## 2 Results
### Functional Annotation of R. glutinosa Unigenes  
To provide putative annotations for the unigenes, all of the assembled unigenes were aligned to the protein databases NR, Swiss-Prot, KEGG, KOG, and Interpro using BLASTx and the nucleotide sequence database NT by BLASTn. A total of 103,938 unigenes (69.11% of all 150,405 unigenes) were annotated, including 97,545 in NR, 83,272 in NT, 65,209 in Swiss-Prot, 74,726 in KEGG, 76,781 in KOG, 82,012 in Interpro, and 25,209 in GO (Figure 2A and Table S3). To study the sequence conservation of _R. glutinosa_ in other plant species, we analyzed the species distribution of the All-Unigene datasets by aligning sequences against the NR database. The result shows that 75.26% of the distinct sequences have top matches (first hit) with the sequences from _Sesamun indicum_, followed by _Coffea caneplora_ (2.46%), _Vitis vinifera_ (2.2%), _Nicotiana sylvestris_ (1.55%), and _N. totometsoiformis_ (1.25%) (Figure 2B).  
\begin{table}
\begin{tabular}{c c c c c c c} \hline \hline \multirow{2}{*}{**Sample**} & **Total Raw** & **Total Clean** & **Total Clean** & **Clean Reads** & **Clean Reads** \\  & **Reads** & **Reads** & **Bases (Gb)** & **Q20 (\%)** & **Q30 (\%)** & **Ratio (\%)** \\ \hline
1706\_RS1 & 35,930,376 & 29,939,804 & 4.49 & 97.89 & 93.55 & 83.33 \\
1706\_RS2 & 35,930,108 & 30,066,360 & 4.51 & 97.91 & 93.56 & 83.68 \\
1706\_RS3 & 35,930,118 & 30,416,510 & 4.56 & 97.91 & 93.6 & 84.65 \\
1706\_nRS1 & 35,930,582 & 30,106,740 & 4.52 & 97.98 & 93.78 & 83.79 \\
1706\_nRS2 & 35,931,096 & 29,693,676 & 4.45 & 98.1 & 93.9 & 82.64 \\
1706\_nRS3 & 34,205,142 & 28,499,086 & 4.27 & 97.91 & 93.59 & 83.32 \\ BJ1\_RS1 & 35,931,216 & 29,457,812 & 4.42 & 97.91 & 93.35 & 81.98 \\ BJ1\_RS2 & 35,931,386 & 29,683,162 & 4.45 & 97.81 & 93.18 & 82.61 \\ BJ1\_RS3 & 35,931,264 & 29,768,646 & 4.47 & 97.86 & 93.27 & 82.85 \\ BJ1\_nRS1 & 35,931,542 & 29,720,528 & 4.46 & 98.16 & 94.02 & 82.71 \\ BJ1\_nRS2 & 35,930,546 & 29,537,004 & 4.43 & 97.83 & 93.39 & 82.21 \\ BJ1\_nRS3 & 35,930,574 & 29,910,368 & 4.49 & 97.82 & 93.36 & 83.24 \\ QH1\_RS1 & 35,930,624 & 29,870,448 & 4.48 & 97.86 & 93.42 & 83.13 \\ QH1\_nRS2 & 35,929,752 & 29,930,562 & 4.49 & 97.59 & 92.8 & 83.3 \\ QH1\_RS3 & 35,930,062 & 29,617,920 & 4.44 & 97.74 & 93.13 & 82.43 \\ QH1\_nRS1 & 35,930,688 & 29,542,912 & 4.43 & 97.8 & 93.29 & 82.22 \\ QH1\_nRS2 & 37,564,468 & 30,470,168 & 4.57 & 98.07 & 93.81 & 81.11 \\ QH1\_nRS3 & 37,564,500 & 30,466,862 & 4.57 & 98.05 & 93.69 & 81.11 \\ W85\_RS1 & 35,930,236 & 30,246,190 & 4.54 & 97.9 & 93.56 & 84.18 \\ W85\_RS2 & 35,930,102 & 30,523,230 & 4.58 & 97.95 & 93.69 & 84.95 \\ W85\_RS3 & 35,930,692 & 30,136,144 & 4.52 & 97.9 & 93.59 & 83.87 \\ W85\_nRS1 & 33,750,468 & 28,498,496 & 4.27 & 97.91 & 93.62 & 84.44 \\ W85\_nRS2 & 35,716,050 & 29,601,754 & 4.44 & 97.88 & 93.52 & 82.88 \\ W85\_nRS3 & 34,297,508 & 29,453,820 & 4.42 & 97.98 & 93.78 & 85.88 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Summary of the sequencing data from different _R. glutinosa_ samples.  
TransDecoder software was used to screen the candidate coding region among the unigenes. The longest ORF (open reading frame) was selected and blast with the SwissProt and Hmmscan database to search for the Pfam protein homology sequence for the prediction of CDS (Coding DNA sequences). In total, more than 102,764 CDS were predicted from All-Unigene sequences (Table S4).  
Taken together, All-Unigene represented by far the most comprehensive transcriptome database of _R. glutinosa_, and the dataset was used as the reference transcriptome database in the gene expression analysis.