Table A1.
Data statistics of raw reads from six samples for RNAseq.
| Sample | Raw reads | Raw reads base (bp) | Q20 (%) | Q30 (%) |
|---|---|---|---|---|
| CK1 | 31,003,104 | 4,650,465,600 | 95.72 | 92.01 |
| CK2 | 37,538,058 | 5,630,708,700 | 95.1 | 91.11 |
| CK3 | 37,726,236 | 5,658,935,400 | 95.31 | 90.95 |
| P1 | 35,871,190 | 5,380,678,500 | 96.92 | 93.53 |
| P2 | 46,131,806 | 6,919,770,900 | 96.48 | 92.26 |
| P3 | 33,488,164 | 5,023,224,600 | 97.32 | 93.81 |
Table A2.
Data statistics of clean reads from six samples after quality control.
| Sample | Clean reads | Clean reads base (bp) | Q20 (%) | Q30 (%) |
|---|---|---|---|---|
| CK1 | 28,585,924 | 4,136,450,402 | 98.48 | 95.62 |
| CK2 | 34,085,674 | 4,903,647,270 | 98.36 | 95.36 |
| CK3 | 34,177,082 | 4,955,215,491 | 98.19 | 94.97 |
| P1 | 33,854,004 | 4,938,319,926 | 98.6 | 95.91 |
| P2 | 43,447,298 | 6,287,507,779 | 98.11 | 94.77 |
| P3 | 32,165,338 | 4,669,426,049 | 98.45 | 95.57 |
Table 1.
Primer sequences used for qRT-PCR validation of differentially expressed genes.
| Gene ID | Primer sequence | Amplicon length (bp) |
|---|---|---|
| DN8346_c0_g1 | Forward: CTGCTGAATGAGTGGGTA | 197 |
| Reverse: AGAAGTTTGAAAGGAGGC | ||
| DN18432_c0_g1 | Forward: AAGTGTCACCTCCTTTAC | 132 |
| Reverse: GGTATTCGTTTTGTCCT | ||
| DN6713_c0_g1 | Forward: CGAGGTCCGTTAGAAGTG | 128 |
| Reverse: TTGCCAGTCTCAGTGTCC | ||
| DN14208_c0_g1 | Forward: GTAAGCCTGGAGAAAAG | 195 |
| Reverse: AGTTGACGGTGTTGGTG | ||
| DN8075_c0_g1 | Forward: GCAACCACCAGGAGCAAC | 88 |
| Reverse: CGGAAATGATGGAGAACCC | ||
| DN14349_c1_g1 | Forward: AAGTGACGAGCCAGGTA | 168 |
| Reverse: TCACAAACATTCGGACA | ||
| DN6594_c0_g1a | Forward: CAACCCCAAGGCTAACA | 303 |
| Reverse: TCACGCACGATTTCACG |
Figure 1:
Sequence length distribution of assembled unigenes.
Figure 2:
Functional annotation statistics of unigenes.
Figure 3:
Functional annotation of unigenes. (A) GO functional annotation statistics on level 2. (B) KOG annotation statistics. (C) KEGG pathway annotation statistics. A. Cellular processes. B. Environmental information processing. C. Genetic information processing. D. metabolism. E. Organismal systems.
Table 2.
Annotated genes differentially expressed in response to punicalagin and related to physiological processes in Bursaphelenchus xylophilus.
| TRINITY_Gene ID | Annotation | Log2 FC | FDR | Type |
|---|---|---|---|---|
| DN8346_c0_g1 | Cytoplasmic dynein heavy chain | 3.0314 | 2.54E-24 | Up |
| DN18432_c0_g1 | ATP synthase F0 subunit 6 (mitochondrion) | −3.5432 | 8.44E-20 | Down |
| DN6713_c0_g1 | Twitchin | 2.6719 | 1.19E-18 | Up |
| DN2658_c0_g1 | Cytochrome c oxidase subunit I (mitochondrion) | −2.2625 | 1.66E-12 | Down |
| DN11917_c0_g2 | Cytochrome b, partial (mitochondrion) | −2.3332 | 3.83E-09 | Down |
| DN9703_c0_g1 | Cytochrome c oxidase subunit 3 (mitochondrion) | -2.2922 | 3.88E-09 | Down |
| DN1325_c0_g2 | Heat shock protein 20 | −2.3758 | 1.70E-05 | Down |
| DN14208_c0_g1 | Small HSP21-like protein | −1.4702 | 6.73E-05 | Down |
| DN14130_c0_g1 | Heat shock protein Hsp-12.2 | −1.3353 | 0.0005945 | Down |
| DN10040_c0_g1 | Electron-transfer-flavoprotein | −1.1439 | 0.01728 | Down |
| DN8075_c0_g1 | Nematode cuticle collagen and collagen triple helix repeat domain containing protein | −1.1863 | 0.01908 | Down |
| DN14349_c1_g1 | Glucosidase 2 subunit beta | −1.0567 | 0.02580 | Down |
| DN22_c0_g1 | NADH dehydrogenase subunit 1 (mitochondrion) | 2.2809 | 0.04550 | Up |
Figure 4:
Annotation of differentially expressed genes (DEGs). (A) Column diagram of DEGs using GO annotation. The bottom x-axis indicates the number of genes annotated on different GO terms. The x-axis indicates the ratios of genes annotated on different GO terms to all terms used for the GO annotation. (B) Scatter diagram of DEGs with GO enrichment. (C) KOG functional classification of DEGs.
Figure 5:
Expression of six differentially expressed genes by (A) RNA-Seq, (B) qRT-PCR and (C) their correlation.
Figure 6:
Annotated, enriched KEGG pathway. (A) Annotated KEGG pathway of phagosome. Genes in blue frames with red borders were up-regulated, genes in blue frames with yellow borders were down-regulated, and genes in blue frames with sky-blue borders were simultaneously up-regulated and down-regulated. (B) Annotated KEGG pathway of oxidative phosphorylation about DEGs. Genes in blue frames with white borders were differentially expressed in the pathway.
Figure A1:
Principal components analysis of variation (A) and correlation coefficient analysis (B) among sequenced transcriptomes to show correlation among samples (control, CK1-3 and the treated samples, P1-3).
Figure A2:
Annotated KEGG pathway of Endocytosis (A), Peroxisome (B) and MAPK signaling pathways (C) about differentially expressed genes. Genes in blue frames with red borders were up-regulated, genes in blue frames with yellow borders were down-regulated and genes in blue frames with sky-blue borders were simultaneously up-regulated and down-regulated.
Figure A3:
Observation of the normal PWNs (A) and punicalagin-treated PWNs twisting abnormally (B) under microscope.