ArticlePloS one2013
De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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70 citing papers in PubMed.
- Next-Generation Metabolic Engineering of Capsaicinoids Biosynthesis in Chilli Pepper: Bridging Genomic Insights to Biotechnological Applications.Biotech (Basel (Switzerland)) · 2026Review
- Transcriptomics in solanaceous crop improvement: advances and opportunities.Frontiers in plant science · 2025Review
- Genome-Wide Identification and Characterization of SNPs and InDels ofPlants (Basel, Switzerland) · 2024Article
- Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database.Horticulture research · 2024Article
- Article
- A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges.Current research in food science · 2023Review
- Biomedical and Antioxidant Potentialities in Chilli: Perspectives and Way Forward.Molecules (Basel, Switzerland) · 2022Review
- Ethylene-Inducible AP2/ERF Transcription Factor Involved in the Capsaicinoid Biosynthesis inFrontiers in plant science · 2022Article
- Integrated Metabolomic-Transcriptomic Analysis Reveals Diverse Resource of Functional Ingredients From Persimmon Leaves of Different Varieties.Frontiers in plant science · 2022Article
- Integrative RNA-Seq analysis ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Capsaicinoid biosynthesis in the pericarp of chili pepper fruits is associated with a placental septum-like transcriptome profile and tissue structure.Plant cell reports · 2021Article
- Omics Technologies to Enhance Plant Based Functional Foods: An Overview.Frontiers in genetics · 2021Review
- Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening.PloS one · 2021Article
- Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists.Scientific reports · 2020Article
- Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites.BMC genomics · 2020Article
- Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages.Scientific reports · 2020Article
- Flower transcriptome dynamics during nectary development in pepper (Capsicum annuum L.).Genetics and molecular biology · 2020Article
- Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of theFrontiers in genetics · 2020Article
- Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers.Horticulture research · 2020Article
- A Plant Virus-Based Vector System for Gene Function Studies in Pepper.Plant physiology · 2019Article
10 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, we applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (Capsicum frutescens L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data. We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. Our results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in C. frutescens and C. annuum sequences, which will be helpful in the identification of polymorphisms within chili pepper populations. These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, our strategy of de novo transcriptome assembly is applicable to a wide range of similar studies.
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