De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids

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.

Transcriptome Analysis of Self- and Cross-pollinated Pistils of Japanese Apricot (Prunus mume Sieb. et Zucc.)

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De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism

“…Filtering out transcripts based on abundance estimation and clustering by sequence identity would have likely removed these assembly artifacts, including transcript variants that were poorly supported by the reads. Nonetheless, only half of the filtered and clustered transcripts were functionally annotated, which is similar to many other de novo-assembled plant transcriptomes, such as tobacco, pepper (Capsicum frutescens), and sweet potato (Ipomoea batatas; Tao et al, 2012;Liu et al, 2013;Nakasugi et al, 2013). RT-PCR followed by sequencing confirmed the existence of the nonannotated transcripts, 80% of which had no predicted protein-coding regions, suggesting that most of these nonannotated transcripts may constitute poorly expressed assembled intergenic noncoding RNAs besides potential dodder-specific transcripts and 39 or 59 untranslated regions.…”

Transcriptional profiling analysis of genic male sterile–fertile Capsicum annuum reveal candidate genes for pollen development and maturation by RNA-Seq technology

“…In the present RNA-Seq system, we generated millions of 49-bp short reads, and these reads were mapped to our transcriptome database and the ESTs database from NCBI. It appeared that more than half of the short reads (69.95 % in fertile and 72.96 % in sterile plants) were uniquely mapped to our reference genes, and these mapping results proved to be much better than in our previous study (Liu et al 2013b). Although this was a preliminary analysis of pepper short-read data, we had gained valuable information which could lead to the identification of differentially expressed genes between the flower buds in fertile and sterile pepper plants.…”