## 2 Results
### Functional Annotation of Unigenes  
For functional annotation analysis, all the assembled unigenes were searched against the public databases using BLAST. The results show that 52,700 (64.39%) unigenes could be annotated in Nr (non-redundant protein) database, 34,565 (42.23%) in Swissprot, 29,536 (36.09%) in KOG (Clusters of eukaryotic Orthologous Group), and 19,013 (23.23%) in KEGG (Kyoto Encyclopedia of Genes and Genomes). Taken together, there were 52,826 (64.55%) unigenes that could be annotated in at least one database (Table 3). GO (Gene Ontology), KOG and KEGG assignments were used to classify the function of the assembled unigenes of _M. canadensis_. For GO annotation, 4396, 4422 and 2566 unigenes were assigned to \"biological process\" category, \"molecular function\" category and \"cellular component\" category, respectively (Supplementary Figure S2). In the \"molecular function\" category, genes assigned to \"binding\" (2260) and \"catalytic activity\" (3326) accounted for the vast majority of this category. In the \"biological process\" category, \"cellular process\" (2891), \"metabolic processes\" (3447) and \"single-organism process\" (2344) were the main subcategories. For KOG classification, 29,536 unigenes were categorized into 25 KOG functional groups. Among them, \"General functional prediction only\" (9523) was the largest group, followed by \"Signal transduction mechanisms\" (5796) and \"Posttranslational modification, protein turnover, chaperones\" (4901) (Supplementary Figure S3). To further understand the biological functions of _M. canadensis_ unigenes, KEGG pathway analysis was performed. As a result, a total of 10,365 unigenes could be mapped to 133 metabolic pathways. \"Metabolism\" (5104) was the largest category (Supplementary Figure S4).  
\begin{table}
\begin{tabular}{c c c c c c} \hline \hline \multirow{2}{*}{**Samples a**} & \multirow{2}{*}{**Raw Reads**} & \multirow{2}{*}{**Clean Reads**} & **Reads** & **Q20 Percentage** & **GC Percentage** \\  & & & **Length (bp)** & **(\%) b** & **(\%) b** \\ \hline CK-1 & 58,914,374 & 57,759,958 & \multirow{2}{*}{150} & \multirow{2}{*}{8,536,291,577} & \multirow{2}{*}{98.69} & \multirow{2}{*}{50.79} \\  & & (98.04\%) & & & \\ CK-2 & 58,863,024 & 57,904,740 & \multirow{2}{*}{150} & \multirow{2}{*}{8,588,205,461} & \multirow{2}{*}{98.88} & \multirow{2}{*}{50.05} \\  & & (98.37\%) & & & \\ CK-3 & 58,109,454 & 57,113,908 & \multirow{2}{*}{150} & \multirow{2}{*}{8,470,135,931} & \multirow{2}{*}{98.83} & \multirow{2}{*}{50.69} \\  & & (98.29\%) & & & \\ MeJA-1 & 61,076,212 & 59,885,296 & \multirow{2}{*}{150} & \multirow{2}{*}{8,855,787,485} & \multirow{2}{*}{98.69} & \multirow{2}{*}{50.55} \\  & & (98.05\%) & & & \\ MeJA-2 & 55,398,094 & 54,424,124 & \multirow{2}{*}{150} & \multirow{2}{*}{8,072,356,234} & \multirow{2}{*}{98.82} & \multirow{2}{*}{50.46} \\ MeJA-3 & 65,765,946 & 64,630,794 & \multirow{2}{*}{150} & \multirow{2}{*}{9,590,111,719} & \multirow{2}{*}{98.82} & \multirow{2}{*}{50.39} \\  & & (98.27\%) & & & \\ \hline \hline \end{tabular}  
* CK and MeJA represent libraries constructed by CK and MeJA-treated samples, respectively. Numbers indicate three biological replicates; b Q20 percentage represents percentage of bases with a Phred value >20.  
\end{table}
Table 1: Summary of Illumina HiSeq4000 sequencing data.  
\begin{table}
\begin{tabular}{c c} \hline \hline Total assembled bases & 59,279,270 \\ Unigene number & 81,843 \\ GC percentage (\%) & 43.92 \\ N50 (bp) & 1126 \\ Average length (bp) & 724 \\ \hline \hline \end{tabular}  
\end{table}
Table 2: Statistics of assembly data.