*''B. cenocepacia'' is a very clinically relevant part of the ''B. cepacia'' complex (BCC), which is a group of hardy (high degree of antibiotic resistance) gram-negative bacteria that typically reside in water or soil (18 different species, with some being plant or human pathogens). ''B. cenocepacia'' is an opportunistic pathogen which causes lung infections in CF (cystic fibrosis) patients; infection by ''B. cenocepacia'' is extremely difficult to treat due to a high level of antibiotic resistance, and thus, infection is tied to increased levels of mortality and a decline in the functioning of the lung. The manuscript covered the genome of ''B. cenocepacia'' J2315, which is a member of a recently emerged (1990s) epidemic lineage of ''B. cenocepacia'' that was extremely transmissible (especially between people with CF); this epidemic lineage is known as the ET12 epidemic strain, that is a part of the IIIA subgroup of ''B. cenocepacia'' (subgroups were found, phylogenetically, through the analysis of the ''recA'' gene). IIIA strains, unlike those associated with the other subgroups, are rarely encountered in a natural environment, suggesting that the strains have strongly adapted to a host-associated pathogen lifestyle (versus that of a soil saprophyte). There also exist many virulence markers that are encountered more frequently with IIIA strains than with other subgroups; the ET12 isolates, additionally, are known to have a cable pilus which permits binding to molecules within the host environment, such as mucins (which are abundant in the lung). J2315, specifically, is an isolate derived from a CF patient and it exhibits strong levels of antibiotic resistance; it is a member of the ET12 lineage which is a part of the IIIA subgroup. The value of the genomic analysis of J2315 lies in the fact that it will give some elucidation regarding the factors responsible for the success of the strain (via CF patient infection); genomic analysis will also help explain how the members of the ET12 lineage adapted, recently, to holding a niche via human infection (instead of holding a niche in the soil, as a soil saprophyte). In short, J2315 represents a unique and extremely significant pathogen in the realm of CF treatment as it possesses properties that allow it thrive even further in the lung environment than other related strains/subgroups; genomic analysis will produce something that will serve as an essential resource for future investigations into J2315 and the disease that is caused by ''Burkholderia cenocepacia''.

*''B. cenocepacia'' is a very clinically relevant part of the ''B. cepacia'' complex (BCC), which is a group of hardy (high degree of antibiotic resistance) gram-negative bacteria that typically reside in water or soil (18 different species, with some being plant or human pathogens). ''B. cenocepacia'' is an opportunistic pathogen which causes lung infections in CF (cystic fibrosis) patients; infection by ''B. cenocepacia'' is extremely difficult to treat due to a high level of antibiotic resistance, and thus, infection is tied to increased levels of mortality and a decline in the functioning of the lung. The manuscript covered the genome of ''B. cenocepacia'' J2315, which is a member of a recently emerged (1990s) epidemic lineage of ''B. cenocepacia'' that was extremely transmissible (especially between people with CF); this epidemic lineage is known as the ET12 epidemic strain, that is a part of the IIIA subgroup of ''B. cenocepacia'' (subgroups were found, phylogenetically, through the analysis of the ''recA'' gene). IIIA strains, unlike those associated with the other subgroups, are rarely encountered in a natural environment, suggesting that the strains have strongly adapted to a host-associated pathogen lifestyle (versus that of a soil saprophyte). There also exist many virulence markers that are encountered more frequently with IIIA strains than with other subgroups; the ET12 isolates, additionally, are known to have a cable pilus which permits binding to molecules within the host environment, such as mucins (which are abundant in the lung). J2315, specifically, is an isolate derived from a CF patient and it exhibits strong levels of antibiotic resistance; it is a member of the ET12 lineage which is a part of the IIIA subgroup. The value of the genomic analysis of J2315 lies in the fact that it will give some elucidation regarding the factors responsible for the success of the strain (via CF patient infection); genomic analysis will also help explain how the members of the ET12 lineage adapted, recently, to holding a niche via human infection (instead of holding a niche in the soil, as a soil saprophyte). In short, J2315 represents a unique and extremely significant pathogen in the realm of CF treatment as it possesses properties that allow it thrive even further in the lung environment than other related strains/subgroups; genomic analysis will produce something that will serve as an essential resource for future investigations into J2315 and the disease that is caused by ''Burkholderia cenocepacia''.

====Methods Employed in the Study====

====Methods Employed in the Study====

*Used strains of ''B. cenocepacia'' in this study: K56-2, BC7, LMG 13307 (BCC0162), CEP0791 (BCC0077), LMG 13320 (BCC0179), FC0504 (BCC0313), LMG 18827 (BCC0016), BCC1261, CEP0826 (BCC0222).

*Used strains of ''B. cenocepacia'' in this study: K56-2, BC7, LMG 13307 (BCC0162), CEP0791 (BCC0077), LMG 13320 (BCC0179), FC0504 (BCC0313), LMG 18827 (BCC0016), BCC1261, CEP0826 (BCC0222).

*J2315 was grown via broth culture and was harvested through centrifugation. Bacterial pellets were suspended in a solution designed for cell lysis; the lysate was then incubated and the DNA was purified (via protein and polysacharride precipitation, which was later removed by centrifugation). DNA was collected from the lysate through ethanol precipitation

*J2315 was grown via broth culture and was harvested through centrifugation. Bacterial pellets were suspended in a solution designed for cell lysis; the lysate was then incubated and the DNA was purified (via protein and polysacharride precipitation, which was later removed by centrifugation). DNA was collected from the lysate through ethanol precipitation

*The whole DNA sequence, using all 6 possible reading frames, was also compared against UniProt, via BLASTX, to improve the quality of previous work (purpose was to identify any possible coding sequences that were missed to earlier work)

*The whole DNA sequence, using all 6 possible reading frames, was also compared against UniProt, via BLASTX, to improve the quality of previous work (purpose was to identify any possible coding sequences that were missed to earlier work)

*Protein structural motifs were identified through the use of Pfam and Prosite, transmembrane domains were found through TMHMM; signal sequences were identified through the use of SignalP version 2.0

*Protein structural motifs were identified through the use of Pfam and Prosite, transmembrane domains were found through TMHMM; signal sequences were identified through the use of SignalP version 2.0