Capsule-forming extracellular polysaccharides are crucial for bacterial host colonization, invasion, immune evasion, and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important foodborne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, whereas disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups and expanded its new 3′-border by identifying glpX as a key gene conserved across all K-serogroups. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication is likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. This is the first time, to the best of our knowledge, that a large scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus and provide a framework for developing diagnostically relevant serotyping methods.

22Capsule-forming extracellular polysaccharides are crucial to bacterial host colonization, 23 invasion, immune evasion and ultimately pathogenicity. Due to warming ocean waters and human 24 encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally 25 important food-borne enteropathogen implicated in acute gastroenteritis, wound infections, and 26 septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and 27 capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. 28 parahaemolyticus, while disclosure of genetic elements encoding 13 O-serogroups have allowed 29 molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 30 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. 31 parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic 32 structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole 33 genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene 34 cluster across different K-serogroups, and expanded its new right-border by identifying glpX as a 35 key gene conserved across all serotypes. A total of 217 genes involved in CPS biosynthesis were 36 annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based 37 on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene 38 clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, 39 gene duplication and nonsense mutations are likely to play instrumental roles in the evolution of 40 CPS in V. parahaemolyticus. It is the first time, to the best of our knowledge, that a large-scale of 41 CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and 3 42 characterized in evolutionary contexts. This work should help advance understanding on the 43 variation of CPS in V. parahaemolyticus, and provide a framework for developing diagnostically 44 relevant serotyping methods. 45 46 Author summary 47 Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio 48 parahaemolyticus has emerged as a globally important food-borne enteropathogen. However, the 49 genetic structure of CPS loci for 71 K-serogroups V. parahaemolyticus have remained 50 unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. 51In this study, we identified and characterized the genetic structure of CPS loci of 40 K-serogroups 52 through whole genome sequencing of 443 V. parahaemolyticus strains. We expanded and 53 identified its new right-border by identifying glpX as a key gene conserved across all serotypes. 54We proposed an evolution model of the CPS gene clusters of 40 K-serogroups. We also found 55 horizontal gene transfer by recombination from other Vibrio species, gene duplication and 56 nonsense mutations are likely to play...

Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes. Here, we generated 121X stLFR co-barcode clean reads and 18X Oxford Nanopore MinION reads and obtained a 595 Mb Mekong tiger perch genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes is more closely related to Sciaenidae than to Tetraodontiformes, resolving a long-time dispute. We depicted the genes involved in pigment development in Mekong tiger perch and results confirmed that the four rate-limiting genes of pigment synthesis had been retained after fish-specific genome duplication. We also estimated the demographic history of Mekong tiger perch, which showed that the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogenetic position of Lobotiformes and biological conservation.