA) networks of lncRNA–miRNA–mRNA involved in PM resistance. A total of 49 DE lncRNAs could potentially act as target mimics for 106 miRNAs. Taken together, our results provide an abundant resource for further exploration of cucumber lncRNAs, mRNAs, miRNAs, and ceRNAs in PM resistance, and will facilitate the molecular breeding for PM resistant varieties to control this severe disease in cucumber.

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Lignin Synthesis Related Genes with Potential Significance in the Response of Upland Cotton to Fusarium Wilt Identified by Transcriptome Profiling

Tropical Plant Biology ◽

10.1007/s12042-020-09278-9 ◽

2021 ◽

Author(s):

Jianan Hou ◽

Fu’an Zhao ◽

Xiaojie Yang ◽

Wu Li ◽

Deyi Xie ◽

...

Keyword(s):

Gene Expression ◽

Fusarium Wilt ◽

Gene Expression Pattern ◽

Transcriptome Profiling ◽

Global Gene Expression ◽

Resistant Cultivar ◽

Susceptible Cultivar ◽

Single Organism ◽

Before And After ◽

Phenylpropanoid Biosynthesis

AbstractFusarium wilt, caused by the fungus Fusarium oxysporum Schlecht. f. sp. vasinfectum (Fov) is a destructive soil-borne cotton disease. To profile the genes and pathways responding to Fov infection, we compared transcriptomic responses before and after F. oxysporum inoculation in a highly resistant cotton cultivar, Yumian21, and a highly susceptible cultivar, Jimian11. Although the overall gene expression pattern was downregulated in both cultivars, the global gene expression in the resistant cultivar was stronger than that in the susceptible cultivar. In addition, the expressed genes of two cultivars mostly differed in “cellular process,” “single-organism process,” “metabolic process,” and “response to stimulus” functional groups in the biological process Gene Ontology category: the upregulated differentially expressed genes (DEG) were largely enriched in the resistant cultivar, while the downregulated DEGs were largely enriched in the susceptible cultivar. Phenylpropanoid biosynthesis and phenylalanine metabolism are the key metabolic pathways in cotton in response to Fov. We found that lignin plays a potential role in cotton resistance to Fov. Two coding genes, caffeic acid 3-O-methyltransferase and peroxidase2, as well as the two transcription factors MYB46 and MYB86, are possibly involved in the accumulation and synthesis of lignin. Furthermore, the result showed that the quantification of lignin could be potentially used as a selection tool to identify Fusarium wilt resistant cotton.

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A molecular framework for control of oriented cell division in the Arabidopsis embryo

10.1101/2021.02.09.430440 ◽

2021 ◽

Author(s):

Prasad Vaddepalli ◽

Thijs de Zeeuw ◽

Sören Strauss ◽

Katharina Bürstenbinder ◽

Che-Yang Liao ◽

...

Keyword(s):

Cell Division ◽

Actin Cytoskeleton ◽

Plant Development ◽

Transcriptome Profiling ◽

Cell Geometry ◽

Auxin Response ◽

Division Plane ◽

Asymmetric Divisions ◽

Extensive Cell ◽

Minimal Surface Area

SummaryPremitotic control of cell division orientation is critical for plant development, as cell walls prevent extensive cell remodelling or migration. Whilst many divisions are proliferative and add cells to existing tissues, some divisions are formative, and generate new tissue layers or growth axes. Such formative divisions are often asymmetric in nature, producing daughters with different fates. We have previously shown that in the Arabidopsis thaliana embryo, developmental asymmetry is correlated with geometric asymmetry, creating daughter cells of unequal volume. Such divisions are generated by division planes that deviate from a default “minimal surface area” rule. Inhibition of auxin response leads to reversal to this default, yet the mechanisms underlying division plane choice in the embryo have been unclear. Here we show that auxin-dependent division plane control involves alterations in cell geometry, but not in cell polarity or nuclear position. Through transcriptome profiling, we find that auxin regulates genes controlling cell wall and cytoskeleton properties. We confirm the involvement of microtubule (MT)-binding proteins in embryo division control. Topology of both MT and Actin cytoskeleton depend on auxin response, and genetically controlled MT or Actin depolymerization in embryos leads to disruption of asymmetric divisions, including reversion to the default. Our work shows how auxin-dependent control of MT- and Actin cytoskeleton properties interacts with cell geometry to generate asymmetric divisions during the earliest steps in plant development.

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Transcriptome profiling of lentil in response to Ascochyta lentis infection

Spanish Journal of Agricultural Research ◽

10.5424/sjar/2019174-14982 ◽

2020 ◽

Vol 17 (4) ◽

pp. e0703 ◽

Cited By ~ 1

Author(s):

Pedro García-García ◽

Francisca Vaquero ◽

F. Javier Vences ◽

Luis E. Sáenz de Miera ◽

Carlos Polanco ◽

...

Keyword(s):

Lignin Biosynthesis ◽

Transcriptome Profiling ◽

Defense Responses ◽

Wild Accession ◽

Auxin Response ◽

Ascochyta Lentis ◽

Acid Pathway ◽

Transcriptomic Level ◽

Moderately Resistant ◽

Resistant Genotypes

Aim of study: The purpose was to identify some general and genotypic-specific defense responses, in order to obtain a set of candidate genes presumably involved in the resistance.Area of study: The experiment was carried out in León, Spain.Material and methods: We have analyzed the response of three lentil genotypes to Ascochyta lentis (isolate AL 84) at transcriptomic level using the Massive Analysis of cDNA Ends (MACE) technique: the susceptible cultivar 'Lupa', the moderately resistant 'ILL5588' and the resistant wild accession 'BG 16880' (L. culinaris subsp. orientalis).Main results: MACE results yielded a total of 50,935 contigs. The average number of detected contigs in each of the six samples was approximately of 40,000. In response to Ascochyta infection, the jasmonic acid pathway and the lignin biosynthesis were up-regulated in resistant genotypes, while they were down-regulated in the susceptible one. The response to chitin, the salicylic pathway and the auxin response were activated only in the resistant L. c. culinaris genotype, while the giberellin synthesis was only induced in the susceptible L. c. culinaris cv. 'Lupa'. A set of 18 lentil gene sequences putatively involved in the response to the pathogen were validated by RT-qPCR.Research highlights: It can be concluded that in response to the infection by Ascochyta, the lignin biosynthesis and the JA pathway were critical for the resistance, while the giberellin synthesis seems to be related with susceptibility to the pathogen.

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Transcriptome Profiling Reveals Potential Genes Involved in Browning of Fresh-cut Eggplant (Solanum Melongena L.)

10.21203/rs.3.rs-60990/v1 ◽

2020 ◽

Author(s):

Xiaohui Liu ◽

Jing Shang ◽

Aidong Zhang ◽

Zongwen Zhu ◽

Dingshi Zha ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Fruits And Vegetables ◽

Molecular Mechanisms ◽

Solanum Melongena ◽

Transcriptome Profiling ◽

Differentially Expressed ◽

Enzymatic Browning ◽

Fruit Samples ◽

Phenylpropanoid Biosynthesis ◽

Fresh Cut

Abstract Background: Fresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the appearance of products and impacts their nutrition. We used the RNA-Seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant (Solanum melongena L.) fruit samples from a browning-sensitive cultivar and a browning-resistant cultivar to investigate the genes and molecular mechanisms involved in browning. Results: A total of 111.55 GB of high-quality reads were generated, the genomes of each sample were compared, and 83.50%–95.14% of the data was mapped to the eggplant reference genome. Furthermore, a total of 19631 differentially expressed genes were identified, among which 12 genes and two WRKY transcription factors were identified as potentially involved in enzymatic browning in fresh-cut eggplant fruit. Moreover, the 14 differentially expressed genes associated with browning were verified using qRT-PCR. Conclusions: Several genes associated with phenolic oxidation, phenylpropanoid biosynthesis, and flavonoid biosynthesis were found to be differentially regulated between the eggplant cultivars with different browning sensitivities. This work is of great theoretical significance, as it provides a basis for future molecular studies and improvement of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

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Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis

BMC Genomics ◽

10.1186/s12864-021-08253-2 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Chang Pyo Hong ◽

Chang-Kug Kim ◽

Dong Jin Lee ◽

Hee Jeong Jeong ◽

Yi Lee ◽

...

Keyword(s):

Fruit Development ◽

Gene Annotation ◽

Average Length ◽

Transcriptome Profiling ◽

Bioactive Compound ◽

Development Stage ◽

Basal Angiosperm ◽

Schisandra Chinensis ◽

Lignan Biosynthesis ◽

Phenylpropanoid Biosynthesis

Abstract Background Schisandra chinensis, an ancient member of the most basal angiosperm lineage which is known as the ANITA, is a fruit-bearing vine with the pharmacological effects of a multidrug system, such as antioxidant, anti-inflammatory, cardioprotective, neuroprotective, anti-osteoporosis effects. Its major bioactive compound is represented by lignans such as schisandrin. Molecular characterization of lignan biosynthesis in S. chinensis is of great importance for improving the production of this class of active compound. However, the biosynthetic mechanism of schisandrin remains largely unknown. Results To understand the potential key catalytic steps and their regulation of schisandrin biosynthesis, we generated genome-wide transcriptome data from three different tissues of S. chinensis cultivar Cheongsoon, including leaf, root, and fruit, via long- and short-read sequencing technologies. A total of 132,856 assembled transcripts were generated with an average length of 1.9 kb and high assembly completeness. Overall, our data presented effective, accurate gene annotation in the prediction of functional pathways. In particular, the annotation revealed the abundance of transcripts related to phenylpropanoid biosynthesis. Remarkably, transcriptome profiling during fruit development of S. chinensis cultivar Cheongsoon revealed that the phenylpropanoid biosynthetic pathway, specific to coniferyl alcohol biosynthesis, showed a tendency to be upregulated at the postfruit development stage. Further the analysis also revealed that the pathway forms a transcriptional network with fruit ripening-related genes, especially the ABA signaling-related pathway. Finally, candidate unigenes homologous to isoeugenol synthase 1 (IGS1) and dirigent-like protein (DIR), which are subsequently activated by phenylpropanoid biosynthesis and thus catalyze key upstream steps in schisandrin biosynthesis, were identified. Their expression was increased at the postfruit development stage, suggesting that they may be involved in the regulation of schisandrin biosynthesis in S. chinensis. Conclusions Our results provide new insights into the production and accumulation of schisandrin in S. chinensis berries and will be utilized as a valuable transcriptomic resource for improving the schisandrin content.

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Comparative transcriptome profiling provides insights into endocarp lignification of walnut (Juglans Regia L.)

10.21203/rs.3.rs-20346/v1 ◽

2020 ◽

Author(s):

Xiaoting Wu ◽

Zechao Zhang ◽

Mintao Sun ◽

Xiuhong An ◽

Shugang Zhao ◽

...

Keyword(s):

Transcription Factors ◽

Molecular Mechanisms ◽

Juglans Regia ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Transcriptome Profiling ◽

Phenotypic Differences ◽

Phenylpropanoid Biosynthesis ◽

Key Genes ◽

Main Component

Abstract Background Lignin is the main component of walnut endocarp, although we know little about the molecular mechanism of lignin formation in walnut endocarp. To understand the molecular mechanisms behind the two kinds of walnut phenotype and explore the genes involved into lignin formation, transcriptome sequencing was conducted in the walnut endocarp of the ‘Zanmei’ (ZM) and ‘Liaoning 7’ (L7) cultivars, which have different endocarp thicknesses. Compared with L7 walnut endocarp, the endocarp of ZM walnut is thicker, which decreases dehiscent nuts and compromised kernels.Results There are more differentially expressed genes (DEGs) in the ZM walnut cultivar. The DEGs involved in the phenylpropanoid biosynthesis were significantly upregulated in both cultivars 45 days after full bloom (DAFB), but more genes were upregulated in ZM than in L7. Moreover, the same DEGs showed different expression levels in the two cultivars. Most of the key genes in ZM had more different multiples than those in L7. Interestingly, when qRT-PCR was used to determine the expression of the key genes in different development stages of the two varieties, the expression patterns were different from those known in other species. Furthermore, transcription factors regulating secondary cell wall and lignin biosynthesis were identified. Quantitative real-time PCR results were consistent with transcriptome data.Conclusion In this study, transcriptome analysis was used to understand the molecular mechanisms of lignin formation in two walnut cultivars with different shell thickness. Several important key genes in the phenylpropanoid biosynthesis pathway were significantly different in the two cultivars, which may be the reason for the phenotypic differences. The analysis of transcription factors revealed that the regulation network in endocarp of walnut may be different from that of drupe such as apricot or peach. This study provides important candidate genes for exploring the complicated metabolic processes involved in the formation of walnut lignin.

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Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

International Journal of Molecular Sciences ◽

10.3390/ijms22168694 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8694

Author(s):

Chang Pyo Hong ◽

Jinsoo Kim ◽

Jinsu Lee ◽

Seung-il Yoo ◽

Wonsil Bae ◽

...

Keyword(s):

Root Growth ◽

Signaling Pathways ◽

Panax Ginseng ◽

Functional Characterization ◽

Secondary Growth ◽

Nitrate Assimilation ◽

Transcriptome Profiling ◽

Perennial Herb ◽

Storage Roots ◽

Ga Signaling

Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots; however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.

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