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 in | The plant genome Vol. 6; no. 2; pp. 1 - 11 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
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Crop Science Society of America
01.07.2013
Wiley |
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| Abstract | 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. |
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| AbstractList | 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. T rigonella 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. T 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 and identified the genes responsible for diosgenin biosynthesis. The GMV-1 variety of 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 -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 Sequence information of the genes that were involved in diosgenin biosynthesis could be used for metabolic engineering of to increase diosgenin content. |
| Author | Srivastava, Navin Tiwari, Tanushree Vaidya, Kanak Chaudhary, Spandan Ghosh, Arpita Katudia, Kalpesh Chikara, Surendra K. Kumar, Vinay |
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| Cites_doi | 10.2135/cropsci2007.09.0519 10.1104/pp.109.144105 10.1186/1471‐2164‐12‐191 10.1016/S0022‐2836(05)80360‐2 10.1093/bioinformatics/btr694 10.1186/1471‐2164‐12‐298 10.1093/bioinformatics/bts094 10.1186/1471‐2164‐11‐400 10.1038/nrg2484 10.1101/gr.9.9.868 10.1093/nar/gkm321 10.1093/jaoac/90.2.358 10.1038/nmeth.1226 10.1016/S1369‐5266(03)00006‐2 10.1007/s001220051056 10.1186/1471‐2164‐11‐180 10.1093/dnares/dsq028 10.1101/gr.074492.107 10.1016/S0271‐5317(02)00457‐8 10.1093/bioinformatics/bti610 10.1186/1471‐2164‐12‐131 |
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| Title | De Novo Transcriptome Sequencing in Trigonella foenum‐graecum L. to Identify Genes Involved in the Biosynthesis of Diosgenin |
| URI | https://onlinelibrary.wiley.com/doi/abs/10.3835%2Fplantgenome2012.08.0021 https://doaj.org/article/f17a66fd94c84dd28a094ed436726251 |
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