Oroxylum indicum subsp. root, (L.) Kurz

Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, Phytochemistry 156, pp. 201-213 : 202

2.1. Sequencing and De novo assembly of O. indicum root transcripts

De novo transcriptome analysis is an excellent platform for generation of comprehensive information to deduce the basic biological, molecular and cellular processes for non-model organisms lacking whole genome sequences. To generate a transcriptome database for O. indicum , cDNA libraries of root tissue were sequenced using Illumina NextSeq 500. A total of 24,625,398 raw reads were generated comprising 3,718,435,098 nucleotides with an average size of 151 bp and 44% GC content ( Table 1 ). Reads with Q < 20 were removed. Reads were mapped to human reference transcriptome which showed absence of contamination of human transcripts. These high quality reads were used for de novo assembly using Trinity ( Hass et al., 2013). It has been reported that the quality of a de novo assembly is dependent on many factors, such as the type of assembler used, followed by parameters like N50 value and coverage ( Reddy et al., 2015). The data has been submitted to NCBI, Sequence Read Archive ( SRA) submission: SUB2988844 .

The assembly resulted in a total of 121,286 transcripts with N50 value of 1783 bp with an average contig length of 1080 bp ( Table 2 ). Furthermore, transcript clustering (CD-HIT-EST) resulted into 81,002 transcripts with an average contig length of 1071 bp and 1788 N50 value ( Table 2 ). These 81,002 transcripts were further targeted for BLASTx analysis for functional annotation.