# De Novo Transcriptome Identifies Olfactory Genes in _Diachassimomorpha Ionigicaudata_ (Ashmead)
## 3 Results
### Transcriptome Annotation  
We first annotated the assembled Ashmead transcriptome on the transcript level. All the transcripts were aligned to public databases for full annotation and Figure 1B showed 74,264, 68,185, 54,536, 58,109, 61,794, 58,113, and 22,546 transcripts were aligned to the NR, NT, UniProt/SwissProt, KEGG pathway, KOG, Pfam, and GO databases, respectively. Thee NR mapping results (Figure 1C) showed the top 10 species aligned by the assembled Ashmead transcripts and the majority of the transcripts were aligned to _Diachasma alloeum_ (45,569 transcripts), _Fopius arisanus_ (5217 transcripts), and _Rhinolophus sincius_ (4920 transcripts). Unsurprisingly, the top two species together with Ashmead were all from the Braconidae family. GO annotation revealed that 11,131, 7722, and 9078 transcripts were involved in \"binding\", \"membrane\", and \"cellular process\", respectively (Figure 1C). Then, we categorized the KEGG pathway annotation (Figure 1E) into six groups: Cellular progresses, environmental information processing, genetic information processing, human diseases, metabolism, and organism systems. Among them, \"signal transduction\" is the most significant pathway, which involved 9231 transcripts. KOG annotation also revealed that 14,221 transcripts were involved in the signal transduction mechanisms (Figure 1F).  
\begin{table}
\begin{tabular}{l c c c c c c c c} \hline \hline  & **G1** & **G2** & **G3** & **M1** & **M2** & **M3** & **C1** & **C2** & **C3** \\ \hline Clean reads & 67,492,576 & 74,983,476 & 70,212,518 & 78,796,858 & 61,848,876 & 72,961,796 & 71,005,592 & 54,703,286 & 70,316,132 \\ Assembled genes & 34,302 & 26,032 & 25,398 & 24,201 & 33,375 & 33,081 & 33,308 & 24,772 & 24,707 \\ Assembled transcripts & 49,914 & 40,912 & 39,528 & 38,089 & 50,517 & 51,704 & 50,530 & 38,856 & 39,637 \\ \hline Unigenes & & & & & & & & \\ Mean Length (bp) & & & & & & & & \\ N50 & & & & & & & & \\ GC (\%) & & & & & & & & \\ Total bases & & & & & & & & \\ \hline Expressed transcripts & 10,736 & 10,320 & 10,645 & 9860 & 10,863 & 11,695 & 16,827 & 11,765 & 14,728 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Overview of the de novo transcriptome of Ashmead.  
Next, TranDecoder predicted 88,215 likely proteins encoded by the assembled Ashmead transcriptome and we annotated them using the Trinote pipeline. It was shown that 59,887, 26,402, 53,725, and 52,572 were aligned to the UniProt/SwissProt, KOG, Pfam, and GO databases, respectively (Figure 1B). In addition, 6642 and 14,672 likely proteins were predicted to contain signal peptides and transmembrane helices (Figure 1B).  
In addition, we predicted 74,963 of the unannotated transcripts using CPC2 had low coding probability. Interestingly, 2128 of the unannotated transcripts were predicted to be possible coding transcripts, which might be specific to the Ashmead and require further experiments to be verified. Next, we predicted 87 transcripts have the potential of producing miRNAs (Table S1). Notably, 84 of them were probably derived from the intron regions of coding genes while 1 and 3 derived from the Ashmead specific coding gene and long noncoding genes, respectively.  
Figure 1: Overview of the assembled Ashmead transcriptome and annotation. (**A**) Length distribution of the assembled Ashmead transcriptome. (**B**) Number of transcripts and likely proteins aligned to different databases. (**C**) Number of the transcripts aligned to other species in the NR mapping results. (**D**) GO annotation for the assembled Ashmead transcriptome. (**E**) KEGG pathway annotation for the assembled Ashmead transcriptome. (**F**) KOG annotation for the assembled transcriptome.