Univrsity of Tehran Press Iranian Journal of Field Crop Science 2008-4811 51 2 2020 06 21 Evaluation of Ferula gummosa Transcriptome by RNA-Seq Evaluation of Ferula gummosa Transcriptome by RNA-Seq 213 221 76111 10.22059/ijfcs.2017.225161.654249 FA Ahmad Sobhani Najafabadi Agronomy and Plant Breeding Dept., Faculty of Agriculture, University of Tehran, Iran. MohammadReza Naghavi Agronomy and Plant Breeding Dept., Faculty of Agriculture, University of Tehran, Iran. Hamid Farahmand Biotechnology Dept., Faculty of Agriculture, University of Tehran, Iran. Ali Reza Abbasi Agronomy and Plant Breeding Dept., Faculty of Agriculture, University of Tehran, Iran. Journal Article 2017 01 15 Ferula gummosa Boiss is a herbaceous plant from the Apiaceae family that is indigenous to East and West of Iran. Galbanum is an oleo-gum-resin with high pharmaceutical and industrial values, which is exuded from F. gummosa in response to wounds. Although galbanum ranks first in terms of Iranian export of pasture medicinal plants, little information exists on the genetic and biochemical mechanisms of these compounds are existed. In this regard, transcriptomics studies of medicinal plants have much to contribute to this field of science. RNA-Seq techniques are now one of the most used and most accurate methods in transcriptomics. In the present study, RNA-Seq was used to evaluate the root and flower of F. gummosa transcriptome. Short reads obtained from Illumina HiSeq2000 were assembled by Trinity software after trimming and filtering for quality scores below 30. The assembled transcriptome with 158,436 transcripts and N50 1,348 bp was annotated using different databases such as NCBI nr-proteins, Plant sub-database of NCBI nr-proteins, Swiss-Prot, TAIR10 and PLAZA 3. In total, 100,275 transcripts were annotated using BLASTX with an E-value cut-off of 10-5. Gene ontology (GO) classification of annotated transcripts was done by Blast2Go and Trinotate pipeline and in total 73,678 transcripts with at least one GO were identified. In terms of biological processes, cellular and metabolic processes are the most GO terms (44.55 %) indicated that the plant is in a metabolically active status. Transcriptome assessment of orthologous genes by NCBI-KOG database led to the identification of 42,452 genes from 3,925 families and 26 functional classes. The largest class of orthologous genes was associated with signal transduction mechanisms (14.29 %), followed by other classes, such as secondary metabolites-transport and catabolism with a frequency of 4.25 % (1,806 transcripts) indicating the most active status of F. gummosa roots and flowers for secondary metabolite production and transportation. Ferula gummosa Boiss is a herbaceous plant from the Apiaceae family that is indigenous to East and West of Iran. Galbanum is an oleo-gum-resin with high pharmaceutical and industrial values, which is exuded from F. gummosa in response to wounds. Although galbanum ranks first in terms of Iranian export of pasture medicinal plants, little information exists on the genetic and biochemical mechanisms of these compounds are existed. In this regard, transcriptomics studies of medicinal plants have much to contribute to this field of science. RNA-Seq techniques are now one of the most used and most accurate methods in transcriptomics. In the present study, RNA-Seq was used to evaluate the root and flower of F. gummosa transcriptome. Short reads obtained from Illumina HiSeq2000 were assembled by Trinity software after trimming and filtering for quality scores below 30. The assembled transcriptome with 158,436 transcripts and N50 1,348 bp was annotated using different databases such as NCBI nr-proteins, Plant sub-database of NCBI nr-proteins, Swiss-Prot, TAIR10 and PLAZA 3. In total, 100,275 transcripts were annotated using BLASTX with an E-value cut-off of 10-5. Gene ontology (GO) classification of annotated transcripts was done by Blast2Go and Trinotate pipeline and in total 73,678 transcripts with at least one GO were identified. In terms of biological processes, cellular and metabolic processes are the most GO terms (44.55 %) indicated that the plant is in a metabolically active status. Transcriptome assessment of orthologous genes by NCBI-KOG database led to the identification of 42,452 genes from 3,925 families and 26 functional classes. The largest class of orthologous genes was associated with signal transduction mechanisms (14.29 %), followed by other classes, such as secondary metabolites-transport and catabolism with a frequency of 4.25 % (1,806 transcripts) indicating the most active status of F. gummosa roots and flowers for secondary metabolite production and transportation.

https://ijfcs.ut.ac.ir/article_76111_affccac51210fcf48f04c6cb80a492f0.pdf