De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis

Abstract

The ripe fruit of Momordica cochinchinensis Spreng, known as gac, is featured by very high carotenoid content. Although this plant might be a good resource for carotenoid metabolic engineering, so far, the genes involved in the carotenoid metabolic pathways in gac were unidentified due to lack of genomic information in the public database. In order to expedite the process of gene discovery, we have undertaken Illumina deep sequencing of mRNA prepared from aril of gac fruit. From 51,446,670 high-quality reads, we obtained 81,404 assembled unigenes with average length of 388 base pairs. At the protein level, gac aril transcripts showed about 81.5% similarity with cucumber proteomes. In addition 17,104 unigenes have been assigned to specific metabolic pathways in Kyoto Encyclopedia of Genes and Genomes, and all of known enzymes involved in terpenoid backbones biosynthetic and carotenoid biosynthetic pathways were also identified in our library. To analyze the relationship between putative carotenoid biosynthesis genes and alteration of carotenoid content during fruit ripening, digital gene expression analysis was performed on three different ripening stages of aril. This study has revealed putative phytoene synthase, 15-cis-phytone desaturase, zeta-carotene desaturase, carotenoid isomerase and lycopene epsilon cyclase might be key factors for controlling carotenoid contents during aril ripening. Taken together, this study has also made availability of a large gene database. This unique information for gac gene discovery would be helpful to facilitate functional studies for improving carotenoid quantities.

De novo transcriptome sequencing of radish (Raphanus sativusL.) and analysis of major genes involved in glucosinolate metabolism

“…In most cases, more than one unique sequence was annotated as encoding the same enzyme. Such sequences may represent different fragments of a single transcript, different members of a gene family, or both [17, 39].

Figure 6 Assembled radish unigenes that may be involved in the glucosinolates metabolism pathway.

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“…This is especially suitable for non-model organisms whose genomic sequences are unknown [14–16]. In recent years, RNA-seq has emerged as a powerful method for discovering and identifying genes involved in biosynthesis of various secondary metabolites, such as, carotenoid biosynthesis in Momordica cochinchinensis [17], cellulose and lignin biosynthesis in Chinese fir [18], tea-specific compounds i.e. flavonoid, theanine and caffeine biosynthesis pathways in tea [19], biosynthesis of flavonoid in Safflower [20], biosynthesis of active ingredients in Salvia miltiorrhiz a [21] and biosynthesis of capsaicinoid in chili pepper [22].…”

Transcriptome Analysis of Salicylic Acid Treatment in Rehmannia glutinosa Hairy Roots Using RNA-seq Technique for Identification of Genes Involved in Acteoside Biosynthesis

“…Recently, transcriptome approaches have become powerful tools to screen candidate genes involved in the biosynthesis of secondary metabolites in plants, particularly in non-model species. Much research has aimed to illuminate the complex biosynthesis pathways of functional ingredients in medicinal plants through the use of RNA-seq digital gene expression analysis, and many secondary metabolism genes have been identified from plants with little genomic sequence information, including Siraitia grosvenorii (Tang et al, 2011), Momordica cochinchinensis (Hyun et al, 2012), Uncaria rhynchophylla (Guo et al, 2014), Pyrus communis (Yang et al, 2015), Eleutherococcus senticosus (Hwang et al, 2015), and S. miltiorrhiza (Gao et al, 2014; Xu et al, 2015, 2016). …”

Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing

“…Transcriptomic studies have been widely adopted to systematically investigate the genes either involved in certain bioprocess and development stage or responses to different abiotic and biotic changes, particularly with the development of high-throughput next generation sequencing (NGS) (Wang et al, 2009; Hyun et al, 2012; Gao et al, 2013; Nejat et al, 2015). A wide spectrums of heat response genes have been identified in different plant species using transcriptomic methods, including Arabidopsis (Rizhsky et al, 2002; Larkindale and Vierling, 2008; Song et al, 2016), rice ( Oryza sativa ) (Sarkar et al, 2014; Wu et al, 2015), maize ( Zea mays ) (Dutra et al, 2015; Frey et al, 2015; Casaretto et al, 2016), tomato ( Solanum lycopersicum ) (Bita et al, 2011; Cheng et al, 2012), potato ( Solanum tuberosum ) (Ginzberg et al, 2009; Tang et al, 2016), carnation ( Dianthus caryophyllus ) (Wan et al, 2015), wheat ( Triticum aestivum ) (Qin et al, 2008), and Brachypodium distachyon (Chen and Li, 2017).…”