De novo assembly and analysis of Cassia obtusifolia seed transcriptome to identify genes involved in the biosynthesis of active metabolites

Abstract

A cDNA library generated from seeds of Cassia obtusifolia was sequenced using Illumina/Solexa platform. More than 12,968,231 high quality reads were generated, and have been deposited in NCBI SRA (SRR 1012912). A total of 40,102 unigenes (>200 bp) were obtained with an average sequence length of 681 bp by de novo assembly. About 34,089 (85%) unique sequences were annotated and 8694 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Among them, 131 unigenes, which are involved in the biosynthesis and (or) regulation of anthraquinone, carotenoid, flavonoid, and lipid, the 4 best known active metabolites, were identified from cDNA library. In addition, three lipid transfer proteins were obtained, which may contribute to the lipid molecules transporting between biological membranes. Meanwhile, 30 cytochrome P450, 12 SAM-dependent methyltransferases, and 12 UDP-glucosyltransferase unigenes were identified, which could also be responsible for the biosynthesis of active metabolites.

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties

“…In the biological process category, most of the CDS were associated with “cellular processes” followed by “metabolic process” in young and mature leaves which may allow for the identification of novel genes involved in the secondary metabolite pathways. Reports on Cassia obtusifolia transcriptome, a member of the same family, also represents with the “cellular processes” followed by “metabolic process” of the transcripts in biological process category [ 81 ]. In the celluar component category, highest number of CDS was associated with “cell” and “cell part” followed by organelle in young and mature leaf samples which indicates the need of large number of transcripts for cell structure and maintaince.…”

“…These results also demonstrated the powerful ability of high-throughput sequencing to identify genes in metabolic pathways. Transcriptome sequencing has been used to elucidate the biosynthetic pathways of Anthraquinones in Cassia obtusifolia [ 81 ], a close relative of senna and Ophiorrhiza pumila [ 50 ]. There are three rate limiting steps, which are catalyzed by Isopentenyldiphosphate isomerase (IPPS), 1-deoxy-Dxylulose-5-phosphate synthase (DXS), and isochorismate synthase (ICS), respectively, in the early stage of anthraquinones formation [ 100 – 102 ].…”

“…In the seed transcriptome C . obtusifolia , 30 CYPs, 12 SAM dependent methyltransferases, and 14 UDP-glucosyltransferase unigenes were identified [ 81 ]. These genes are therefore promising candidates for catalyzing the modifications of the anthraquinone which may also be involved in the biosynthesis of active metabolites.…”

Comparative Transcriptome Analysis Uncovers Genes and Pathways Relating to Downy Mildew Resistance in Isabgol (Plantago ovata Forsk.)

“…In the present study, maximum GO terms were assigned for cellular component indicating need for large number of CDS for cellular component activity. Maximum GO terms were assigned for cellular component category in plants such as Humulus lupulus, Brassica rapa, Oryza sativa, Bupleurum chinense, Cassia obtusifolia and Chrysanthemum[51][52][53][54][55][56]. In the cellular component category, highest number of CDS were associated with "membrane" followed by "cell" in infected and control leaf samples which indicates the need of large number of transcripts for…”

Selection and evaluation of reference genes for expression analysis of Cassi

“…Recently, we obtained the transcriptome of C. obtusifolia seeds. 26) Several genes, which are relevant to formation of seed, the biosynthesis of bioactive metabolites and stress response, were screened from the transcriptome data. In the study, 10 candidate reference genes, including 1 each encoding elongation factor 1α (EF1α2) and β-Tubulin (β-TUB2), 2 genes encoding the actin (ACT1 and ACT2), cyclophilin (CYP1 and CYP2), Ubiquitin (UBQ1 and UBQ2), and α-Tubulin (α-TUB1 and α-TUB2), were chosen from the transcriptome data of C. obtusifolia.…”