## 3 Results
### Transcriptome Analysis
#### 3.2.2 Annotation of Unigenes  
The NCBI, KEGG, InterPro and GO databases were used to compare all of the obtained unigenes. For _H. cagayunensis_, only 109,240 (75.85%) of the 144,042 unigenes were compared to the NCBI Nr database and produced significant matches, whereas the InterPro database annotation results reported a total of 54,331 (37.72%) significant matches (Table 4). A total of 20.92% (22,854 unigenes) of the unigene annotation results against the NCBI Nr database showed homology with proteins from _Coffea arabica_ (Figure 3a). Other matches with the NCBI Nr database were also dominated by proteins from other plant groups such as _Coffea eugenioides_ (10,752 unigenes), _Citrobacter freundii_ (6596 unigenes), and _Coffea caenophora_ (6492 unigenes). In terms of predicted protein similarity distribution, 96% of the unigene sequences had similarities higher than 60%, while 40% of unigene sequences showed similarities between 28% and 60% (Figure 4a). \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Statistic** & _H. cagayanensis_ & _H. lacunosa_ & _H. coriacea_ \\ \hline \multicolumn{4}{c}{**Unigenes Annotation**} \\ \hline NCBI-Nr & 109,240 (75.84\%) & 42,479 (69.00\%) & 72,610 (70.55\%) \\ KEGG & 25,186 (17.49\%) & 24,703 (40.10\%) & 23,752 (23.08\%) \\ InterPRO & 54,331 (37.72\%) & 55,079 (89.41\%) & 52,269 (50.79\%) \\ Gene Ontology (GO) & 89,203 (61.93\%) & 33,581 (54.52\%) & 56,914 (55.30\%) \\ \hline \hline \end{tabular}
\end{table} 
Table 4: A annotated unigenes from flower part of _H. cagayanensis_, _H. lacunosa_, and _H. coriacea_ by databases. \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Statistic** & _H. cagayanensis_ & _H. lacunosa_ & _H. coriacea_ \\ \hline \multicolumn{4}{c}{**Unigenes**} \\ \hline Total unigenes & 144,042 & 156,830 & 102,914 \\ GC\% & 42.68 & 42.66 & 41.49 \\ Contig N50 (bp) & 989 & 1178 & 1545 \\ Minimum contig length (bp) & 186 & 187 & 199 \\ Maximum contig length (bp) & 9665 & 11,303 & 9825 \\ Median contig length (bp) & 350 & 315 & 547 \\ Average contig length (bp) & 619.35 & 649.54 & 909.36 \\ Total bases & 89,212,671 & 101,866,954 & 93,585,886 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Statistical summary of transcriptome assemblages for all species. Meanwhile, for _H. lacunosa_, the results showed that 42,479 (69 %) unigenes were successful compared with 61,598 database unigenes in NCBI Nr. The annotation results of the InterPro database showed 55,079 (89.41%) matches (Table 3). Approximately 17% (7217 unigenes) of the unigene annotation results with the NCBI Nr database showed homology with protein from _Coffea arabica_ (Figure 3b). Other protein matches in the NCBI Nr database were also dominated by other plant groups such as _Coffea eugenoides_ (3668 unigenes) and _Coffea canephora_ (2358 unigenes). The predicted protein similarity distribution found that 95.15% of unigene sequences had similarities higher than 60%, and 4.85% of unigene sequences were between 31% and 60% (Figure 4b). Figure 3: The homological species distribution annotation of **(a)**_H. cagayunensis_; **(b)**_H. lacunosa_; and **(c)**_H. coriacea_ unigenes against the NCBI-NR database. Analysis of _H. coriacea_ showed that 72,610 (70.55%) unigenes were successfully matched with 102,914 unigenes in the NCBI Nr database. Moreover, 52,269 (50.79%) corresponding unigenes were in the InterPro database (Table 3). Unigen annotation results with NCBI Nr database showed 29.21% (21,207 unigenes) of homology with protein _Coffea arabica_,  
Figure 4: A annotation unigenes of flower part of (**a**) _H. acagavanensis_; (**b**) _H. lacunose_; and (**c**) _H. coriacea_ from NR database: the percentage of similarity of sequences identified using blastx program. Coffea eugenioides (11,767 unigenes), _C. canephora_ (7215 unigenes), _Nyssa sinensis_ (3274 unigenes), _Sesamum indicum_ (2124 unigenes), and _Olea europaea_ var. _sylvestris_ (489 unigenes) (Figure 3c). The protein similarity distribution found that 93% of unigene sequences had similarities higher than 60%.