Yu Bai
ABSTRACT
The flour beetles Tribolium castaneum (Herbst) was noted as an important model organism for studies of insect physiology, for pest control and other topic[1]. As a product pest, T. castaneum is widely distributed all over the world. We reported and analyzed the genomic characteristics of local T. castaneum using next-generation sequencing. It is hoped to carry out pest control through its variation characteristics of SNP, Indel, SV and CNV. Through the variation detection, it was found that there were a lot of variations in the energy metabolism pathway, which was closely related to the antioxidant and cold resistance. It can be used as a genomic variation level reference for the subsequent prevention and control of local T. castaneum.
- Dippel, S., Oberhofer, G., Hu, Y., Schwirz, J., Schacht, M., Lehmann, S., Montino, A., Posnien, N., ... Bucher, G. (2020). Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC genomics, 21(1), 47.Google Scholar
- Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754--1760. Google ScholarDigital Library
- Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England), 25(16), 2078--2079. Google ScholarDigital Library
- Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., Shi, X., Fulton, R. S., Ley, T. J., Wilson, R. K., Ding, L., & Mardis, E. R. (2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature methods, 6(9), 677--681.Google Scholar
- Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011). CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome research, 21(6), 974--984.Google Scholar
- Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research, 38(16), e164.Google Scholar
Index Terms
- Resequencing and Analysis of Whole Genome of Local Tribolium castaneum Using Next-generation Sequencing
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