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Background : Several members of the genus Clausena have a great potential as a candidate for the identification of new drug lead molecules, but lack of their genomic information can be a hindrance for the verification of the genetic background for future use. To broaden and delve into the genomic features of this genus, Clausena excavata, an important medicinal plant in many Asian countries, was used for RNA-seq analysis.
Methods and Results : A ten ㎍ of the total RNA was used for mRNA isolation using oligo-dT beads and random sheared mRNAs were used to prepare a cDNA library for a illumina hiseq 2500 analysis. In total, 17,580,456 trimmed clear reads from the illumina hiseq 2500 were used for de novo assembly using three assemblers, CLC genomics workbench, velvet-oases, and Trinity. A total of 16,638 non-redundant unigenes with an average length of 755 bp were generated by the assembly. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2,305 genes in the cellular component, 5,577 in the biological processes, and 8,056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4,374 genes. Among annotated genes, 3,006 were mapped to 123 metabolic pathways by KEGG metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five Clausena species; eight of them exhibited polymorphism.
Conclusion : In the present study, genomic resources of the genus Clausena were enriched through RNA-seq and SSR markers, which will serve as valuable resources for genomic/genetic studies of the genus Clausena and close relatives.
