# Identifying Terpenoid Biosynthesis Genes in _Euphoria maculata_ via Full-Length cDNA Sequencing
## 3 Results  
### E. maculata Transcriptome Analysis Using PacBio Iso-Seq  
We clustered raw sequencing reads from the full-length cDNA libraries into consensus transcripts using the TOFU pipeline (GitHub version) supported by PacBio (Table 1). We obtained approximately 62 million polymerase reads with an average length of 56,777 bp in the \(\leq\)4 kb library and 51,584 bp in the \(\geq\)4 kb library. We obtained 467,479 CCSs with an average length of 2471 bp and a CCS read score of 0.989 in the \(\leq\)4 kb library and  
Figure 1: Schematic representation of full-length cDNA analysis in _E. maculata._465,085 CCSs with an average length of 4040 bp and a read score of 0.983 in the \(\geq\)4 kb library. Using the standard Iso-Seq protocol for transcript clustering, we obtained 47,860 high-quality (HQ) isoforms and 405 low-quality (LQ) isoforms in the \(\leq\)4 kb library and 33,573 HQ and 993 LQ isoforms in the \(\geq\)4 kb library (Table 1). Then, we processed 81,433 HQ transcripts with the COding GENome reconstruction Tool (Cogent v7.0.0, [[https://github.com/Magdoll/Cogent](https://github.com/Magdoll/Cogent)]([https://github.com/Magdoll/Cogent](https://github.com/Magdoll/Cogent)); accessed on 1 April 2022) to develop a fake genome of 20,722 reads (containing 18,481 reconstructed contigs and 2241 unassigned sequences). The fake genome was then used as a reference to map the HQ transcripts, which produced 20,172 isoforms (Figure 1, Table 2). The transcript length showed a normal distribution with the greatest number of transcripts in the 2000-2999-bp range (Figure 2).  
\begin{table}
\begin{tabular}{c c c} \hline \hline
**Analysis Metric** & **Under 4 kb** & **Over 4 kb** \\ \hline \multicolumn{3}{c}{**Polymerase reads**} \\ Total Polymerase Read length (bp) & 31,143,923,142 & 31,036,246,900 \\ Total Polymerase Reads & 548,527 & 601,659 \\ Average Polymerase Read Length (bp) & 56,777 & 51,584 \\ \multicolumn{3}{c}{**Subreads**} \\ Total Subreads & 18,525,814 & 8,597,836 \\ N50 & 2504 & 3893 \\ Average Subread Length (bp) & 1630 & 3739 \\ \multicolumn{3}{c}{**Circular consensus sequence (CCS) reads**} \\ Total CCS reads & 467,479 & 465,085 \\ Total CCS read length (bp) & 1,155,280,061 & 1,879,756,017 \\ Average CCS read length (bp) & 2471 & 4040 \\ \multicolumn{3}{c}{**Transcript clustering**} \\ Number of polished high-quality isoforms & 47,860 & 33,573 \\ Number of polished low-quality isoforms & 405 & 993 \\ \hline \hline \end{tabular}
\end{table}
Table 1: PacBio summary of RNA-seq data from two RNA libraries of _E. maculata_.  
\begin{table}
\begin{tabular}{c c c} \hline \hline
**Iso Seq Result** & **Number of Reads** & **Length (bp)** \\ \hline High-quality consensus Seq. & 76,631 & 216,086,311 \\ Reconstructed Coding Contig & 19,902 & 60,494,776 \\ Unassigned Seq & 3344 & 10,608,597 \\ Fake Genome & 20,722 & 71,103,373 \\ Minimum read length & & 100 \\ Maximum read length & & 13,544 \\ Average read length & & 3059 \\ Number of Isoforms & Number of Transcripts & Percentage (\%) \\
1 & 13,492 & 66.9 \\
2 & 3946 & 19.6 \\
3 & 1269 & 6.3 \\
4 & 630 & 3.1 \\
5 & 381 & 1.9 \\
6 & 185 & 0.9 \\
7 & 116 & 0.6 \\
8–25 & 153 & 0.8 \\ Total & 20,172 & 100 \\ \hline \hline \end{tabular}
\end{table}
Table 2: IsoSeq results and statistics of isoforms in the transcriptomes of _E. maculata_.