Molecular data analysis of selected
housekeeping and informational genes from nineteen <i>Campylobacter jejuni</i> genomes

Vathsala Mohan; Mark Stevenson

doi:10.12688/f1000research.2-87.v1

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Data Article

Molecular data analysis of selected housekeeping and informational genes from nineteen Campylobacter jejuni genomes

[version 1; peer review: 2 not approved]

Vathsala Mohan¹, Mark Stevenson²

PUBLISHED 14 Mar 2013

Author details Author details

¹ AgResearch Ltd, Grasslands, Palmerston North, New Zealand
² Epicentre, Institute of Veterinary and Biomedical Sciences, Massey University, Palmerston North, New Zealand

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Abstract

Campylobacter jejuni (C. jejuni) is a rapidly evolving bacterial species with massive genetic recombination potential to generate niche specific genotypes. Generally the housekeeping gene lineage has been evidenced to undergo lateral gene transfer and recombination fairly frequently compared to the information processing gene lineage. During such exchanges, gene amelioration takes place over time acquiring the host genomes’ molecular characteristics. In this study fifty genes that comprised twenty five housekeeping lineage genes and twenty five information processing lineage genes from nineteen C. jejuni genomes were studied. These nineteen genomes included seven C. jejuni isolates that belonged to the same genotype or multilocus sequence type ST-474. The genes from both lineages were tested for recombination and the guanine-cytosine (GC) variation. This paper details about the data collected and the analyses performed in the corresponding research article entitled ”Campylobacter jejuni genomes exhibit notable GC variation within housekeeping genes”. Further, this paper provides details on the results that are not included in the research paper to provide completeness to the study conducted. The gene sequences from the seven C. jejuni ST-474 isolates were submitted to the GenBank and the corresponding gene IDs are provided for referencing purposes.

Associated Research Article Vathsala Mohan, Mark Stevenson » Campylobacter jejuni genomes exhibit notable GC variation within housekeeping genes, F1000Research 2013, 2:89 (https://doi.org/10.12688/f1000research.2-89.v1)

Corresponding author: Vathsala Mohan

Competing interests: No competing interests were disclosed.

Grant information: This work was part of Vathsala Mohan’s PhD work and this project was supported by:

1. Building Research Capability in Strategically Relevant Areas (BRCSRA) fund;
2. Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North (RM12767); and
3. The Royal Society of New Zealand Marsden Fund (MAU0802).

This was an original research work and the funders had no role in any of the processes or in the preparation of the manuscript.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2013 Mohan V and Stevenson M. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

How to cite: Mohan V and Stevenson M. Molecular data analysis of selected housekeeping and informational genes from nineteen Campylobacter jejuni genomes [version 1; peer review: 2 not approved]. F1000Research 2013, 2:87 (https://doi.org/10.12688/f1000research.2-87.v1) First published: 14 Mar 2013, 2:87 (https://doi.org/10.12688/f1000research.2-87.v1) Latest published: 14 Mar 2013, 2:87 (https://doi.org/10.12688/f1000research.2-87.v1)

Background

Mulitlocus sequence typing (MLST) is a technique devised to sub-divide bacterial populations¹. MLST exploits the internal fragments that are approximately 470 to 500 base pairs of the housekeeping genes and constructs allelic profiles based on variations in the nucleotide sequences of (usually) seven housekeeping genes. Bacterial isolates are grouped into different clusters². C. jejuni is a zoonotic pathogen that causes gastroenteritis in humans worldwide and the natural competency and plasticity of C. jejuni have not been investigated outside the MLST housekeeping genes^3–8. This technique has subsequently been exploited to structure and investigate the association of C. jejuni populations where, previous researches inferred that a mutation at any site can occur somewhere in the population within the space of a week^7–9. Hybrid alleles were shown to be more common in some of the MLST loci (tkt, aspA, gltA and glyA) and in the MOMP gene of C. jejuni (interchangeably designated as porA) as a result of recombination and, has been interpreted as a consequential measure of convergence of C. jejuni and C. coli^7,8,10.

Housekeeping alleles of C. jejuni strains (genotypes) share 86% nucleotide sequence identity with each other however, the housekeeping alleles cover lesser than < 0.2% of the entire genome¹¹. The molecular differences at the genome level and/or at the full gene level may not be detected even when MLST is combined with other antigenic genes such as porA. Moreover, the housekeeping alleles or genes are involved in specific metabolic function which may not reflect the evolutionary events in other genes involved in a different function in a genome. Further, there is no evidence to suggest that MLST alleles are identical at their full length level and it is not known if a detailed knowledge of MLST alleles can capture the true evolutionary history of the other genes in a genome.

Objectives

Based on these background information and knowledge gap, the nucleotide sequence data from two different lineages of genes, the metabolic housekeeping and the informational genes were collected from 19 C. jejuni genomes. The main objectives were

(1) To select genes those are categorised as housekeeping genes.

(2) To ensure the presence of these genes in all of the C. jejuni genomes compared without segmentation.

(3) To categorise them according to the functions they are involved in.

(4) To create two different nucleotide datasets for comparison and,

(5) To test different genetic hypotheses.

Materials and methods

Selection of metabolic and informational housekeeping genes

Although genes have been classified as housekeeping and informational genes, the list of genes that can be categorised as housekeeping genes have not be defined very clearly. Hence in this study we collected the set of genes that have been used in routine multilocus sequence typing (MLST) schemes for different bacterial species from the PubMLST database and from previous phylogenetic studies that used housekeeping genes for analyses^12–14. The gene names were matched with the C. jejuni NCTC 11168 genome (GenBank accession number NC002163) that is fully annotated and has been used as reference in many other genome comparative studies^15–20. Following the identification of genes, a total of 50 genes were selected and these were further examined for their presence in other C. jejuni reference genomes to be analysed in this study. Full length nucleotide sequences of the selected set of housekeeping genes were retrieved in FASTA format from the GenBank from all of the selected C. jejuni genomes. Further the genes were classified into operational genes (metabolic housekeeping genes) and informational genes based on their function by referring to the KEGG pathway and the gene function websites. The positions of the categorised selected subset of genes (metabolic housekeeping and informational genes) are marked on the reference C. jejuni NCTC 11168 (GenBank accession number NC002163) circular genome and are shown in Figure 1A and Figure 1B, respectively. Here after in this paper the genes are referred to as housekeeping genes (metabolic housekeeping genes) and informational genes for the purpose of plain comparison and interpretation.

Figure 1A. Represents the housekeeping genes (n = 25) on the circular NCTC 11168 C. jejuni genome and the MLST housekeeping genes used in typing of C. jejuni are in red fonts.

Figure 1B. Represents the informational genes (n = 25) located on the circular NCTC 11168 C. jejuni genome.

Reference C. jejuni genomes and nucleotide sequences from MLST ST-474 isolates

Details of the reference C. jejuni genomes, housekeeping and informational genes, their names and their functions are provided in Table 1, Table 2 and Table 3, respectively. Twelve fully sequenced C. jejuni genomes were used to compare 50 selected genes. The gene sequences were downloaded from the GenBank database. Seven C. jejuni MLST ST-474 isolates were sequenced at the Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand. The gene predictions were kindly provided by Dr. Biggs Patrick from Massey Genome Service, Massey University, Palmerston North for the seven C. jejuni MLST ST-474 isolates. These genomes were studied in partial fulfilment of the PhD project by the first author of this paper. The nucleotide sequences for the selected genes (n = 50) were retrieved from the gene predictions from the seven C. jejuni ST-474 genomes in FASTA format and gene sequences for five of the four ST-474 isolates P179a, H704a, H73020, P569a and P694a were submitted to the GenBank and their sequence ids are given in Table 4 and Table 5 for metabolic and informational or repair genes, respectively. In addition this data is accessible below:

Table 1. Campylobacter jejuni subsp. jejuni reference genomes.

Species	Strain	Size (Mb)	%GC	ORFs	Disease/source	Year and place of isolation	GenBank
Campylobacter jejuni subsp. jejuni	NCTC 11168	1.64	30.5	1643	Clinical Food poisoning	1977, UK	AL111168
Campylobacter jejuni subsp. jejuni	RM1221	1.78	30.3	1838	Chicken	2005*, USA	CP000025
Campylobacter jejuni subsp. jejuni	81–176	1.6	30.6	1653	Clinical Food poisoning	1981, USA	CP000538
Campylobacter jejuni subsp. jejuni	81116	1.63	30.5	1626	Clinical Food poisoning	2007, UK	CP000814
Campylobacter jejuni subsp. jejuni	CG8421	1.6	30.4	1512	Clinical Food poisoning	ns	ABGQ00000000
Campylobacter jejuni subsp. jejuni	HB93-13	1.7	30.6	1710	Clinical GBS	2006*, USA	AANQ00000000
Campylobacter jejuni subsp. jejuni	CG8486	1.65	30.4	1425	Clinical Food poisoning	ns	AASY00000000
Campylobacter jejuni subsp. jejuni	CF93-6	1.67	30.5	1757	Clinical MFS	2006*, Japan	AANJ00000000
Campylobacter jejuni subsp. jejuni	84–25	1.67	30.4	1748	Clinical Meningitis	2006*, USA	AANT00000000
Campylobacter jejuni subsp. jejuni	260.94	1.65	30.5	1716	Clinical GBS	ns	AANK00000000
Campylobacter jejuni subsp. jejuni	IA3902	1.64	30.5	1718	Sheep abortion	2010, USA	CP001876
Campylobacter jejuni subsp.doylei	269.97	1.85	30.6	2094	Human blood	2007, UK	CP000768
Campylobacter jejuni subsp. jejuni-P179a	ST-474	-	-	-	Poultry	New Zealand	-
Campylobacter jejuni subsp. jejuni-P110b	ST-474	-	-	-	Poultry	New Zealand	AEIO00000000.1
Campylobacter jejuni subsp. jejuni-P694a	ST-474	-	-	-	Poultry	New Zealand	-
Campylobacter jejuni subsp. jejuni-P569a	ST-474	-	-	-	Poultry	New Zealand	-
Campylobacter jejuni subsp. jejuni-H22082	ST-474	-	-	-	Human	New Zealand	AEIP01000008.1
Campylobacter jejuni subsp. jejuni-H704a	ST-474	-	-	-	Human	New Zealand	-
Campylobacter jejuni subsp. jejuni-H73020	ST-474	-	-	-	Human	New Zealand	-

ST: Multilocus sequence sequence type; GBS: Guillain-Barré syndrome; ORFs: Open reading frames; Mb: Mega bases; GC: Guanine: Cytosine; ns: not stated; *:Date of start of project.

Table 2. Metabolic genes selected from the MLST schemes of different bacterial species for comparison.

Gene	Gene ID	Name of the gene	Function
argF	Cj0994c	Probable ornithine carbamoyltransferase	Amino acid biosynthesis - Glutamate family
aroE	Cj0405	Probable shikimate 5-dehydrogenase	Amino acid biosynthesis - Aromatic amino acid family
atpD	Cj0107	Probable ATP synthase F1 sector beta subunit	Energy metabolism
dapE	Cj1048c	Probable succinyl-diaminopimelate desuccinylase	Amino acid biosynthesis - Aspartate family
ftsZ	Cj0696	Probable cell division protein	Cell division
fumC	Cj1364c	Probable fumarate hydratase	Probable fumarate hydratase
gapA	Cj1403c	Glyceraldehyde 3-phosphate dehydrogenase	Energy metabolism
gltB	Cj0007	Probable glutamate synthase (NADPH) large subunit	Energy metabolism TCA
groEL	Cj1221	60 kD chaperonin	Heat Shock
hemN	Cj0580c	Probable oxidoreductase	Oxygen-independent coproporphyrinogen-III oxidases
ilvD	Cj0013	Probable dihydroxy-acid dehydratase	Amino acid biosynthesis - Glutamate family
infB	Cj0136	Probable translation initiation factor IF-2	Protein translation
lysA	Cj0314	Probable diaminopimelate decarboxylase	Amino acid biosynthesis - Aspartate family
nuoD	Cj1576c	Probable NADH dehydrogenase I chain D	Energy metabolism - Respiration - Aerobic
pycA	Cj1037c	Possible pyruvate carboxylase A subunit	Central intermediary metabolism - Gluconeogenesis
sdhA	Cj0437	Probable succinate dehydrogenase flavoprotein subunit	Energy metabolism - Tricarboxylic acid cycle
trpB	Cj0348	Probable tryptophan synthase beta chain	Amino acid biosynthesis
trpC	Cj0498	Probable indole-3-glycerol phosphate synthase	Amino acid biosynthesis - Aromatic amino acid family
aspA	Cj0087	Aspartase	Central intermediary metabolism
glnA	Cj0699c	Glutamine synthetase	Central intermediary metabolism
gltA	Cj1682c	Central intermediary metabolism	Citrate synthase
glyA	Cj0402	Serine hydroxy methyl transferase	Central intermediary metabolism
glmM	Cj0360	Phospho glucosamine mutase	Central intermediary metabolism
tkt	Cj1645	Transketolase	Central intermediary metabolism
uncA/atpA	Cj0105	ATP synthase a subunit	Central intermediary metabolism

Table 3. Genes of repair mechanism, their gene ID, name, function and the pathways they are involved in.

Genes	Gene ID	Name of the gene	Function	Pathway
dnaE_	Cj0718	DNA polymerase III subunit alpha	It is a main replicative polymerase(Catalyses DNA-template-directed extension of the 3’- end of a DNA strand by one nucleotide at a time)	Purine metabolism, pyrimidine metabolism, metabolic pathways, DNA replication, mismatch repair and homologous recombination
gidA_	Cj1188c	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	Involved in the modification of the wobble third base in tRNAs (5- carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; also known as a glucose-inhibited cell division protein A)	tRNA modification and regulation
guaA_	Cj1248	Probable GMP synthase (glutamine-hydrolysing)	Purine ribonucleotide biosynthesis	Purine metabolism
gyrA_	Cj1027c	DNA gyrase subunit A	Negatively supercoils closed circular double-stranded DNA or prevents from super-coiling that is deleterious to bacterial survival	Direct DNA repair mechanism
gyrB_	Cj0003	DNA gyrase subunit B	Negatively super-coils closed circular double-stranded DNA	Direct DNA repair mechanism
ligA	Cj0586	NAD-dependent DNA ligase	Catalyses the formation of phosphodiester linkages and is essential for DNA replication and repair of damaged DNA (between 5’-phosphoryl and 3’-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction)	Direct DNA repair mechanism, DNA replication, base excision repair, nucleotide excision repair and mismatch repair
mfdrepair	Cj1085c	Transcription-repair coupling factor	Prevents or corrects mutagenic nucleotides by removing them from DNA strands during replication	Nucleotide excision repair – DNA
mutS	Cj1052c	Recombination and DNA strand exchange inhibitor protein	Involved in blocking homologous recombination and inhibits DNA strand exchange (has ATPase activity stimulated by recombination intermediates)	Mismatch excision repair – DNA repair
mutY_	Cj1620c	Probable A/G-specific adenine glycosylase	Corrects incorrectly paired bases during DNA replication and involved in recombinational repair	Base excision repair – DNA repair
ogt	Cj0836	Methylated-DNA-protein-cysteine methyltransferase	Direct DNA repair by alkylation reversal	Direct DNA repair
polA	Cj0338c	DNA polymerase I	Has 3’-5’ exonuclease, 5’-3’ exonuclease and 5’-3’polymerase activities, primarily functions to fill gaps during DNA replication and repair	Replication and DNA repair
pyrC_	Cj0259	Dihydroorotase Pyrimidine	ribonucleotide biosynthesis: catalyses the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis	Pyrimidine nucleotide biosynthesis
pyrG_	Cj0027c	CTP synthetase	Catalyses the ATP-dependent amination of UTP to CTP with either Lglutamine or ammonia as the source of nitrogen	Pyrimidine nucleotide biosynthesis
recA_	Cj1673c	Recombinase A	Involved in recombinational repair of DNA damage. Catalyses the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single stranded DNA by duplex DNA, and the ATP-dependent hybridisation of homologous single-stranded DNAs	Recombinational repair
recJ_	Cj0028	Putative single-stranded-DNAspecific exonuclease	Synthesis and modification of macromolecules - DNA replication, restriction/modification, recombination and repair	Recombinational repair
recN	Cj0642	Putative DNA repair protein	DNA repair protein	Recombinational repair
recR	Cj1263	Recombination protein	Involved in a recombinational process of DNA repair	Recombinational repair
rplB_	Cj1704c	50S ribosomal protein L2	One of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation	Ribosomal gene
rpoB_	Cj0479	DNA-directed RNA polymerase subunit beta’	RNA synthesis, RNA modification and DNA transcription	RNA polymerase
rpoD_	Cj1001	RNA polymerase sigma factor	Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria	RNA polymerase
ruvA	Cj0799c	Holliday junction DNA helicase	Plays an essential role in ATPdependent branch migration of the Holliday junction	Branch migration repair mechanism
ssb	Cj1071	Single-stranded DNA-binding protein	Binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA	Other repair mechanisms
uvrA_	Cj0342c	Excinuclease ABC subunit A uvrA is an ATPase and a DNAbinding protein.	A damage recognition complex composed of two uvrA and two uvrB subunits scans DNA for abnormalities	Nucleotide excision repair
uvrB Nucleotide excision repair	Cj0680c	Excinuclease ABC subunit B	The UvrABC repair system catalyzes the recognition and processing of DNA lesions	The beta hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion
xseA	Cj0325	Exo-deoxyribonuclease VII large subunit	Bi-directionally degrades single stranded DNA into large acid insoluble oligonucleotides	Mismatch excision repair :Repair, ribosomal and nucleotide metabolic genes employed for MLST typing of other bacterial species

Table 4. GenBank sequence ids for metabolic genes for the five ST-474 isolates.

Isolates	Sequence_ids	Genes
H704a_1	KC405082	argF
H704a_2	KC405083	aroE
H704a_3	KC405084	aspA
H704a_4	KC405085	atpD
H704a_5	KC405086	dapE
H704a_6	KC405087	ftsZ
H704a_7	KC405088	fumC
H704a_8	KC405089	gapA
H704a_9	KC405090	glmM
H704a_10	KC405091	glnA
H704a_11	KC405092	gltA
H704a_12	KC405093	gltB
H704a_13	KC405094	glyA
H704a_14	KC405095	groEL
H704a_15	KC405096	hemN
H704a_16	KC405097	ilvD
H704a_17	KC405098	infB
H704a_18	KC405099	lysA
H704a_19	KC405100	nuoD
H704a_20	KC405101	pycA
H704a_21	KC405102	sdhA
H704a_22	KC405103	tkt
H704a_23	KC405104	trpB
H704a_24	KC405105	trpC
H704a_25	KC405106	atpA
H73020_1	KC405107	argF
H73020_2	KC405108	aroE
H73020_3	KC405109	aspA
H73020_4	KC405110	atpD
H73020_5	KC405111	dapE
H73020_6	KC405112	ftsZ
H73020_7	KC405113	fumC
H73020_8	KC405114	gapA
H73020_9	KC405115	glmM
H73020_10	KC405116	glnA
H73020_11	KC405117	gltA
H73020_12	KC405118	gltB
H73020_13	KC405119	glyA
H73020_14	KC405120	groEL
H73020_15	KC405121	hemN
H73020_16	KC405122	ilvD
H73020_17	KC405123	infB
H73020_18	KC405124	lysA
H73020_19	KC405125	nuoD
H73020_20	KC405126	pycA
H73020_22	KC405127	sdhA
H73020_21	KC405128	tkt
H73020_23	KC405129	trpB
H73020_24	KC405130	trpC
H73020_25	KC405131	atpA
P179a_1	KC405132	argF
P179a_2	KC405133	aroE
P179a_3	KC405134	aspA
P179a_4	KC405135	atpD
P179a_5	KC405136	dapE
P179a_6	KC405137	ftsZ
P179a_7	KC405138	fumC
P179a_8	KC405139	gapA
P179a_9	KC405140	glmM
P179a_10	KC405141	glnA
P179a_11	KC405142	gltA
P179a_12	KC405143	gltB
P179a_13	KC405144	glyA
P179a_14	KC405145	groEL
P179a_15	KC405146	hemN
P179a_16	KC405147	ilvD
P179a_17	KC405148	infB
P179a_18	KC405149	lysA
P179a_19	KC405150	nuoD
P179a_20	KC405151	pycA
P179a_21	KC405152	sdhA
P179a_22	KC405153	tkt
P179a_23	KC405154	trpB
P179a_24	KC405155	trpC
P179a_25	KC405156	atpA
P569a_1	KC405157	argF
P569a_2	KC405158	aroE
P569a_3	KC405159	aspA
P569a_4	KC405160	atpD
P569a_5	KC405161	dapE
P569a_6	KC405162	ftsZ
P569a_7	KC405163	fumC
P569a_8	KC405164	gapA
P569a_9	KC405165	glmM
P569a_10	KC405166	glnA
P569a_11	KC405167	gltA
P569a_12	KC405168	gltB
P569a_13	KC405169	glyA
P569a_14	KC405170	groEL
P569a_15	KC405171	hemN
P569a_16	KC405172	ilvD
P569a_17	KC405173	infB
P569a_18	KC405174	lysA
P569a_19	KC405175	nuoD
P569a_20	KC405176	pycA
P569a_21	KC405177	sdhA
P569a_22	KC405178	tkt
P569a_23	KC405179	trpB
P569a_24	KC405180	trpC
P569a_25	KC405181	atpA
P694a_1	KC405182	argF
P694a_2	KC405183	aroE
P694a_3	KC405184	aspA
P694a_4	KC405185	atpD
P694a_5	KC405186	dapE
P694a_6	KC405187	ftsZ
P694a_7	KC405188	fumC
P694a_8	KC405189	gapA
P694a_9	KC405190	glmM
P694a_10	KC405191	glnA
P694a_11	KC405192	gltA
P694a_12	KC405193	gltB
P694a_13	KC405194	glyA
P694a_14	KC405195	groEL
P694a_15	KC405196	hemN
P694a_16	KC405197	ilvD
P694a_17	KC405198	infB
P694a_18	KC405199	lysA
P694a_19	KC405200	nuoD
P694a_20	KC405201	pycA
P694a_21	KC405202	sdhA
P694a_22	KC405203	tkt
P694a_23	KC405204	trpB
P694a_24	KC405205	trpC
P694a_25	KC405206	atpA

Table 5. GenBank sequence Ids of the genes involved in the repair mechanism for the five ST-474 isolates.

Isolate_number	Sequence Ids	Genes
H704axseA	KC408804	xseA
H73020xseA	KC408805	xseA
P179a_xseA	KC408806	xseA
P569axseA	KC408807	xseA
P694axseA	KC408808	xseA
H704auvrB	KC408809	uvrB
H73020uvrB	KC408810	uvrB
P179auvrB	KC408811	uvrB
P569auvrB	KC408812	uvrB
P694auvrB	KC408813	uvrB
H704auvrA	KC408814	uvrA
H73020uvrA	KC408815	uvrA
P179auvrA	KC408816	uvrA
P569auvrA	KC408817	uvrA
P694auvrA	KC408818	uvrA
H704assb	KC408819	ssb
H73020ssb	KC408820	ssb
P179assb	KC408821	ssb
P569assb	KC408822	ssb
P694assb	KC408823	ssb
H704aruvA	KC408824	ruvA
H73020ruvA	KC408825	ruvA
P179aruvA	KC408826	ruvA
P569aruvA	KC408827	ruvA
P694aruvA	KC408828	ruvA
H704arpoD	KC408829	rpoD
H73020rpoD	KC408830	rpoD
P179arpoD	KC408831	rpoD
P569arpoD	KC408832	rpoD
P694arpoD	KC408833	rpoD
H704arpoB	KC408834	rpoB
H73020rpoB	KC408835	rpoB
P179arpoB	KC408836	rpoB
P569arpoB	KC408837	rpoB
P694arpoB	KC408838	rpoB
H704arplB	KC408839	rplB
H73020_rplB	KC408840	rplB
P179arplB	KC408841	rplB
P569arplB	KC408842	rplB
P694arplB	KC408843	rplB
H704arecR	KC408844	recR
H73020recR	KC408845	recR
P179arecR	KC408846	recR
P569arecR	KC408847	recR
P694arecR	KC408848	recR
H704arecN	KC408849	recN
H73020recN	KC408850	recN
P179arecN	KC408851	recN
P569arecN	KC408852	recN
P694arecN	KC408853	recN
H704arecJ	KC408854	recJ
H73020recJ	KC408855	recJ
P179arecJ	KC408856	recJ
P569arecJ	KC408857	recJ
P694arecJ	KC408858	recJ
H704arecA	KC408859	recA
H73020recA	KC408860	recA
P179arecA	KC408861	recA
P569arecA	KC408862	recA
P694arecA	KC408863	recA
H704apyrG	KC408864	pyrG
H73020pyrG	KC408865	pyrG
P179apyrG	KC408866	pyrG
P569apyrG	KC408867	pyrG
P694apyrG	KC408868	pyrG
H704apyrC	KC408869	pyrC
H73020pyrC	KC408870	pyrC
P179apyrC	KC408871	pyrC
P569apyrC	KC408872	pyrC
P694apyrC	KC408873	pyrC
H704apolA	KC408874	polA
H73020polA	KC408875	polA
P179apolA	KC408876	polA
P569apolA	KC408877	polA
P694apolA	KC408878	polA
H704aogt	KC408879	ogt
H73020ogt	KC408880	ogt
P179aogt	KC408881	ogt
P569aogt	KC408882	ogt
P694aogt	KC408883	ogt
H704amutY	KC408884	mutY
H73020mutY	KC408885	mutY
P179amutY	KC408886	mutY
P569amutY	KC408887	mutY
P694amutY	KC408888	mutY
H704amutS	KC408889	mutS
H73020mutS	KC408890	mutS
P179amutS	KC408891	mutS
P569amutS	KC408892	mutS
P694amutS	KC408893	mutS
H704amfd	KC408894	mfd
H73020mfd	KC408895	mfd
P179amfd	KC408896	mfd
P569amfd	KC408897	mfd
P694amfd	KC408898	mfd
H704aligA	KC408899	ligA
H73020ligA	KC408900	ligA
P179aligA	KC408901	ligA
P569aligA	KC408902	ligA
P694aligA	KC408903	ligA
H704agyrB	KC408904	gyrB
H73020gyrB	KC408905	gyrB
P179agyrB	KC408906	gyrB
P569agyrB	KC408907	gyrB
P694agyrB	KC408908	gyrB
H704agyrA	KC408909	gyrA
H73020gyrA	KC408910	gyrA
P179agyrA	KC408911	gyrA
P569agyrA	KC408912	gyrA
P694agyrA	KC408913	gyrA
H704aguaA	KC408914	guaA
H73020_guaA	KC408915	guaA
P179aguaA	KC408916	guaA
P569aguaA	KC408917	guaA
P694aguaA	KC408918	guaA
H704agidA	KC408919	gidA
H73020gidA	KC408920	gidA
P179agidA	KC408921	gidA
P569agidA	KC408922	gidA
P694agidA	KC408923	gidA
H704adnaE	KC408924	dnaE
H73020dnaE	KC408925	dnaE
P179adnaE	KC408926	dnaE
P569adnaE	KC408927	dnaE
P694adnaE	KC408928	dnaE

Analysis of Guanine-Cytosine content and recombination

The length of the house keeping and the informational genes and sites of recombination can be found below:

The results of the guanine-cytosine (GC) analysis with the GC range for all of the genes from 19 C. jejuni genomes can be found below:

The overall GC and GC3 contents of individual genes were compared using DnaSP v5²¹. The frequency distribution graphs of GC contents from all the 19 genomes compared were generated in R programming language²². Inferences on recombination within each gene under investigation were drawn using Dual-Brothers within Geneious v.5.3.4²³. This function uses a double change point model that detects spatial variation in the phylogenetic tree topology and spatial variation of the nucleotide substitution process²³. The gene sequences were aligned using Geneious v5.3.4 and the recombination detection functionality was applied on each gene alignment to infer changes in the topologies and substitution processes. In addition, the aligned sequences were examined using DnaSP v5 to identify the sites involved in recombination. The number of recombination events, referred to as Rm was estimated using DnaSP v5. The GC variance for the genes were estimated using the variance function in Microsoft Office Excel and the relationship between the GC variance and the recombination events was analysed using linear models by having Rm as a dependent variable, and the log GC variance and the length as independent variables.

Figure 2–Figure 9 describe the guanine-cytosine (GC) variation in the housekeeping and the informational genes. The plots describe the frequency distribution of GC content across 19 C. jejuni genomes and the number inside the parenthesis denotes the number of recombination sites for the respective genes.

Figure 2. Guanine-cytosine (GC) variation in the metabolic housekeeping genes – A.

The plots describe the distribution of GC across 19 C. jejuni genomes and the number inside the parenthesis denotes the number of recombination sites.

Figure 3. Guanine-cytosine (GC) variation in the metabolic housekeeping genes – A.

The plots describe the distribution of GC across 19 C. jejuni genomes and the number inside the parenthesis denotes the number of recombination sites.

Figure 4. Guanine-cytosine (GC) variation in the metabolic housekeeping genes – A.

The plots describe the distribution of GC across 19 C. jejuni genomes and the number inside the parenthesis denotes the number of recombination sites.

Figure 5. Guanine-cytosine (GC) variation in the MLST housekeeping genes – A.

The plots describe the distribution of GC across 19 C. jejuni genomes and the number inside the parenthesis denotes the number of recombination sites.

Figure 6. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

This plot describes the GC distribution across all 19 C. jejuni genomes. The number of recombination sites is provided in parentheses.

Figure 7. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

This plot describes the GC distribution across all 19 C. jejuni genomes. The number of recombination sites is provided in parentheses.

Figure 8. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

This plot describes the GC distribution across all 19 C. jejuni genomes. The number of recombination sites is provided in parentheses.

Figure 9. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

This plot describes the GC distribution across all 19 C. jejuni genomes. The number of recombination sites is provided in parentheses.

Author Contributions

VM did the data collection, analyses and wrote the paper in partial fulfillment of her PhD thesis. MS was VM’S supervisor and worked alongside her to get this manuscript out.

Grant Information

This work was part of Vathsala Mohan’s PhD work and this project was supported by:

1. Building Research Capability in Strategically Relevant Areas (BRCSRA) fund;

2. Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North (RM12767); and

3. The Royal Society of New Zealand Marsden Fund (MAU0802).

This was an original research work and the funders had no role in any of the processes or in the preparation of the manuscript.

Competing Interests

No competing interests were disclosed.

Acknowledgements

I thank Prof. Nigel French and Dr. Patrick Biggs, mEpiLab, IVABS, Massey University, for giving their comments on this piece of work. I thank Dr. Patrick Biggs for kindly providing me with the gene predictions for my PhD work. I thank Massey University Doctoral Scholarship and New Zealand International Doctoral Scholarship for funding me. This work was carried out in mEpiLab, IVABS, Massey University, New Zealand.

References

1. Maiden MCJ: Multilocus Sequence Typing of Bacteria. Annu Rev Microbiol. 2006; 60: p. 561–588.
2. Maiden MCJ, Bygraves JA, Feil E, et al:Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998; 95: p. 3140–3145.
3. Colles FM, Dingle KE, Cody AJ, et al:Comparison of Campylobacter populations in wild geese with those in starlings and free-range poultry on the same farm. Appl Environ Microbiol. 2008; 74: p. 3583–3590.
4. Dingle KE, Colles FM, Wareing DR, et al:Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol. 2001; 39: p. 14–23.
5. McCarthy ND, Colles FM, Dingle KE, et al:Host-associated genetic import in Campylobacter jejuni. Emerg Infect Dis. 2007; 13: p. 267–272.
6. Sheppard SK, Colles F, Richardson J, et al:Host association of Campylobacter genotypes transcends geographic variation. Appl Environ Microbiol. 2010; 76: p. 5269–5277.
7. Sheppard SK, McCarthy ND, Falush D, et al:Convergence of Campylobacter Species: implications for Bacterial Evolution. Science. 2008; 320: p. 237–239.
8. Sheppard SK, McCarthy ND, Jolley KA, et al:Introgression in the genus Campylobacter: Generation and spread of mosaic alleles. Microbiology. 2011; 157: p. 1066–1074.
9. Wilson DJ, Gabriel E, Leatherbarrow AJ, et al:Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni. Mol Biol Evol. 2009; 26: p. 385–397.
10. Clark CG, Beeston A, Bryden L, et al:Phylogenetic relationships of Campylobacter jejuni based on porA sequences. Can J Microbiol. 2007; 53: p. 27–38.
11. Dingle KE, Maiden MC: In Campylobacter: Molecular and Cellular Biology. ed. M.E.K.E.p. Ketley JM. Ketley JM, Konkel ME, Eds Horizon Bioscience, Wymondham, Norfolk, UK, 2005.
12. Wertz JE, Goldstone C, Gordon DM, et al:A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol. 2003; 16: p. 1236–1248.
13. Christensen H, Kuhnert P, Olsen JE, et al:Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol. 2004; 54: p. 1601–1609.
14. Margos G, Gatewood AG, Aanensen DM, et al:MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proc Natl Acad Sci U S A. 2008; 24: p. 8730–8735.
15. Fouts DE, Mongodin EF, Mandrell RE, et al:Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species. PLoS Biol. 2005; 3: e15.
16. Gundogdu O, Bentley SD, Holden MT, et al:Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics. 2007; 8: p. 162.
17. Hofreuter D, Tsai J, Watson RO, et al:Unique features of a highly pathogenic Campylobacter jejuni strain. Infect Immun. 2006; 74: p. 4694-4707.
18. Lefebure T, Stanhope MJ: Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 2009; 19: p. 1224–1232.
19. Parker CT, Quiñones B, Miller WG, et al:Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J Clin Microbiol. 2006; 44: p. 4125–4135.
20. Parkhill J, Wren BW, Mungall K, et al:The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature. 2000; 403: p. 665–668.
21. Librado P, Rozas J: DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25: p. 1451–1452.
22. Zhou BB, Elledge SJ: The DNA damage response: putting checkpoints in perspective. Nature. 2000; 408: p. 433–439.
23. Minin VN, Dorman KS, Fang F, et al:Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics. 2005; 21: p. 3034–3042.

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¹ AgResearch Ltd, Grasslands, Palmerston North, New Zealand
² Epicentre, Institute of Veterinary and Biomedical Sciences, Massey University, Palmerston North, New Zealand

Competing interests

No competing interests were disclosed.

Grant information

This work was part of Vathsala Mohan’s PhD work and this project was supported by:

1. Building Research Capability in Strategically Relevant Areas (BRCSRA) fund;
2. Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North (RM12767); and
3. The Royal Society of New Zealand Marsden Fund (MAU0802).

This was an original research work and the funders had no role in any of the processes or in the preparation of the manuscript.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Mohan V and Stevenson M. Molecular data analysis of selected housekeeping and informational genes from nineteen Campylobacter jejuni genomes [version 1; peer review: 2 not approved]. F1000Research 2013, 2:87 (https://doi.org/10.12688/f1000research.2-87.v1)

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Reviewer Report 07 Feb 2014

Daniel Falush, Department of Evolutionary Genetics, Max Planck Institute, Leipzig, Germany

Not Approved

https://doi.org/10.5256/f1000research.1102.r3557

I do not understand either from the abstract or reading the earlier paper why this data was collected. Neither the strain collection nor the quantities calculated have any obvious special features. The information presented is of a similar character to ... Continue reading

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Reviewer Report 02 May 2013

David Ussery, Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark

Not Approved

https://doi.org/10.5256/f1000research.1102.r921

This short article describes a comparison of 'housekeeping genes' with 'information processing genes', across 19 Campylobacter jejuni genomes. I cannot fully evaluate this paper as the data is not available. I understand that this is a new journal, and as ... Continue reading

This short article describes a comparison of 'housekeeping genes' with 'information processing genes', across 19 Campylobacter jejuni genomes. I cannot fully evaluate this paper as the data is not available. I understand that this is a new journal, and as such perhaps F1000Research has not agreed that all sequences should be deposited to GenBank or EMBL before publication, but I find this frustrating that the results are published, but the data is missing.

Since currently there are only 11 C. jejuni genomes listed as 'complete', I was curious as to what additional genomes were used in this study. See:http://www.ncbi.nlm.nih.gov/genome/browse/

Unfortunately, it seems that only about half of the finished genomes were used (that is, 6 out of 11), and an additional set of apparently randomly chosen 6 unfinished, draft genome sequences were used, in addition to the apparently draft sequences of another 7 genomes of sequence type ST-474. Although it is stated that seven of the genomes have been deposited to GenBank, they are still not present in the database of complete genomes, as of 1 May, 2013 (the article was published about 6 weeks ago, on 14 March, 2013). In Table 1, I can see accession numbers for DRAFT sequences for two of the seven ST-474 genomes, and the remaining five do not appear to be listed in the NCBI genomes project pages, which includes even planned projects with no data yet. But the two ST-474 genomes listed in Table 1 do not appear to have the sequence type (ST-474) in the GenBank file; instead, all that is listed is "rare MLST strain". This missing meta-data makes it difficult to know if the other five genomes are perhaps there, but I cannot find them, even if I search for the strain name (e.g., P179a) provided for in Table 1.

Figure 1 shows the location of the housekeeping genes in the NCTC 11168 genome (which I recognise because I know that the GenBank accession number is for that strain - but wouldn't it be much more clear to just label this chromosome as 'C. jejuni', and then put the strain name (NCTC 11168)? I am curious as to whether there's a significant AT content difference in the genes in the top half (e.g., closer to the replication origin), compared to the lower half (replication terminus). How does this difference compare to that found between the two gene sets?

From my perspective, Figures 2 - 9 are not very informative at all. These could be collapsed perhaps into a SINGLE box and whisker's plot, where the distributions could easily be compared with each other.

Competing Interests: No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

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Daniel Falush, Department of Evolutionary Genetics, Max Planck Institute, Leipzig, Germany

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Not Approved

I do not understand either from the abstract or reading the earlier paper why this data was collected. Neither the strain collection nor the quantities calculated have any obvious special features. The information presented is of a similar character to statistics that are automatically generated for example by the pubMLST database. There is no reason to clog up the scientific literature with such reports.

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No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

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02 May 2013 | for Version 1

David Ussery, Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark

51 Views Cite this report Responses(0)

Not Approved

This short article describes a comparison of 'housekeeping genes' with 'information processing genes', across 19 Campylobacter jejuni genomes. I cannot fully evaluate this paper as the data is not available. I understand that this is a new journal, and as such perhaps F1000Research has not agreed that all sequences should be deposited to GenBank or EMBL before publication, but I find this frustrating that the results are published, but the data is missing.

Since currently there are only 11 C. jejuni genomes listed as 'complete', I was curious as to what additional genomes were used in this study. See:http://www.ncbi.nlm.nih.gov/genome/browse/

Unfortunately, it seems that only about half of the finished genomes were used (that is, 6 out of 11), and an additional set of apparently randomly chosen 6 unfinished, draft genome sequences were used, in addition to the apparently draft sequences of another 7 genomes of sequence type ST-474. Although it is stated that seven of the genomes have been deposited to GenBank, they are still not present in the database of complete genomes, as of 1 May, 2013 (the article was published about 6 weeks ago, on 14 March, 2013). In Table 1, I can see accession numbers for DRAFT sequences for two of the seven ST-474 genomes, and the remaining five do not appear to be listed in the NCBI genomes project pages, which includes even planned projects with no data yet. But the two ST-474 genomes listed in Table 1 do not appear to have the sequence type (ST-474) in the GenBank file; instead, all that is listed is "rare MLST strain". This missing meta-data makes it difficult to know if the other five genomes are perhaps there, but I cannot find them, even if I search for the strain name (e.g., P179a) provided for in Table 1.

Figure 1 shows the location of the housekeeping genes in the NCTC 11168 genome (which I recognise because I know that the GenBank accession number is for that strain - but wouldn't it be much more clear to just label this chromosome as 'C. jejuni', and then put the strain name (NCTC 11168)? I am curious as to whether there's a significant AT content difference in the genes in the top half (e.g., closer to the replication origin), compared to the lower half (replication terminus). How does this difference compare to that found between the two gene sets?

From my perspective, Figures 2 - 9 are not very informative at all. These could be collapsed perhaps into a SINGLE box and whisker's plot, where the distributions could easily be compared with each other.

Competing Interests

No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

Respond to this report

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[1] 1. Maiden MCJ: Multilocus Sequence Typing of Bacteria. Annu Rev Microbiol. 2006; 60: p. 561–588.

[2] 2. Maiden MCJ, Bygraves JA, Feil E, et al:Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998; 95: p. 3140–3145.

[3] 3. Colles FM, Dingle KE, Cody AJ, et al:Comparison of Campylobacter populations in wild geese with those in starlings and free-range poultry on the same farm. Appl Environ Microbiol. 2008; 74: p. 3583–3590.

[4] 4. Dingle KE, Colles FM, Wareing DR, et al:Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol. 2001; 39: p. 14–23.

[5] 5. McCarthy ND, Colles FM, Dingle KE, et al:Host-associated genetic import in Campylobacter jejuni. Emerg Infect Dis. 2007; 13: p. 267–272.

[6] 6. Sheppard SK, Colles F, Richardson J, et al:Host association of Campylobacter genotypes transcends geographic variation. Appl Environ Microbiol. 2010; 76: p. 5269–5277.

[7] 7. Sheppard SK, McCarthy ND, Falush D, et al:Convergence of Campylobacter Species: implications for Bacterial Evolution. Science. 2008; 320: p. 237–239.

[8] 8. Sheppard SK, McCarthy ND, Jolley KA, et al:Introgression in the genus Campylobacter: Generation and spread of mosaic alleles. Microbiology. 2011; 157: p. 1066–1074.

[9] 9. Wilson DJ, Gabriel E, Leatherbarrow AJ, et al:Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni. Mol Biol Evol. 2009; 26: p. 385–397.

[10] 10. Clark CG, Beeston A, Bryden L, et al:Phylogenetic relationships of Campylobacter jejuni based on porA sequences. Can J Microbiol. 2007; 53: p. 27–38.

[11] 11. Dingle KE, Maiden MC: In Campylobacter: Molecular and Cellular Biology. ed. M.E.K.E.p. Ketley JM. Ketley JM, Konkel ME, Eds Horizon Bioscience, Wymondham, Norfolk, UK, 2005.

[12] 12. Wertz JE, Goldstone C, Gordon DM, et al:A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol. 2003; 16: p. 1236–1248.

[13] 13. Christensen H, Kuhnert P, Olsen JE, et al:Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol. 2004; 54: p. 1601–1609.

[14] 14. Margos G, Gatewood AG, Aanensen DM, et al:MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proc Natl Acad Sci U S A. 2008; 24: p. 8730–8735.

[15] 15. Fouts DE, Mongodin EF, Mandrell RE, et al:Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species. PLoS Biol. 2005; 3: e15.

[16] 16. Gundogdu O, Bentley SD, Holden MT, et al:Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics. 2007; 8: p. 162.

[17] 17. Hofreuter D, Tsai J, Watson RO, et al:Unique features of a highly pathogenic Campylobacter jejuni strain. Infect Immun. 2006; 74: p. 4694-4707.

[18] 18. Lefebure T, Stanhope MJ: Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 2009; 19: p. 1224–1232.

[19] 19. Parker CT, Quiñones B, Miller WG, et al:Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J Clin Microbiol. 2006; 44: p. 4125–4135.

[20] 20. Parkhill J, Wren BW, Mungall K, et al:The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature. 2000; 403: p. 665–668.

[21] 21. Librado P, Rozas J: DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25: p. 1451–1452.

[22] 22. Zhou BB, Elledge SJ: The DNA damage response: putting checkpoints in perspective. Nature. 2000; 408: p. 433–439.

[23] 23. Minin VN, Dorman KS, Fang F, et al:Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics. 2005; 21: p. 3034–3042.

Molecular data analysis of selected housekeeping and informational genes from nineteen Campylobacter jejuni genomes

Abstract

Background

Objectives

Materials and methods

Selection of metabolic and informational housekeeping genes

Figure 1A. Represents the housekeeping genes (n = 25) on the circular NCTC 11168 C. jejuni genome and the MLST housekeeping genes used in typing of C. jejuni are in red fonts.

Figure 1B. Represents the informational genes (n = 25) located on the circular NCTC 11168 C. jejuni genome.

Reference C. jejuni genomes and nucleotide sequences from MLST ST-474 isolates

Table 1. Campylobacter jejuni subsp. jejuni reference genomes.

Table 2. Metabolic genes selected from the MLST schemes of different bacterial species for comparison.

Table 3. Genes of repair mechanism, their gene ID, name, function and the pathways they are involved in.

Table 4. GenBank sequence ids for metabolic genes for the five ST-474 isolates.

Table 5. GenBank sequence Ids of the genes involved in the repair mechanism for the five ST-474 isolates.

Analysis of Guanine-Cytosine content and recombination

Figure 2. Guanine-cytosine (GC) variation in the metabolic housekeeping genes – A.

Figure 3. Guanine-cytosine (GC) variation in the metabolic housekeeping genes – A.

Figure 4. Guanine-cytosine (GC) variation in the metabolic housekeeping genes – A.

Figure 5. Guanine-cytosine (GC) variation in the MLST housekeeping genes – A.

Figure 6. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

Figure 7. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

Figure 8. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

Figure 9. Guanine-cytosine (GC) distribution in the ribosomal and repair genes – A.

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