How can Sequence Alignment Method Affect the Phylogenetic Relationship Results?
Keywords:
bioinformatics, software, Geneious, NCBI, geneticsAbstract
Sequence alignment is a fundamental step before analysing the phylogenetic relationships between organisms. The effect of the alignment method on the phylogenetic relationship results has not been well studied. Three methods for sequence alignment are available in Geneious software: (1) Geneious alignment, (2) ClustalW, and (3) MUSCLE. The study aimed to investigate the impacts of these three alignment methods on the phylogenetic relationships between test organisms. Therefore, the phylogenetic tree was established for the same organisms (honey bee species and subspecies) after using the three alignment methods, and then the results were compared. The constructed tree after using ClustalW differed than Geneious alignment and MUSCLE without a clear effect on relationship between the closely related organisms. Based on this study, it is better for researchers to test different alignment methods before constructing the final phylogenetic tree to select the most suitable one.
References
Abou-Shaara, H.F., Bayoumi, S.R. Using mitochondrial DNA similarity percentages to analyze the maternal source of hybrid bees from two honey bee subspecies. Scientific Papers: Animal Science and Biotechnologies, 2019, 52, 32-40.
Eimanifar, A., T. Kimball, R., L. Braun, E., Ellis, J. D., The complete mitochondrial genome of the Cape honey bee, Apis mellifera capensis Esch.(Insecta: hymenoptera: apidae). Mitochondrial DNA Part B, 2016, 1, 817-819. https://doi.org/10.1080/23802359.2016.1241682
Eimanifar, A., T. Kimball, R., L. Braun, E., M. Moustafa, D., Haddad, N., Fuchs, S., Grunewald, B., Ellis, J. D., The complete mitochondrial genome of the Egyptian honey bee, Apis mellifera lamarckii (Insecta: Hymenoptera: Apidae). Mitochondrial DNA Part B, 2017a, 2, 270-272. https://doi.org/10.1080/23802359.2017.1325343
Abou-Shaara, H.F. A scientific note on the evolutionary relationships between honey bees and their enemies. Agronomical Research in Moldavia, 2018, 51, 101-107. https://doi.org/10.2478/cerce-2018-0009
Takahashi, J. I., Rai, J., Wakamiya, T., Okuyama, H., Characterization of the complete mitochondrial genome of the giant black Himalayan honeybee (Apis laboriosa) from Nepal. Conservation Genetic Resources, 2018, 10, 59-63. https://doi.org/10.1007/s12686-017-0765-6
Abou-Shaara, H.F. Utilizing bioinformatics to detect genetic similarities between African honey bee subspecies. Journal of Genetics, 2019, 98, 96. https://doi.org/10.1007/s12041-019-1145-7
Thompson, J. D., Gibson, T. J., Higgins, D. G., Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics, 2003, 1, 2-3. https://doi.org/10.1002/0471250953.bi0203s00
Edgar, R. C., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 2004, 32, 1792-1797. https://doi.org/10.1093/nar/gkh340
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Mentjies, P., Drummond, A. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 2012, 28, 1647-1649. https://doi.org/10.1093/bioinformatics/bts
Haddad, N., Adjlane, N., Loucif-Ayad, W., Dash, A., Rajashekar, B., Al-Nakeeb, K., Sicheritz-Ponten, T., Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae). Mitochondrial DNA Part B, 2017, 2, 548-549. https://doi.org/10.1080/23802359.2017.1365647
Gibson, J. D., Hunt, G. J., The complete mitochondrial genome of the invasive Africanized honey bee, Apis mellifera scutellata (Insecta: Hymenoptera: Apidae). Mitochondrial DNA Part A, 2016, 27, 561-562. https://doi.org/10.3109/19401736.2014.905858
Haddad, N. J., Mitochondrial genome of the Levant Region honeybee, Apis mellifera syriaca (Hymenoptera: Apidae). Mitochondrial DNA Part A, 2016, 27, 4067-4068. https://doi.org/10.3109/19401736.2014.1003846
Eimanifar, A., Kimball, R. T., Braun, E. L., Fuchs, S., Grünewald, B., Ellis, J. D., The complete mitochondrial genome and phylogenetic placement of Apis nigrocincta Smith (Insecta: Hymenoptera: Apidae), an Asian, cavity-nesting honey bee. Mitochondrial DNA Part B, 2017b, 2, 249-250. https://doi.org/10.1080/23802359.2017.1318683
Tan, H. W., Liu, G. H., Dong, X., Lin, R. Q., Song, H. Q., Huang, S. Y., Yuan,Z.G., Zhao,G.H., Zhu, X. Q., The complete mitochondrial genome of the Asiatic cavity-nesting honeybee Apis cerana (Hymenoptera: Apidae). Plos one, 2011, 6, e23008. https://doi.org/10.1371/journal.pone.0023008
Wakamiya, T., Tingek, S., Okuyama, H., Kiyoshi, T., Takahashi, J. I., The complete mitochondrial genome of the cavity-nesting honeybee, Apis koschevnikovi (Insecta: Hymenoptera: Apidae). Mitochondrial DNA Part B, 2017, 2, 24-25. https://doi.org/10.1080/23802359.2016.1275847
Wang, A. R., Kim, M. J., Park, J. S., Choi, Y. S., Thapa, R., Lee, K. Y., Kim, I., Complete mitochondrial genome of the dwarf honeybee, Apis florea (Hymenoptera: Apidae). Mitochondrial DNA, 2013, 24, 208-210. https://doi.org/10.3109/19401736.2012.744986
Arias, M.C., Sheppard, W.S. Phylogenetic relationships of honey bees (Hymenoptera: Apinae: Apini) inferred from nuclear and mitochondrial DNA sequence data. Molecular Phylogenetic and Evolution, 2005, 37, 25-35. https://doi.org/10.1016/j.ympev.2005.02.017.
