## 2 Results
### Expression Analysis for Radial Striation and Non-Radial Striation of Four R. glutinosa Cultivars  
In order to obtain the gene expression profiles of each individual tissue, reads from different tissues were mapped to the obtained non-redundant unigenes. According to the FPKM (fragments per kb per million fragments) values, the mappable reads were used to estimate the transcription levels. Among 24 samples of _R. glutinosa_, more than 60.0% of unigenes both in radial striation and non-radial striation from 1706 and W85 had FPKM values greater than 1, showing a higher number of transcriptionally active unigenes, while radial striation and non-radial striation from BJ1 and QH1 showed a lower number (Figure 3A). However, expression levels of unigenes from BJ1 and QH1 samples showed a higher degree of dispersion than those from the 1706 and W85 samples (Figure 3B). Figure 2: Characteristics of homology search of _R. glutinosa_ unigenes. (**A**) Venn diagram of shared and unique unigenes in _R. glutinosa_. Annotation according to the nr, nt, Swiss-Prot, KEGG, COG, GO, and Interpro databases; (**B**) number and percentage of unigenes matching the 25 top species using BLASTx in the nr database. In order to analyze the global similarities and differences among tissues and cultivars of _R. glutinosa_, PCA and box-whisker plots were conducted. The first four principal components (PCs) accounted for 82.37% of the variation (Figure S3). The 24 samples were divided into different groups according to the PCA loading plot, and six replicates from the same cultivar clustered closely in the same region. However, the radial striation and non-radial striation of the same cultivar were not clustered together (Figure S3). This may be because radial striations and non-radial striations both belong to _R. glutinosa_ tuberous root. Most samples from the All-Unigenes database showed expression patterns similar to these tissues. To identify _R. glutinosa_ genes that were significantly up- or downregulated in non-radial striation compared to corresponding radial striation controls, DeSeq2 was used to generate log\({}_{2}\) fold change values for each gene. The unigenes that had at least a two-fold change with an Adjusted _p_-value \(\leq\) 0.05 were screened and taken as differentially expressed transcripts (DETs). It was interesting that 1706_RS vs. 1706_nRS comparisons had the most differentially expressed unigenes: 3247 in total, with 1789 upregulated genes and 1458 downregulated genes. Only 1166 DETs were determined between W85_RS vs. W85_nRS, with 533 upregulated genes and 633 downregulated unigenes (Figure 4A). In total, 362 unigenes were found to be differentially expressed in all comparisons. The tissue-specific expression of these unigenes revealed that only 1660, 864, 321, and 241 genes from 1706, BJ1, QH1, and W85, respectively, were found to be differentially expressed in RS vs. nRS comparisons (Figure 4B). In detail, 143 common upregulated genes were found among the four comparisons, including the phenylalanine ammonialyase gene (_PAL_, _CL2036.Contig6_), the geranoid 8-hydroxylase gene (_G10H_, _CL1629.Contig4_), and the bHLH transcription factor gene (_CL15084.Contig2_) (Figure S4A; Table S5). In contrast, up to 219 common downregulated genes were found in the same comparisons, including the auxin-responsive protein gene (_ARF_, _CL15166.Contig1_), the aluminum-activated malate transporter gene (_ALMT_, _Unigene23223_), and the ABC transporter B family member gene (_ABCG_, _CL15718.Contig2_) (Figure S4B; Table S6). Figure 3: Unigenes expressed number and level on different tissues. (**A**) The number of expressed genes in each sample; (**B**) Expressional levels of unigenes of all the samples. Up and down lines of colored squares indicate upper and lower quartiles, and middle lines indicate medians. Black balls indicate outliers of expression values.