- Genomic Islands (GIs) are one of the most important mobile components that quickly help bacteria acquire large fragments of foreign genes. - multocida are unknown in the evolution of bacterial populations.. - multocida , the GIs accounted for 5.8% of the core genes in the pan-genome, mainly related to functional metabolic activities. - multocida evolution and adaptation to the environment are reflected by the proportion and function of the pan-genome acquired from GIs, and the large quantities of GI data will aid in additional population genetics studies.. - 10 kb) acquired through horizontal gene transfer (HGT) between different hosts, that might in- crease the versatility and adaptability of the recipient and enable certain bacteria to occupy entirely new niches. - Full list of author information is available at the end of the article. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - are divided into pathogenicity, resistance, xenobiotic- degradation, metabolic, symbiosis or fitness islands by the environmental context of the bacterium and the one or more important functional genes among them [13, 14].. - Apart from containing gap aligned areas, the average gen- ome length of the donors was 2,323,144 bp, ranging from 2.20 to 2.70 Mbp. - The quantity of the encoded proteins ranged from 1903 (Razi 0002, avian) to 2313 (FDAARGOS_261, human). - multocida, a comparison of the 114 isolates with each other discerned 3948 COGs (Cluster of orthologous genes) in the pan-genome. - The core set of the pan-genome was at a rate of COGs), and the dispensable genes was COGs). - multocida fluctuated slightly with the increase of the strain. - most of the cases were close to zero, and the unique genes increased in pro- portion with the increase of strains, and thus, the ability of the strain to obtain foreign elements was stable (Fig. - A functional clustering of the pan-genome was per- formed with COG (Fig. - The sizes of the pan-genome and core genes are plotted as a function of the number (n) of strains sequentially added. - the accessory genes of the pan-genome, were more relevant for information stor- age, processing and metabolism, such as carbohydrate transport and metabolism and cell wall or cell mem- brane biosynthesis. - distinguishing characteristics were determined accord- ing to the separation site and the sequence classifica- tion in the phylogenetic tree (Fig. - Comparing the results of the core genes with the MLST (Additional file 5: Figure S2), the classification results and the STs of these strains were consistent, meaning they were in the same branch or extremely adjacent branches, as la- belled with the same colour in the diagram (Fig. - The number of new genes and unique genes as a function of the number of sequenced genomes, respectively. - 3 Characterization of the gene sets of all strains showing diverse function. - The height of each column rectangle represents the proportion of the functional categories. - Two ST13, ATCC 43137 and HB03 of the 5 swine-sourced were aggregated, and 1 ST74, 3480, and 1 ST50, HN06, were clustered. - Three of the 4 human-sourced strains were significantly dif- ferent from all other strains and clustered into one group, while SMC1 was close but not in the same large branch. - Circle 2 shows the different geographical locations of the strain in the key colours on the right side, including North America (America and Canada), Asia (China, Thailand, India, Sri Lanka, Pakistan, Malaysia, and Iran), Europe (UK and France), South America (Peru) and unknown geographic sources (Table S1). - Circle 3 shows the host source of the isolates. - The regions of GIs without precise starting point were predicted and the interrupted GI fragments were dis- carded totally because of the limitations of the strains sequence themselves. - ICE accounted for 11% (32) of the total.. - Due to the differences in software re- arrangement in the prediction of the draft genome strains, only the GI regions of the 17 complete genome strains were compared with their predicted prophage area, and of the possible phage regions were found to be approximately the same as those of the GIs (Additional file 10: Table S7). - The particular correlation of the population genome and GIs By comparing the core genes of the pan-genome of P.. - multocida with the genes contained in the GIs,. - approximately 5.8% (55) of the functional core genes were detected in the GIs. - These genes existed in the non-gene island region of the same host strain many times and in the GIs region only at the two ends of the GI. - In the accessory gene set, approximately of the func- tional genes existed in the GIs. - Similar to the main functional categories of the accessory gene set, the GI genes were compared with the general situation of the accessory gene set in the GIs by GO annota- tion and were mainly related to biological processes and cellular component (Fig. - The unique genes in the strains were compared with those con- tained in GIs, and 200 of the 565 unique genes were found in the GIs, accounting for approximately 35.4% of the total. - The functional proportions of all gene sets of the 280 GIs and the size regions occu- pied by the unique genes in each proportion were obtained (Fig. - Of the predicted strain phage, 66 strains contained integrase/recombinase/transpo- sase. - Therefore, the phylogenetic tree based on the mobile elements in these prophage of 66 strains was used as a proxy for the phylogeny of the GIs. - The phylogenetic relationship ex- hibited by the important mobile elements was basic- ally consistent with the phylogenetic relationship of the core genes.. - In the bioenergetics-constrained prokaryotic genome size, the adaptive evolutionary process of populations is revealed through the pan-genome [29, 30]. - our conclusions were similar to Hurtado et al [31] conclusions, indicating that this type of strain strengthens the ability of the “survival of the fittest” alone [32]. - HGT events with beneficial effects would increase the fitness of the acceptors, eventually being fixed in the population. - In the process, new genes with. - small fluctuations and the growing number of unique genes are the embodiment of the ability to obtain for- eign elements stably and regularly (Fig. - 4, where most of the similarly located P. - multo- cida strains were in the same large branch, and most of the same host-derived were in the same phylogenetic tree. - As shown in Additional file 13: Figure S3, an arc of the same colour represents the same large branch. - 5 The functional properties of all the genes in the 280 GIs and their attribution in the pan-genome. - The genomic sums of the 280 GIs predicted from 114 P. - y-axis shows the percentages of the core genes of GIs. - y-axis shows the percentages of the unique genes of GIs. - y-axis shows the percentages of the accessory GI genes. - all strains in the phylogenetic tree had a high degree of similarity, except for the canis-sourced strain OH1905.. - OH1905 was not located on a single branch as on NCBI, but was located on the same large branch as P-1662 and some of the avian-source strains. - This may be due to the different strains of the screening results making a slight change in common genes determined by these data, for example there are 306_PMUL, OH4807 in Add- itional file 13: Figure S3-A, while FDAARGOS_219 in Additional file 13: Figure S3-B. - this gene was only present in the strain P1933 (WP and the pathogenicity and resistance is- land GIPm3480_1 of the strains 3480 and GIPmHNO . - The HNH-TerS-TerL supramolecular com- plex in the GIs plus a complete capsid could cleave the cos-site of the phage. - This is helpful to the island invasion packaging mechanism of the phage by certain helper phages to be excised, replicated, and packaged in an encap- sulated form that can infect phage particles, thereby mak- ing GIs with no mobility inherent to their mobility [42, 43].. - coli HicAB, affects the growth and death of the strains [49]. - of the core genes in the pan-genome, 42.3% of the accessory genes, and 35.4% of the unique genes. - multocida, the genes with higher frequencies in the foreign strains were also transferred. - however, because of their unique location characteristics at both ends of the GI, it is more likely that the host’s own genes have moved to the GI area after the GI was transferred to the host. - Moreover, 42.3% of the accessory genes were derived from GIs. - Most of the genes that have similar functional proportions to the accessory genes, possibly due to the greater demand for such func- tional categories during the survival and reproduction of these strains or the fact that most of the strains themselves contain many of the functional categories associated with biological processes to make GIs more likely to contain such genes. - As shown in Additional file 16: Table S9, there were 200 unique genes contributed by the GIs to strain 36,950, including most of the drug-resistant genes asso- ciated with the specific phenotype of the strain, such as aminoglycosides, macrolides, and beta-lactams. - Most of the GI-related genes found in HS_SKN01 were related to ICE. - multocida were disparately affected by GIs, which played an important role in the amplification of the pan-genome of bacteria flora, especially the genes re- lated to virulence, tolerability and environmental adapt- ability. - These types of genes enable the bacteria to transfer benefits to themselves through the horizontal GI transfer, thereby enhancing symbiosis and adapta- tion of the bacteria.. - The GI genes found in the population genome of P. - We identified 280 GIs, accounting for 5.8% of the core genes in the pan-genome, 42.3% of the accessory genes. - and 35.4% of the unique genes. - Therefore, in the context of population genetics of P. - Sequen- cing of the 10 isolates was conducted using an Illumina HiSeq 2500. - The median sizes of the pan-genomes data were generated using the mathemat- ical model heap’s law, n pan = k pan N γ [25]. - The construction of the phylogenetic tree. - The p-distance of the tree based on core genes was calculated as 0.020, and the average Jukes-Canter (JC) distance was 0.009.. - And the phylo- genetic tree based on integrase/recombinase/transpo- sase of prophage was constructed in the same way.. - The existing GIs were preliminarily screened on the basis of the unique or minimal number of comparative genomic characteristics of GI by Mauve [70].. - the functions of these genes are involved in the insertion and deletion of the region that is flanked by DR structures and are absent from the chromosome with which they are closely associated [6, 72]. - The detailed information of the. - Calculation of intersection between GI and pan-genome These genes present on the GIs in the core genes, the accessory genes and unique genes. - The common part of the core genes and GIs were analysed by the COG data- base for their functional clustering results, and the com- mon parts of the unique genes and GIs were the same.. - In the background of the newest gene ontology files, the shared parts of the accessory genes and the GIs were used to obtain the gene enrichment at the 3rd level of GO in the native format with the Web Gene Ontology Annotation Plot (WEGO) [73].. - The de- tailed information of the predicted prophage of 114 strains as Additional file 9: File S2 could be seen in https://fig- share.com/s/405c87082feea840e2da (DOI: https://doi.org/. - Specific information of the GIs on 17 complete genome. - A summary of the number of the GIs of 97 whole genome. - Enriched genes of GIs in the accessory gene. - Comparison of the phylogenetic tree 147 Pm from NCBI. - The significant functional genes in the common part of the GIs and the unique genes of the pan-genome. - The detailed information of the GIs and prophage of 114 strains (Additional file 6: File S1 and Additional file 9: File S2) could be seen in https://figshare.com/s/405c87082feea840e2da (DOI: https://doi.org/. - JH, DZ and YY performed MLST analysis and the construction of the phylogenetic tree. - Pathogenicity islands: the tip of the iceberg.. - Bacteriophages: an appraisal of their role in the treatment of bacterial infections. - An overview of the structures of protein-DNA complexes. - Crystal structure of the ATP-binding subunit of an ABC transporter. - Identification and characterization of the dTDP-rhamnose biosynthesis and transfer genes of the. - Structure and dynamics of the pan- genome of Streptococcus pneumoniae . - Conjugative transposons: the tip of the iceberg. - PHASTER: a better, faster version of the PHAST phage search tool
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