Transcriptome analysis of cumin (Cuminum cyminum L.) using RNA-Seq
2018
Sadeghi, Daruish | Mortazavian, Mohammad-Mahdi | Bakhtiyarizadeh, Mohammad-Reza
Cumin (<em>Cuminum cyminum</em> L.) is a flowering plant from Apiaceae family and native to the East Mediterranean to India. The main component of essential oil in cumin seeds is cumin aldehyde (63% of total oil). Despite the importance of the cumin derivative drugs little information is available on the genome and the molecular mechanisms involved in metabolic pathway of this plant. Transcriptomic studies have greatly contributed to better understand in metabolic pathways of medicinal plants. At the moment, the use of next-generation sequencing techniques, especially RNA-seq technique were considered as the suitable promising and most accurate methods of transcriptomic evaluation. In the present study, we report cumin transcriptome for the first time. Flower tissue was used to extract RNA from four samples for RNA-seq analysis. According to the results, more than 153000000 reads with length of 50 NT were achieved. Trinity software, using 25 and 32 K-mers, was used to assemble the reads. Selection of the best assembly was followed using BUSCO software based on the integer transcript sequences. After assembly of reads, 50973 genes with an average length of 725 NT and N50 value of 1136 NT were obtained. Moreover, 53103 transcripts were identified from all genes. From this number, 35860 transcripts had at least one homologous in Nr database. More than 66.7% of all transcripts had at least one homologous in GO database (biological process, molecular function, cellular compound). Most of the genes were related to transcriptional regulation and membrane activities. In the present study, the first transcriptome profile is reported in cumin which data can be used in subsequent studies to assess expression of genes and other genetic studies in this plant.
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