Coronavirus Phylogeny Analysis Based On Z-curve Theory

With the rapid development of human and other model organism genome-sequencing projects, more and more whole genomic sequences are available. It's reasonable to believe that the accumulation of large amount of sequence data will lead to a great breakthrough in theory. But the data are not equal to knowledge, how to extract useful information is a most important problem. Z-curve is a powerful tool to analyze the genomic sequences intuitively. Based on the Z-curve theory, a genome can be uniquely represented by a three dimensional space curve. The global and local features can be grasped at a glance. Z-curve theory is the theoretical foundation of this paper. It is introduced briefly at the beginning of chapter III. In this paper a new method based on the Z-curve parameters to analyze the coronavirus phylogeny is proposed.In chapter I, we mainly introduced the background of bioinformatics and its development. Some biology knowledge used in this paper is also introduced briefly in this charpter.The chapter II is mainly about the molecular evolution and phylogenetics. In this chapter, some important concepts of molecular evolution, methods of phylogeny research and approaches of phylogenetic tree construction are introduced briefly. The content of this chapter is useful to chapter III.The chapter III is the most important part of this paper. In this chapter, a new systematic way of inferring evolutionary relatedness among coronaviruses including SARS-CoVs from different hosts is proposed, which is based on all coding sequences. This method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The Z-curve parameters used in this approach are from a further development of the Z-curve methodology. A DNA sequence can be represented by a series of Z-curve parameters. Comparing these Z-curve parameters of different species can get their evolutionary distance, and after the distances of every two species are figured out, an evolutionary distance matrix can be acquired. Through the matrix the phylogenetic trees can be reconstructed. The results with this method not only reflected the relatedness of SARS-CoV and other coronaviruses but also opened out the revolution process of SARS-CoVs. In addition, to repeat the two tasks, we also made use of the codon usage rates derived from coronavirus RdRp genes and all...