## 3 Results
### Functional Annotation and Classification of Unigenes  
In order to provide putative annotations for the assembled unigenes, the 175,089 unigenes were aligned against public databases including NR, SwissPro, KEGG, KOG, and GO databases using BLASTX or BLASTY (E-value \(\leq 1.0\times 10^{-5}\)). A total of 121,096 unigenes (69.16% of the total unigenes) were matched to at least one of these databases. Then, 68.88% unigenes were matched to the proteins in the NR database, followed by 40.14% in the SwissProt database, 49.43% in the KEGG database, 36.65% in the KOG database, and 40.72% in the GO database (Table 3). Species homology distribution of \(D\). _loddigesii_ transcripts were determined based on NR annotation. The highest number of unigenes matched was \(D\). _catenatum_ (107,679 unigenes; 89.29%), _Phalaenopsis equestris_ (5328; 4.42%), and _Apostasia shenzhenica_ (778; 0.65%).  
The functional classification of the \(D\). _loddigesii_ transcriptome was performed by analyzing the BLAST results against the GO and COG databases. A total of 71,288 unigenes were assigned to 58 functional GO subcategories consisting of 28 in 'biological process', 12 in'molecular function', and 18 in 'cellular constituent'. The most representative terms in the biological processes group were 'cellular process' (48,302; 67.76%) and'metabolic process' (42,720; 59.93%); the top two terms in the cellular components groups were 'cell' (57,332; 80.42%) and 'cell part' (57,246; 80.3.0%), while the 'binding' (44,898; 62.98%) and 'catalytic activity' (42,720; 59.93%) were the dominant terms in the molecular functions groups (Figure S1).  
Based on the alignment of paralogs or orthologs, 64,171 unigenes have significant hits in the KOG database. These unigenes were clustered into 25 functional categories. Among the 25 categories, the category with the largest unigene number was 'general function prediction only' (17,814; 27.76%), which was followed by'signal transduction mechanisms' (6342; 9.88%) and 'post-translational modification, protein turnover, chaperones' (6316; 9.84%) (Figure S2).  
\begin{table}
\begin{tabular}{c c c} \hline
**Sample ID** & **TH** & **TL** \\ \hline Raw reads & 134,806,660 & 136,435,192 \\ Clean reads & 127,791,342 & 130,146,106 \\ Clean bases (Gb) & 19.17 & 19.53 \\ Clean reads rate (\%) & 92.28 & 95.23 \\ Clean Q20 bases rate (\%) & 97.79 & 97.72 \\ Clean Q30 bases rate (\%) & 93.36 & 93.23 \\ \hline \end{tabular}
\end{table}
Table 1: Summary information of the \(D\). _loddigesii_ RNA-seq data.  
\begin{table}
\begin{tabular}{c c c c c c} \hline
**Item** & **Total Number** & **N50** & **Mean Length** & **Total Bases** \\  & **(bp)** & **(bp)** & **(bp)** & **(bp)** \\ \hline Transcripts & 230,951 & 1627 & 952 & 219,753,857 \\ Unigenes & 175,089 & 1745 & 1168 & 204,522,529 \\ \hline \end{tabular}
\end{table}
Table 2: Statistics of the de novo transcriptome assembly for \(D\). _loddigesii_.  
\begin{table}
\begin{tabular}{c c c c c c c} \hline
**Database** & **NR** & **SwissProt** & **KEGG** & **KOG** & **GO** & **Total** & **Total** \\  & & & & & & **Annotation** & **Unigene** \\ \hline Number of annotated unigenes & 120,597 & 70,272 & 86,544 & 64,171 & 71,288 & 121,096 & 175,089 \\ Percentage (\%) & 68.88 & 40.14 & 49.43 & 36.65 & 40.72 & 69.16 & 100 \\ \hline \end{tabular}
\end{table}
Table 3: Summary of annotations on the unigenes in the \(D\). _loddigesii_ transcriptome against public databases.