RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus

Loke, Kok-Keong; Rahnamaie-Tajadod, Reyhaneh; Yeoh, Chean-Chean; Goh, Hoe-Han; Mohamed‐Hussein, Zeti‐Azura; Noor, Normah Mohd; Zainal, Zamri; Ismail, Ismanizan

doi:10.1016/j.gdata.2015.11.003

Cited by 22 publications

(18 citation statements)

References 14 publications

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“…The genomic studies have been progressively revolutionized by the high-throughput next-generation sequencing (NGS) technologies. The advancement of RNA-sequencing (RNA-Seq) technology and computational biology tools enables to obtain rapid, and cost-effective transcriptomic resources providing a better insight into transcriptional and post-transcriptional regulation of secondary metabolite biosynthetic pathways associated genes in various non-model plant species such as Chlorophytum borivilianum [29], Camellia sinensis [21], Cymbopogon winterianus [30], and Polygonum minus [31]. In hop, it is well documented that lupulin glands in cones contain a significantly high amount of PF and BA compared to leaves and bracts [9], which raises the need to unravel the organ-or tissue-specific expression patterns of related genes of enzymes and regulators.…”

Section: Transcriptome Sequence Analysis and De Novo Assemblymentioning

confidence: 99%

Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop (Humulus lupulus L.)

Mishra

Kocábek

Nath

et al. 2019

IJMS

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The hop plant (Humulus lupulus L.) produces several valuable secondary metabolites, such as prenylflavonoid, bitter acids, and essential oils. These compounds are biosynthesized in glandular trichomes (lupulin glands) endowed with pharmacological properties and widely implicated in the beer brewing industry. The present study is an attempt to generate exhaustive information of transcriptome dynamics and gene regulatory mechanisms involved in biosynthesis and regulation of these compounds, developmental changes including trichome development at three development stages, namely leaf, bract, and mature lupulin glands. Using high-throughput RNA-Seq technology, a total of 61.13, 50.01, and 20.18 Mb clean reads in the leaf, bract, and lupulin gland libraries, respectively, were obtained and assembled into 43,550 unigenes. The putative functions were assigned to 30,996 transcripts (71.17%) based on basic local alignment search tool similarity searches against public sequence databases, including GO, KEGG, NR, and COG families, which indicated that genes are principally involved in fundamental cellular and molecular functions, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in leaf, bract, and lupulin glands tissues of hop. The expression profile of transcript encoding enzymes of BCAA metabolism, MEP, and shikimate pathway was most up-regulated in lupulin glands compared with leaves and bracts. Similarly, the expression levels of the transcription factors and structural genes that directly encode enzymes involved in xanthohumol, bitter acids, and terpenoids biosynthesis pathway were found to be significantly enhanced in lupulin glands, suggesting that production of these metabolites increases after the leaf development. In addition, numerous genes involved in primary metabolism, lipid metabolism, photosynthesis, generation of precursor metabolites/energy, protein modification, transporter activity, and cell wall component biogenesis were differentially regulated in three developmental stages, suggesting their involvement in the dynamics of the lupulin gland development. The identification of differentially regulated trichome-related genes provided a new foundation for molecular research on trichome development and differentiation in hop. In conclusion, the reported results provide directions for future functional genomics studies for genetic engineering or molecular breeding for augmentation of secondary metabolite content in hop.

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Section: Transcriptome Sequence Analysis and De Novo Assemblymentioning

confidence: 99%

Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop (Humulus lupulus L.)

Mishra

Kocábek

Nath

et al. 2019

IJMS

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“…The annotations were performed using Trinotate annotation pipeline (Loke et al, 2016a). The Blast2GO program (https://www.blast2go.com/) was also used to annotate proteins based on cellular component, molecular function and biological process (Fig.…”

Section: Methodsmentioning

confidence: 99%

Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herbPersicaria minorleaves upon methyl jasmonate elicitation

Aizat

Ibrahim

Rahnamaie-Tajadod

et al. 2018

PeerJ

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BackgroundJasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown.MethodIn this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression.ResultsFrom this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson’s r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147).DiscussionMeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.

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“…8 Metabolit terbanyak pada daun kesum adalah terpenoid dan flavonoid. 14 dan perkembangan spora jamur. 15 Senyawa flavonoid memiliki mekanisme kerja dengan mengganggu homeostasis mitokondria dan integritas membran sel jamur.…”

Section: Pendahuluanunclassified

Aktivitas anti jamur ekstrak etanol daun kesum (<em>Polygonum minus Huds.</em>) terhadap jamur <em>Trichophyton mentagrophytes</em>

et al. 2019

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Dermatofitosis merupakan penyakit kulit yang diakibatkan oleh kolonisasi jamur dermatofita yang menyerang jaringan keratin epidermis bagian superfisial seperti kulit, kuku, dan rambut. Salah satu spesies terbanyak penyebab dermatofitosis yaitu Trichophyton mentagrophytes. Tanaman Kesum (Polygonum minus Huds.) memiliki kandungan senyawa metabolit sekunder yang berpotensi sebagai anti jamur. Tujuan: Penelitian ini bertujuan untuk mengetahui aktivitas anti jamur ekstrak etanol daun Kesum terhadap jamur Trichophyton mentagrophytes, dan mengetahui diameter zona hambat oleh ekstrak etanol daun Kesum terhadap Trichopyton mentagrophytes. Metode: Aktivitas anti jamur diuji dengan metode difusi cakram. Analisis metabolit sekunder ekstrak etanol daun Kesum menggunakan metode kromatografi lapis tipis. Kontrol positif yang digunakan adalah Itrakonazol 8µg, dan kontrol negatif adalah DMSO 10%. Hasil: Ekstrak etanol daun Kesum memiliki aktivitas anti jamur pada konsentrasi 40% dan 80% dengan rata-rata diameter zona hambat 10,125 mm dengan kategori sedang dan 20,625 mm dengan kategori sangat kuat. Hasil skrining fitokimia didapatkan terpenoid, flavonoid, alkaloid, saponin dan fenol. Simpulan: Ekstrak etanol daun Kesum berpotensi sebagai obat anti dermatofita terhadap Trichophyton mentagrophytes.

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RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus

Cited by 22 publications

References 14 publications

Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop (Humulus lupulus L.)

Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop (Humulus lupulus L.)

Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herbPersicaria minorleaves upon methyl jasmonate elicitation

Aktivitas anti jamur ekstrak etanol daun kesum (<em>Polygonum minus Huds.</em>) terhadap jamur <em>Trichophyton mentagrophytes</em>

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