Transcriptomic analysis of  treated by a potential phytonematicide, punicalagin

Qun-Qun Guo; Gui-Cai Du; Ting-Ting Zhang; Mei-Juan Wang; Chao Wang; Hong-Tao Qi; Rong-Gui Li

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Transcriptomic analysis of Bursaphelenchus xylophilus treated by a potential phytonematicide, punicalagin

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| 18 mar 2020

Journal of Nematology

Tom 52 (2020): Zeszyt 1 (January 2020)

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Data publikacji: 18 mar 2020

Zakres stron: 1 - 14

DOI: https://doi.org/10.21307/jofnem-2020-001

© 2020 Qun-Qun Guo et al., published by Sciendo.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Sequence length distribution of assembled unigenes.

Functional annotation statistics of unigenes.

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.

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.

Expression of six differentially expressed genes by (A) RNA-Seq, (B) qRT-PCR and (C) their correlation.

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.

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).

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.

Observation of the normal PWNs (A) and punicalagin-treated PWNs twisting abnormally (B) under microscope.

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

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

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_g1^a	Forward: CAACCCCAAGGCTAACA	303
	Reverse: TCACGCACGATTTCACG

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

eISSN:: 2640-396X
Język:: Angielski

Częstotliwość wydawania:: Volume Open
Dziedziny czasopisma:: Life Sciences, other

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Transcriptomic analysis of Bursaphelenchus xylophilus treated by a potential phytonematicide, punicalagin

Data publikacji: 18 mar 2020

Zakres stron: 1 - 14

DOI: https://doi.org/10.21307/jofnem-2020-001

© 2020 Qun-Qun Guo et al., published by Sciendo.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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Figure A3:

Annotated genes differentially expressed in response to punicalagin and related to physiological processes in Bursaphelenchus xylophilus.

Data statistics of raw reads from six samples for RNAseq.

Primer sequences used for qRT-PCR validation of differentially expressed genes.

Data statistics of clean reads from six samples after quality control.