Background is highlighted while an important resource of calanolides, which are dipyranocoumarins that inhibit the reverse transcriptase of human immunodeficiency virus type 1 (HIV-1 RT). . Ivabradine HCl (Procoralan) This species contains a large number and variety of secondary metabolites including flavonoids, triterpenes, coumarins, chromones, and xanthones , some of which exhibit interesting anti-leishmanial, anti-bacterial, anti-cancer, anti-parasitic, and anti-viral properties [4, 5]. Two chemotypes have been classified according Ivabradine HCl (Procoralan) to their geographical origin. Chemotype 1 (CTP 1), which grows in Sierra de Santa Marta, State of Veracruz, Mexico, produces mammea type coumarins with high cytotoxic activity against human tumor cells and antibacterial properties against and . Meanwhile, chemotype 2 (CTP 2) grows in San Andres Tuxtla, State of Veracruz, Mexico, and produces calanolides, a series of tetracyclic dipyranocoumarins that exhibit an inhibitory effect against the reverse transcriptase of the human immunodeficiency virus type 1 (HIV-1?RT) [2, 7]. There are three different calanolides (A, B and C) that have been found in and exhibit a significant inhibition on replication of the HIV-1 virus. Interestingly, these bioactive compounds show no toxicity to MT2 human lymphocytes . Additional studies have shown that a high dose of B and C calanolides causes an increased number of spleen megakaryocytes and no alteration of hepatocytes . Calanolide A, which possesses the highest inhibition of viral replication, has been synthesized and has been reported to have similar actions to the natural product [9, 10]. This molecule is in fact in clinical development as a novel therapeutic agent against HIV-1 infection [11, 12]. In plants, calanolides can be detected mainly in leaves (from CTP2), even if indeed they result from seedlings of this had been germinated from seed and cultivated inside a greenhouse Ivabradine HCl (Procoralan) . Calanolides can be also detected in plant callus , cell suspension cultures, and leaves from 12-month-old plants that were regenerated from the young, nodal-stems of plants . The metabolic pathways in the biosynthesis of calanolides involve multiple and complex series of enzymatic reactions in which L-phenylalanine and the genomic basis of the synthesis and function of metabolic compounds such as calanolides remains poorly understood. Here, we present the first report of a complete transcriptome analysis of (CT2) for future gene identification and functional genomics studies of this species. We carried out transcriptome sequencing and assembly of RNA libraries derived from terminal leaves, stems, and roots that come from regenerated seedlings. We provide annotation to public databases and categorize the transcripts into biological functions and pathways. In addition, calanolide biosynthetic pathways are suggested, and based on the homologies of some genes, we propose some of Rabbit Polyclonal to TMBIM4 them to be promising candidates for future analyses of the calanolide biosynthetic pathway. Results and discussions Sequencing and Ivabradine HCl (Procoralan) assembly A total of 16,842,368 paired-end reads (2×150) were generated (5,276,841 for leaves, 5,000,558 for stem and 6,240,602 for roots). Prior to the assembly process, the paired reads were trimmed and/or merged together using the SeqPrep pipeline (see methods for more details). A assembly was generated using Oases , a Bruijn graph-based assembler designed as an extension of Velvet  mainly used to assemble short-read sequences derived from transcriptomics data. Velvet/Oases produced a total of 61,620 contigs ranged from 0.1 to 10?kb, with an average length of 547.28?bp (Additional file 1). The GC contents of the contig set was approximately 44.7?%, which is similar to the GC content of the coding regions from other species within the Malpighiales order (reviewed in ). The N50 of these contigs was also estimated and resulted in a moderately high value of 867?bp. A fairly large number (40,727) of assembled contigs (40,727, which represents a 66.01?% of the Ivabradine HCl (Procoralan) total), were between 200?bp and 500?bp in length, indicating the presence of assembled fragments. For practical purposes, in the presented work, all contigs from the dataset are known as unigenes..