Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 30135
Computing the Similarity and the Diversity in the Species Based on Cronobacter Genome

Authors: E. Al Daoud

Abstract:

The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.

Keywords: Genome, species, blastp, conserved genes, cronobacter.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1314484

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 363

References:


[1] L. Sian, “Brain evolution: Genetic layering,” Nature reviews Neuroscience. Vol.18, No. 6, pp 324-324, 2017.
[2] P. Blanco-Arias, C. A. Sargent, and N. A. Affara, “A comparative analysis of the pig, mouse, and human” PCDHX genes. Mamm. Genome. Vol 15, pp 296–306, 2004.
[3] A. Varki1 and K. T. Altheide “Comparing the human and chimpanzee genomes: Searching for needles in a haystack,” Genome Res. Vol. 15, pp 1746-1758, 2005.
[4] Z. He, D. Han, O. Efimova, P. Guijarro, Q. Yu, A. Oleksiak, S. Jiang, K. Anokhin, B. Velichkovsky, S. Grünewald, et al. “Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques,” Nat. Neurosci Vol. 20, pp 886–895, 2017.
[5] J. R. Dixon, D. U. Gorkin, B. Ren, “Chromatin Domains: The Unit of Chromosome Organization,” Mol Cell Vol. 62, pp 668–680, 2016.
[6] B. I. Bae, D. Jayaraman, C. A. Walsh “Genetic changes shaping the human brain” Dev Cell Vol 32, pp 423–434, 2015.
[7] B. B. Lake, “Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain,” Science Vol. 352, pp 1586–1590, 2016.
[8] A. Peltzer, G. Jäger, A. Herbig, A. Seitz, C. Kniep, J. Krause and K. Nieselt, "EAGER: efficient ancient genome reconstruction," Genome Biol. Vol. 17, No. 1, pp 60-74, 2016.
[9] M. A. McMahon, M. Rahdar, M. Porteus “Gene editing: not just for translation anymore,” Nat Methods Vol. 9, pp 28–31, 2012.
[10] L. Pozzi, C. M. Bergey and A. S. Burrell, “The use (and misuse) of phylogenetic trees in comparative behavioral analyses,” International Journal of Primatology, Vol 35, pp 32–54, 2014.
[11] B. Buchfink, C. Xie, and D. H. Huson, “Fast and sensitive protein alignment using DIAMOND,” Nat. Methods, Vol. 12, pp 59–60, 2015.
[12] D. He, O. Fiz-Palacios, C. J. Fu, J. Fehling, C. C. Tsai and S. L. Baldauf, “An alternative root for the eukaryote tree of life,” Curr Biol, Vol 24 pp 465-470, 2014.
[13] KEGG, http://www.genome.jp/kegg/catalog. Last access on October, 2017.