Phylogenomics And Comparative Phylogeny Analysis In The Genus Streptomyces

Streptomyces is the main component of the terrestrial microbiota and the largest group of prokaryotic microbes and rich in species diversity.Because it is the major sources of various active secondary metabolites,Streptomyces has been a major group for research and excavation in the study of prokaryotic microorganisms resources.In the early days,because of the need for patenting and the lack of uniform classification and identification standards,a large number of new species have been described,which directly led to the problem of over-classification of species in the group.Due to the huge numbers of described species and particularity of the genome(large genome and complex structure of secondary metabolic gene clusters),the existing analysis methods cannot perform orthologous inferring on them,resulted that the phylogenomic trees of this genus base on Supermatrix cannot be obtained.For solving this problem,in this paper design a new orthologous inference algorithm——MGFinder.The MGFinder algorithm uses network analysis methods to perform gene family analysis on 382 available whole genome sequences of genus Streptomyces,based on the theoretical concept of orthologous genes.After feasibility analysis and parameter test adjustments,39 orthologous gene could be obtained using MGFinder,which effectively solved the problem of orthologous gene inference.Based on the inferred orthologous gene family,phylogenetic analysis of Streptomyces species was performed,revealing the phylogenetic relationship between Streptomyces species on genomics.Simultaneously,the results of ORGIs(Overall Genome-Related Indexs),phylogeny and phenotypic features comparison,according to rules of ICNP(International Code of Nomenclature of Prokaryotes),reveal that 29 Streptomyces species were proposed to be reclassified as later heterotypic synonyms,further improving the problem of over-classification of Streptomyces.Because of the morphological development of Streptomyces is an important feature of this group,so studying the evolution process of its morphological development is of great significance for understanding the systematic evolution of Streptomyces.In this study,we focus on the key genes related to morphological development,comparative phylogenetic analysis was used to compare the phylogenetic history of morphological genes with the genome-based species,revealed the evolutionary history of morphological development and its relationship with speciational evolution among Streptomyces species.