RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection
Abstract
:1. Introduction
2. Results
2.1. K8 and HY Survival Curve Analysis
2.2. Gene Expression in K8 and HY Strains
2.3. Analysis of DEGs in HY and K8 Strains
2.4. Functional Classifications and Comparison of DEGs in K8 and HY Strains
2.5. Comparison of DEGs between HY and K8 Strains
3. Discussion
4. Materials and Methods
4.1. Silkworm Strains and Fungal Strain
4.2. Survival Curves Assay of K8 and HY Strains
4.3. Preparation of Silkworm Samples for Sequencing
4.4. RNA Extraction, Illumina Sequencing, and Data Processing
4.5. Annotation and Analysis of Sequence Data
4.6. qPCR Analysis
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sample | Raw Reads | Clean Reads | Clean Base | Total Mapped | Total Mapped Ratio | Unique Match |
---|---|---|---|---|---|---|
HY-control-1 | 14,538,847 | 14,283,926 | 714,196,300 | 12,821,136 | 89.76% | 48.20% |
HY-control-2 | 13,093,162 | 12,957,649 | 647,882,450 | 11,439,009 | 88.28% | 53.63% |
HY-control-3 | 14,750,894 | 14,604,137 | 730,206,850 | 12,986,072 | 88.92% | 62.05% |
HY-immersion-1 | 18,735,786 | 18,318,940 | 915,947,000 | 16,445,941 | 89.78% | 52.31% |
HY-immersion-2 | 14,899,363 | 14,591,964 | 729,598,200 | 13,070,880 | 89.58% | 51.16% |
HY-immersion-3 | 12,500,104 | 12,366,585 | 618,329,250 | 11,040,402 | 89.28% | 54.10% |
HY-injection-1 | 15,171,911 | 14,914,968 | 745,748,400 | 13,195,864 | 88.47% | 74.54% |
HY-injection-2 | 15,078,479 | 14,804,938 | 740,246,900 | 12,837,562 | 86.71% | 72.23% |
K8-control-1 | 17,655,181 | 17,298,316 | 864,915,800 | 15,429,685 | 89.20% | 45.02% |
K8-control-2 | 12,458,912 | 12,334,197 | 616,709,850 | 10,425,374 | 84.52% | 57.16% |
K8-control-3 | 13,424,038 | 13,277,104 | 663,855,200 | 11,612,998 | 87.47% | 53.37% |
K8-immersion-1 | 15,981,466 | 15,699,938 | 784,996,900 | 14,060,649 | 89.56% | 40.49% |
K8-immersion-2 | 17,412,127 | 17,068,312 | 853,415,600 | 15,368,966 | 90.04% | 50.74% |
K8-immersion-3 | 12,750,866 | 12,610,756 | 630,537,800 | 11,102,951 | 88.04% | 47.15% |
K8-injection-1 | 14,183,649 | 13,929,356 | 696,467,800 | 12,446,506 | 89.35% | 74.64% |
K8-injection-2 | 14,573,110 | 14,328,895 | 716,444,750 | 12,705,750 | 88.67% | 74.15% |
Average | 14,825,493 | 14,586,874 | 729,343,691 | 12,936,859 | 88.60% | 56.93% |
Pathway ID | Description | p Value | |||
---|---|---|---|---|---|
Immersion | Injection | ||||
K8 | HY | K8 | HY | ||
ko00232 | Caffeine metabolism | 0.0045 | |||
ko04974 | Protein digestion and absorption | 0.0266 | |||
ko00020 | Tricarboxylic acid (TCA) cycle | 0.0304 | 0.0340 | ||
ko04972 | Pancreatic secretion | 0.0353 | 0.0410 | ||
ko00720 | Carbon fixation pathways in prokaryotes | 0.0494 | |||
ko00052 | Galactose metabolism | 0.0011 | |||
ko04512 | ECM-receptor interaction | 0.0158 | 0.0214 | ||
ko00561 | Glycerolipid metabolism | 0.0221 | 0.0087 | ||
ko04145 | Phagosome | 0.0404 | 0.0006 | 3.9 × 10−5 | |
ko04142 | Lysosome | 0.0452 | 0.0001 | ||
ko00603 | Glycosphingolipid biosynthesis—globo series | 0.0469 | |||
ko00531 | Glycosaminoglycan degradation | 0.0469 | |||
ko00604 | Glycosphingolipid biosynthesis—ganglio series | 0.0469 | |||
ko04711 | Circadian rhythm—fly | 0.0004 | 0.0294 | ||
ko05130 | Pathogenic Escherichia coli infection | 0.0007 | 0.0119 | ||
ko00511 | Other glycan degradation | 0.0024 | 0.0023 | ||
ko05215 | Prostate cancer | 0.0041 | 0.0381 | ||
ko04919 | Thyroid hormone signaling pathway | 0.0062 | 0.0496 | ||
ko04390 | Hippo signaling pathway | 0.0088 | |||
ko04975 | Fat digestion and absorption | 0.0105 | |||
ko05166 | Human T-cell lymphotropic virus I (HTLV-I) infection | 0.0105 | 0.0486 | ||
ko04612 | Antigen processing and presentation | 0.0115 | 0.0109 | ||
ko05200 | Pathways in cancer | 0.0118 | |||
ko05217 | Basal cell carcinoma | 0.0126 | |||
ko00010 | Glycolysis/Gluconeogenesis | 0.0130 | |||
ko05164 | Influenza A | 0.0138 | 0.0128 | ||
ko04151 | PI3K-Akt signaling pathway | 0.0155 | 0.0141 | ||
ko04391 | Hippo signaling pathway—fly | 0.0179 | |||
ko04621 | Nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway | 0.0179 | |||
ko00591 | Linoleic acid metabolism | 0.0186 | |||
ko00565 | Ether lipid metabolism | 0.0192 | |||
ko04141 | Protein processing in endoplasmic reticulum | 0.0199 | 0.0025 | ||
ko04510 | Focal adhesion | 0.0206 | |||
ko04662 | B cell receptor signaling pathway | 0.0226 | 0.0214 | ||
ko03320 | Peroxisome proliferator-activated receptor (PPAR) signaling pathway | 0.0255 | 0.0242 | ||
ko05131 | Shigellosis | 0.0270 | |||
ko00592 | α-Linolenic acid metabolism | 0.0270 | |||
ko00600 | Sphingolipid metabolism | 0.0278 | |||
ko05169 | Epstein-Barr virus infection | 0.0280 | 0.0260 | ||
ko05205 | Proteoglycans in cancer | 0.0284 | |||
ko05222 | Small cell lung cancer | 0.0301 | 0.0285 | ||
ko04014 | Ras signaling pathway | 0.0306 | |||
ko04540 | Gap junction | 0.0309 | 0.0293 | ||
ko05134 | Legionellosis | 0.0309 | |||
ko04146 | Peroxisome | 0.0325 | |||
ko04916 | Melanogenesis | 0.0333 | |||
ko04144 | Endocytosis | 0.0352 | |||
ko01040 | Biosynthesis of unsaturated fatty acids | 0.0419 | |||
ko05160 | Hepatitis C | 0.0456 | 0.0433 | ||
ko04660 | T cell receptor signaling pathway | 0.0465 | 0.0441 | ||
ko04910 | Insulin signaling pathway | 0.0484 | 0.0459 | ||
ko04931 | Insulin resistance | 0.0055 | |||
ko05145 | Toxoplasmosis | 0.0062 | |||
ko05162 | Measles | 0.0094 | |||
ko00310 | Lysine degradation | 0.0118 | |||
ko04623 | Cytosolic DNA-sensing pathway | 0.0170 | |||
ko00380 | Tryptophan metabolism | 0.0181 | |||
ko05110 | Vibrio cholerae infection | 0.0201 | |||
ko04920 | Adipocytokine signaling pathway | 0.0221 | |||
ko05323 | Rheumatoid arthritis | 0.0285 |
KEGG Term | p-Value | Corrected p-Value |
---|---|---|
ko04622:RIG-I-like receptor signaling pathway | 0.0005 | 0.0459 |
ko00983:Drug metabolism—other enzymes | 0.0012 | 0.0459 |
ko00830:Retinol metabolism | 0.0012 | 0.0459 |
Name | Length | KO Name | KO ID | Description |
---|---|---|---|---|
BGIBMGA004606 | 507 | - | - | Heat shock protein hsp20.4 [Bombyx mori] |
BGIBMGA004882 | 759 | - | - | bmp-2 [Bombyx mori] |
BGIBMGA013238 | 1347 | - | - | P450 6B5-like|cytochrome P450 CYP6AE7 [Bombyx mori] |
BGIBMGA003907 | 402 | CYP3A | K07424 | Cytochrome P450 |
BGIBMGA003908 | 1044 | CYP9 | K15003 | P450 9e2-like|E-class P450, group II; Cytochrome P450 |
BGIBMGA010047 | 810 | - | - | Quinoprotein amine dehydrogenase, β chain-like |
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Xing, D.; Yang, Q.; Jiang, L.; Li, Q.; Xiao, Y.; Ye, M.; Xia, Q. RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection. Int. J. Mol. Sci. 2017, 18, 234. https://doi.org/10.3390/ijms18020234
Xing D, Yang Q, Jiang L, Li Q, Xiao Y, Ye M, Xia Q. RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection. International Journal of Molecular Sciences. 2017; 18(2):234. https://doi.org/10.3390/ijms18020234
Chicago/Turabian StyleXing, Dongxu, Qiong Yang, Liang Jiang, Qingrong Li, Yang Xiao, Mingqiang Ye, and Qingyou Xia. 2017. "RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection" International Journal of Molecular Sciences 18, no. 2: 234. https://doi.org/10.3390/ijms18020234