Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Insects
2.2. Measurement of Lac Secretion Rates
2.3. RNA Extraction and Sequencing
2.4. Data Analysis
2.5. De Novo Assembly and Gene Annotation
2.6. Quantitative PCR (qPCR) Analysis
2.7. Analysis of Differential Expression Gene (DEG)
2.8. Data Availability
3. Results
3.1. The Characteristics and Dynamic Regularity of K. chinensis
3.2. Overview of Transcriptomic Analyses
3.3. Genes Expressed Differentially between Insects at Different Stages
3.4. Reduced Protein Synthesis in Lac Secretion-Active Stages
3.5. Reduced and Unbalanced Central Metabolic Pathways
3.6. Shifted Metabolism of Fatty Acids, Lipids, and Terpenes
3.7. Candidate Genes Potentially Involved in Lac Synthesis and Secretion
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Chen, X.M.; Chen, Y.Q.; Zhang, H.; Shi, L. Lac Insects Breeding and Lac Processing; Chinese Forestry Press: Beijing, China, 2008. [Google Scholar]
- Chen, X.M. Biodiversity of Lac Insects; Yunnan Science and Technology Press: Yunnan, China, 2005. [Google Scholar]
- Chen, X.M.; Feng, Y. Lac insects. In An Introduction to Resource Entomology; Science Press: Beijing, China, 2009; Chapter 1; pp. 12–28. [Google Scholar]
- Rohmer, M. The mevalonate-independent methylerythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis, including carotenoids. Pure Appl. Chem. 1999, 12, 2279–2284. [Google Scholar] [CrossRef]
- Bede, J.C.; Teal, P.E.A.; Goodman, W.G.; Tobe, S.S. Biosynthetic Pathway of Insect Juvenile Hormone III in Cell Suspension Cultures of the Sedge Cyperus iria. Plant Physiol. 2001, 127, 584–593. [Google Scholar] [CrossRef] [PubMed]
- Hsieh, M.H.; Goodman, H.M. The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis. Plant Physiol. 2005, 2, 641–650. [Google Scholar] [CrossRef] [PubMed]
- Shamim, G.; Pandey, D.M.; Ramani, R.; Sharma, K.K. Identification of genes related to resin biosynthesis in the Indian lac insect, Kerria lacca (Hemiptera: Tachardiidae). Int. J. Trop. Insect Sci. 2014, 34, 149–155. [Google Scholar] [CrossRef]
- Ranjan, S.K.; Mallick, C.B.; Saha, D.; Vidyarthi, A.S.; Ramani, R. Genetic variation among species, races, forms and inbred lines of lac insects belonging to the genus Kerria (Homoptera, Tachardiidae). Genet. Mol. Biol. 2011, 34, 511–519. [Google Scholar] [CrossRef] [PubMed]
- Chen, H.; Chen, X.M.; Feng, Y.; Yang, Z.X. Cladistic Analysis of Phylogenetic Relationships among 7 Species of Lac Insects (Homoptera: Tachardiidae). For. Res. 2008, 5, 599–604. [Google Scholar]
- Chen, X.M.; Chen, H.; Feng, Y.; He, R.; Yang, Z.X. Status of Two Species of Lac Insects in the Genus Kerria from China Based on Morphological, Cellular, and Molecular Evidence. J. Insect Sci. 2011, 11, 106. [Google Scholar] [CrossRef]
- Shamim, G.; Ranjan, S.K.; Kandasamy, T.; Mohanasundaram, A.; Sharma, K.K.; Ramani, R. Phylogenetic study of Lac Insects of Kerria spp. using intron length polymorphism (EPIC-PCR). J. Entomol. Zool. Stud. 2014, 2, 258–264. [Google Scholar]
- Chen, H.; Chen, X.M.; Feng, Y.; He, R.; Zhang, W.F.; Yang, Z.X. Molecular phylogeny and biogeography of lac insects (Hemiptera: Kerriidae) inferred from nuclear and mitochondrial gene sequences. Mol. Biol. Rep. 2013, 10, 5943–5952. [Google Scholar] [CrossRef]
- Costechareyre, D.; Chich, J.F.; Strub, J.M.; Rahbé, Y.; Condemine, G. Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides. PLoS ONE 2013, 8, e54118. [Google Scholar] [CrossRef]
- Anathakrishnan, R.; KSinha, D.; Murugan, M.; Zhu, K.Y.; Chen, M.S.; Zhu, Y.C.; Smith, C.M. Comparative gut transcriptome analysis reveals differences between virulent and avirulent Russian wheat aphids, Diuraphis noxia. Arthropod Plant Interact. 2014, 8, 79–88. [Google Scholar] [CrossRef]
- Yang, P.; Zhu, J.Y.; Gong, Z.J.; Xu, D.L.; Chen, X.M.; Liu, W.W.; Lin, X.D.; Li, Y.F. Transcriptome Analysis of the Chinese White Wax Scale Ericerus pela with Focus on Genes Involved in Wax Biosynthesis. PLoS ONE 2012, 7, e35719. [Google Scholar] [CrossRef] [PubMed]
- Chen, H.; Juan, L.; Kai, C.; Lu, Q.; Wang, C.; Wu, H.X.; Yang, Z.X.; Ding, W.F.; Shao, S.X.; Wang, H.Y.; et al. Molecular mechanisms of tannin accumulation in Rhus galls and genes involved in plant-insect interactions. Sci. Rep. 2018, 8, 9841. [Google Scholar] [CrossRef] [PubMed]
- Liu, P.F.; Wang, W.W.; Ling, X.F.; Lu, Q.; Zhang, J.W.; He, R.; Chen, H. Regulation of Hormone-Related Genes in Ericerus pela (Hemiptera: Coccidae) for Dimorphic Metamorphosis. J. Insect Sci. 2019, 19. [Google Scholar] [CrossRef]
- Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.D.; et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 7, 644–652. [Google Scholar] [CrossRef]
- Kanehisa, M.; Araki, M.; Goto, S.; Hattori, M.; Hirakawa, M.; Itoh, M.; Katayama, T.; Kawashima, S.; Okuda, S.; Tokimatsu, T.; et al. KEGG for linking genomes to life and the environment. Nuclenic Acids Res. 2008, 36, 480–484. [Google Scholar] [CrossRef]
- Camacho, C.G.; Coulouris, V.; Avagyan, N.M.; Papadopoulos, J.; Bealer, K.; Madden, T.L. BLAST+: Architecture and applications. BMC Bioinform. 2009, 10, 421. [Google Scholar] [CrossRef]
- Kanehisa, M.; Goto, S. KEGG: Kyoto Encyclopaedia of Genes and Genomes. Nucleic Acids Res. 2002, 1, 27–30. [Google Scholar] [CrossRef]
- Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT Method. Methods 2001, 4, 402–408. [Google Scholar] [CrossRef]
- Anders, S.; Huber, W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11, R106. [Google Scholar] [CrossRef]
- Wang, L.; Feng, Z.; Wang, X.; Wang, X.; Zhang, X. DEGseq: An R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2010, 1, 136–138. [Google Scholar] [CrossRef] [PubMed]
- Brisson, J.A.; Richards, S. Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010, 8, e1000313. [Google Scholar] [CrossRef] [Green Version]
- Chen, Y.Q.; Chen, X.M.; Li, K.; Shi, L.; Chen, Z.Y. A study on population dynamics of lac insect and its lac secreting. J. Northwest For. Univ. 2005, 1, 170–174. [Google Scholar]
- Chen, X.M.; Feng, Y. Study on population density and secretion of lac insect. For. Res. 1993, 4, 462–465. [Google Scholar]
Database | Numbers of Unigene | Percent (%) |
---|---|---|
Nr | 54,037 | 29.38 |
Nt | 18,328 | 9.96 |
Swiss-Prot | 49,924 | 27.14 |
PFAM | 49,642 | 26.99 |
KEGG | 30,464 | 16.56 |
COG | 36,724 | 19.96 |
GO | 50,406 | 27.4 |
Annotated in all databases | 8950 | 4.86 |
Total unigenes | 183,899 | 100 |
Metabolic Pathway | Up | Down | ||
---|---|---|---|---|
Number | Average Log2 Fold | Number | Average Log2 Fold | |
Protein metabolism: Synthesis, modification, and degradation | ||||
Ribosomal proteins | 1 | 1.19 | 113 | −5.66 |
Initiation and elongation factors | 1 | 7.77 | 27 | −5.52 |
Chaperones and protein folding | 6 | 2.41 | 34 | −5.90 |
Proteases and protein degradation related | 9 | 1.66 | 75 | −5.47 |
Others | 0 | - | 1 | −5.52 |
Total | 17 | 3.26 | 250 | −5.61 |
Central metabolic pathways and energy metabolism | ||||
Glycolysis | 2 | 1.03 | 7 | −5.92 |
Citrate acid cycle (TCA cycle) | 4 | 1.38 | 14 | −5.12 |
Pentose phosphate pathways | 3 | 1.55 | 3 | −6.13 |
Respiratory chain and energy metabolism related | 2 | 1.02 | 37 | −5.81 |
Others | 0 | - | 9 | −4.99 |
Total | 22 | 1.25 | 70 | −5.59 |
Non-central metabolic pathways | ||||
Metabolism of fatty acids, lipids, terpenes | 24 | 1.96 | 23 | −4.68 |
Metabolism of nitrogen compounds | 9 | 2.01 | 22 | −5.31 |
UDP-glucuronosyl and UDP-glucosyl transferase | 4 | 1.72 | 0 | |
Other metabolism | 6 | 2.03 | 32 | −4.92 |
Total | 43 | 1.93 | 77 | −4.97 |
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Wang, W.; Liu, P.; Lu, Q.; Ling, X.; Zhang, J.; Chen, M.-S.; Chen, H.; Chen, X. Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses. Insects 2019, 10, 430. https://doi.org/10.3390/insects10120430
Wang W, Liu P, Lu Q, Ling X, Zhang J, Chen M-S, Chen H, Chen X. Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses. Insects. 2019; 10(12):430. https://doi.org/10.3390/insects10120430
Chicago/Turabian StyleWang, Weiwei, Pengfei Liu, Qin Lu, Xiaofei Ling, Jinwen Zhang, Ming-Shun Chen, Hang Chen, and Xiaoming Chen. 2019. "Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses" Insects 10, no. 12: 430. https://doi.org/10.3390/insects10120430
APA StyleWang, W., Liu, P., Lu, Q., Ling, X., Zhang, J., Chen, M. -S., Chen, H., & Chen, X. (2019). Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses. Insects, 10(12), 430. https://doi.org/10.3390/insects10120430