title: Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A.
abstract: Salmonella Paratyphi A (S. Paratyphi A) is a highly adapted, human-specific pathogen that causes paratyphoid fever. Cases of paratyphoid fever have recently been increasing, and the disease is becoming a major public health concern, especially in Eastern and Southern Asia. To investigate the genomic variation and evolution of S. Paratyphi A, a pan-genomic analysis was performed on five newly sequenced S. Paratyphi A strains and two other reference strains. A whole genome comparison revealed that the seven genomes are collinear and that their organization is highly conserved. The high rate of substitutions in part of the core genome indicates that there are frequent homologous recombination events. Based on the changes in the pan-genome size and cluster number (both in the core functional genes and core pseudogenes), it can be inferred that the sharply increasing number of pseudogene clusters may have strong correlation with the inactivation of functional genes, and indicates that the S. Paratyphi A genome is being degraded.
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
authors.forename: Weili
authors.initials: W
authors.lastname: Liang
authors.forename: Yongbing
authors.initials: Y
authors.lastname: Zhao
authors.forename: Chunxia
authors.initials: C
authors.lastname: Chen
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Cui
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.forename: Biao
authors.initials: B
authors.lastname: Kan
mesh_terms: D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012482:Salmonella paratyphi A / Q000235:genetics*