De Novo Transcriptome Sequencing in Trigonella foenum‐graecum L. to Identify Genes Involved in the Biosynthesis of Diosgenin

Trigonella foenum‐graecum L. (fenugreek) is a viable alternative for production of diosgenin because of its shorter growing cycle, lower production costs, and consistent yield and quality. We studied de novo transcriptome analysis along with the diosgenin pathway in Trigonella foenum‐graecum and ide...

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Published inThe plant genome Vol. 6; no. 2; pp. 1 - 11
Main Authors Vaidya, Kanak, Ghosh, Arpita, Kumar, Vinay, Chaudhary, Spandan, Srivastava, Navin, Katudia, Kalpesh, Tiwari, Tanushree, Chikara, Surendra K.
Format Journal Article
LanguageEnglish
Published Crop Science Society of America 01.07.2013
Wiley
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Summary:Trigonella foenum‐graecum L. (fenugreek) is a viable alternative for production of diosgenin because of its shorter growing cycle, lower production costs, and consistent yield and quality. We studied de novo transcriptome analysis along with the diosgenin pathway in Trigonella foenum‐graecum and identified the genes responsible for diosgenin biosynthesis. The GMV‐1 variety of Trigonella foenum‐graecum has been used in the present study for transcriptome analysis by sequencing messenger ribonucleic acid (RNA) with a SOLiD 4 Genome Analyzer. Deep sequencing data of the transcriptome was assembled using various assembly tools along with functional annotation of genes, and pathway analysis for diosgenin biosynthesis was deciphered. A total of 42 million high quality reads were obtained. De novo assembly was performed using Velvet at different k‐mer, Oases, and CLC Genomics Workbench, which generated 20,561 transcript contigs. CAP3 was used to reduce the redundancy of contigs obtained through these assemblers. A total of 18,333 transcript contigs were functionally annotated. Kyoto Encyclopedia of Genes and Genomes pathway mapping showed that 6775 transcripts were related to plant biochemical pathways including the diosgenin biosynthesis pathway. The large number of transcripts reported in the current study will serve as a valuable genetic resource for Trigonella foenum‐graecum. Sequence information of the genes that were involved in diosgenin biosynthesis could be used for metabolic engineering of Trigonella foenum‐graecum to increase diosgenin content.
Bibliography:All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.
Kanak Vaidya and Arpita Ghosh contributed equally to this work.
ISSN:1940-3372
1940-3372
DOI:10.3835/plantgenome2012.08.0021