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針對鏈球菌屬泛基因體的大規模比較分析顯示特定功能支配性

為了解決Dell G5的問題，作者林依璿 這樣論述：

Members of the genus Streptococcus have diverse habitats, including beneficial bacteria used in food fermentation, normal flora in animals and humans, and important pathogenic bacteria capable of infecting humans and a wide range of animals. In human, Streptococcus colonized different parts of the

body, and streptococcal infection can cause a variety of diseases. Although not normally viewed as a standard model microorganism, Streptococcus is the most sequenced bacterial genus to date. There is an immense interest on the various Streptococcus species by the scientific community and post a cli

nical importance on the understanding of this group of bacteria. The purpose of the present study was to understand the functional rationale underlying proteins with varying magnitudes of conservation among Streptococcus species. This research use comparative genomics to analyze the genomes and char

acterize the orthologous relations of the predicted genes of 52 fully sequenced Streptococcus strains. The computer-based analysis allows fast identification of genomic features that have been highly conserved in multiple streptococcal species, as well as less conserved and unique genes that give ea

ch organism its own novel characteristics. I used the phylogenetic and pan-genome concepts to evaluate the overall genomic variations of the Streptococcus. The evolutionary clades generated from both 16S rRNA single gene and concatenated core genes approaches showed concordance with the taxonomic cl

assification. Based on the 52 genomes analyzed in this study, the size of the streptococcal pan-genome exceeds 10,000 genes, which is five times the average streptococcal genome size. The regression analysis suggests an open pan-genome of this genus. The species boundary of the genus Streptococcus i

s a continuum as the variable genes make up about 77% of a genome. Beside the core (17%) and unique (6%) genes, the variable genes were further divided into three subtypes, group-core, group-distributed and distributed, depending on the degree of protein conservation within the 12 streptococcal grou

ps. Functional analysis using COG and KO showed comparable results. The core and distributed genes generally encode proteins with known functions whereas group-specific and unique genes are significantly under-annotated. I used two pattern/motif-based strategies to infer putative biological function

ality. The first involves the prediction of subcellular localization, and the second uses protein domain to infer protein function. The proteins encoded by core genes are significantly enriched in cytoplasm. The group-specific and unique genes encode proteins that reside mostly in non-cytoplasmic co

mpartments, especially on bacterial cell wall and secreted into extracellular space. Protein domain analysis showed ABC transporter components and the other surface-associated protein domains are amongst the top predicted protein domain in group-specific proteins. Group-specific and unique proteins

are also found to significantly harbor tandem repeats of certain Pfam domains. This type of domain architecture is especially associated with surface-exposed membrane, cell wall and secretory proteins. In summary, this dissertation explored the ability to extract genus-, group- and strain-specific b

iological features from streptococcal genome comparison. The delineation of the genus Streptococcus using comparative genomics approaches is a step forward in our understanding of the biological functions of the proteins in this group of medically important microorganisms.