Identification and Characterization of the CPP Gene Family in the Genome of Aedes aegypti L. (Yellow Fever Mosquito) (Diptera: Culicidae)

Yıl 2023, Cilt: 27 Sayı: 6, 1174 - 1184, 18.12.2023

Murat Turan

https://doi.org/10.16984/saufenbilder.1338063

Öz

Aedes aegypti is an important vector organism responsible for carrying numerous arboviral pathogens and serious diseases, including yellow fever, Zika, Chikungunya, and Dengue fever. The CPP gene family, one of the crucial molecular defense systems, plays a significant role in the regulation of growth and development by controlling the production of proteins. In this study, a comprehensive genome analysis of the CPP gene family in Ae. aegypti was conducted. Each gene was thoroughly characterized, gene structures were examined, and conserved motifs were investigated. Additionally, the properties of these proteins were comprehensively analyzed. Expression analyses were performed to reveal the effects of CPP genes on development by calculating Reads Per Kilobase Million (RPKM) values. The findings emphasize the importance of CPP genes in controlling arboviral pathogens and understanding general stress responses in insects. The information derived from this research could contribute to the development of more effective intervention strategies for Ae. aegypti and other vector carriers to cope with stress. In conclusion, the systematic analysis of the CPP gene family in the Ae. aegypti genome is a crucial step in the management and development of effective disease prevention strategies for this species. Moreover, this study provides a significant foundation for future functional genomics research in understanding the structure and function of CPP genes.

Anahtar Kelimeler

Aedes aegypti, CPP gene family, Yellow fever mosquito, Characterization

Teşekkür

The author would like to thank Dr. Emre İlhan for his contributions.

Kaynakça

• [1] U. Ullah, Z. A. Buttar, A. Shalmani, I. Muhammad, A. Ud-Din, H. Ali, “Genome-wide identification and expression analysis of CPP-like gene family in Triticum aestivum L. under different hormone and stress conditions”, Open Life Sciences, vol. 17, pp. 544-562, 2022.
• [2] L. Zhang, H. K. Zhao, Y. M. Wang, C. P. Yuan, Y. Y. Zhang, H. Y. Li, X. F. Yan, Q. Y. Li, Y. S. Dong, “Genomewide identification and expression analysis of the CPP-like gene family in soybean”, Genetics and Molecular Research, vol. 14, no.1, pp. 1260- 1268, 2015.
• [3] T. Lu, Y. Dou, C. Zhang, “Fuzzy clustering of CPP family in plants with evolution and interaction analyses”, BMC Bioinformatics, vol. 14, no. Suppl 13, S10, 2013.
• [4] Z. Yang, S. Gu, X. Wang, W. Li, Z. Tang, C. Xu, “Molecular Evolution of the CPP-like Gene Family in Plants: Insights from Comparative Genomics of Arabidopsis and Rice”, Journal of Molecular Evolution, vol. 67, pp. 266- 277, 2008.
• [5] Y. Zhou, L. Hu, S. Ye, L. Jiang, S. Liu, “Genome-wide identification and characterization of cysteine-rich polycomb-like protein (CPP) family genes in cucumber (Cucumis sativus) and their roles in stress responses”, Biologia, vol. 73, pp. 425-435, 2018.
• [6] A. Rakhimzhanova, A. G. Kasapoğlu, A. Sapakova, E. İlhan, R. Zharmukhametova, M. Turan, L. Zekenova, S. Muslu, L. Kazhygeldiyeva, M. Aydın, A. Çiltaş, “Expression analysis and characterization of the CPP gene family of Melatonin-treated common bean cultivars under different abiotic stresses,” South African Journal of Botany, vol. 160, pp. 282-294, 2023.
• [7] M. Li, F. Wang, J. Ma, H. Liu, H. Ye, P. Zhao, J. Wang, “Comprehensive Evolutionary Analysis of CPP Genes in Brassica napus L. and Its Two Diploid Progenitors Revealing the Potential Molecular Basis of Allopolyploid Adaptive Advantage Under Salt Stress”, Frontiers in Plant Science, vol. 13, 873071, 2022.
• [8] Y. Sun, X. Jia, D. Chen, Q. Fu, J. Chen, W. Yang, H. Yang, X. Xu, “GenomeWide Identification and Expression Analysis of Cysteine-Rich Polycomblike Protein (CPP) Gene Family in Tomato”, International Journal of Molecular Sciences, vol. 24, 5762, 2023.
• [9] X. Y. Song, Y. Y. Zhang, F. C. Wu, L. Zhang, “Genome-wide analysis of the maize (Zea may L.) CPP-like gene family and expression profiling under abiotic stress”, Genetics and Molecular Research, vol. 15, no. 3, gmr.15038023, 2016.
• [10] F. Ding, J. Fua, D. Jiang, M. Hao, G. Lina, “Mapping the spatial distribution of Aedes aegypti and Aedes albopictus”, Acta Tropica, vol. 178, pp. 155–162, 2018.
• [11] J. Vontas, E. Kioulos, N. Pavlidi, E. Morou, A. della Torre, H. Ranson, “Insecticide resistance in the major dengue vectors Aedes albopictus and Aedes aegypti”, Pesticide Biochemistry and Physiology, vol. 104, pp. 126–131, 2012.
• [12] C. Lowenberger, “Innate immune response of Aedes aegypti”, Insect Biochemistry and Molecular Biology, vol. 31, pp. 219–229, 2001.
• [13] M. I. Salazar, J. H. Richardson, I. Sánchez-Vargas, K. E. Olson, B. J. Beaty, “Dengue virus type 2: replication and tropisms in orally infected Aedes aegypti mosquitoes”, BMC Microbiology, vol. 7, 9, 2007.
• [14] B. Kamgang, S. Marcombe, F. Chandre, E. Nchoutpouen, P. Nwane, J. Etang, V. Corbel, C. Paupy, “Insecticide susceptibility of Aedes aegypti and Aedes albopictus in Central Africa”, Parasites & Vectors, vol. 4, 79, 2011.
• [15] D. J. Gubler, G. G. Clark, “Community involvement in the control of Aedes aegypti”, Acta Tropica, vol. 61, pp. 169-179, 1996.
• [16] K. Kamimura, I. T. Matsuse, H. Takahashi, J. Komukai, T. Fukuda, K. Suzuki，M. Aratani, Y. Shirai, M. Mogi, “Effect of temperature on the development of Aedes aegypti and Aedes albopictus”, Medical Entomology and Zoology, vol. 53, no. 1, pp. 53-58, 2002.
• [17] S. Leta, T. J. Beyene, E. M. De Clercq, K. Amenu, M. U. G. Kraemer, C. W. Revie, “Global risk mapping for major diseases transmitted by Aedes aegypti and Aedes albopictus”, International Journal of Infectious Diseases, vol. 67, pp. 25–35, 2018.
• [18] B. J. Matthews, O. Dudchenko, S. B. Kingan, S. Koren, I. Antoshechkin, J. E. Crawford, W. J. Glassford, M. Herre, S. N. Redmond, N. H. Rose, G. D. Weedall, Y. Wu, S. S. Batra, C. A. Brito-Sierra, S. D. Buckingham, C. L. Campbell, S. Chan, E. Cox, B. R. Evans, T. Fansiri, et al., “Improved reference genome of Aedes aegypti informs arbovirus vector control”, Nature, vol. 563, no. 7732, pp. 501-507, 2018.
• [19] A. Compton, J. Liang, C. Chen, V. Lukyanchikova, Y. Qi, M. Potters, R. Settlage, D. Miller, S. Deschamps, C. Mao, V. Llaca, I. V. Sharakhov, Z. Tu, “The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere”, G3 (Bethesda), vol. 10, no. 10, pp. 3811-3819, 2020.
• [20] A. Zamyatin, P. Avdeyev, J. Liang, A. Sharma, C. Chen, V. Lukyanchikova, N. Alexeev, Z. Tu, M. A. Alekseyev, “Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis”, Gigascience, vol. 10, no. 3, giab017, 2021.
• [21] J. Ghurye, S. Koren, S. T. Small, S. Redmond, P. Howell, A. M. Phillipy, N. J. Besansky, “A chromosome-scale assembly of the major African malaria vector Anopheles funestus”, Gigascience., vol. 8, no. 6, giz063, 2019.
• [22] O. Dudchenko, S. S. Batra, A. D. Omer, S. K. Nyquist, M. Hoeger, N. C. Durand, M. S. Shamim, I. Machol, E. S. Lander, A. P. Aiden, E. L. Aiden, “De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds”, Science, vol. 356, no. 6333, pp. 92-95, 2017.
• [23] E. S. Tvedte, M. Gasser, B. C. Sparklin, J., Michalski, C. E. Hjelmen, J. S. Johnston, X. Zhao, R. Bromley, L. J. Tallon, L. Sadzewicz, D. A. Rasko, J.C. Dunning Hotopp, “Comparison of long read sequencing technologies in interrogating bacteria and fly genomes”, G3 (Bethesda), vol. 11, no. 6, jkab083, 2021.
• [24] M. D. Adams, S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne, P. G. Amanatides, S. E. Scherer, P. W. Li, R. A. Hoskins, R. F. Galle, R. A. George, S. E. Lewis, S. Richards, M. Ashburner, S. N. Henderson, G. G. Sutton, J. R. Wortman, M. D. Yandell, Q. Zhang, L. X. Chen, et al., “The genome sequence of Drosophila melanogaster”, Science, vol. 287, no. 5461, pp. 2185-2195, 2000.
• [25] I. Letunic, S. Khedkar, P. Bork, “SMART: recent updates, new developments and status in 2020”, Nucleic Acids Research, vol. 49, pp. D458–D460, 2021.
• [26] J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, D. G. Higgins, “The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools”, Nucleic Acids Research, vol. 25, pp. 4876-4882, 1997.
• [27] I. Letunic, P. Bork, “Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation”, Nucleic Acids Research, vol. 49, pp. W293–W296, 2021.
• [28] T. A. Hall, “BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT”, Nucleic Acids Symposium Series, vol. 41, pp. 95-98, 1999.
• [29] C. Chen, H. Chen, Y. Zhang, H. R. Thomas, M. H. Frank, Y. He, R. Xia, “TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data”, Molecular Plant, vol. 13, no. 8, pp. 1194-1202, 2020.
• [30] E. Gasteiger, C. Hoogland, A. Gattiker, S. Duvaud, M. R. Wilkins, R. D. Appel, A. Bairoch, “Protein Identification and Analysis Tools on the Expasy Server,” In John M. Walker (Ed): The Proteomics Protocols Handbook, Humana Press, pp. 571-607, 2005.
• [31] V. Thumuluri, J. J. A. Armenteros, A. R. Johansen, H. Nielsen, O. Winther, “DeepLoc 2.0: multi-label subcellular localization prediction using protein language models”, Nucleic Acids Research, vol. 50, no. W1, pp. W228– W234, 2022.
• [32] B. Hu, J. Jin, A. Y. Guo, H. Zhang, J. Luo, G. Gao, “GSDS 2.0: an upgraded gene feature visualization server,” Bioinformatics, vol. 31, pp. 1296- 1297, 2015.
• [33] T. L. Bailey, N. Williams, C. Misleh, W. W. Li, “MEME: discovering and analyzing DNA and protein sequence motifs,” Nucleic Acids Research, vol. 34, pp. W369-W373, 2006.
• [34] A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, pp. 621-628, 2008.