Genetic exchange and reassignment in Porphyromonas gingivalis

Figures & data

Table 1. Occurrences of transposase, fimbrilin and CRISPR features in 35 P. gingivalis genomes*

		Fimbrilin types		CRISPR features
Strains	Transposase ^a	FimA type ^b	Mfa1 type^c	CAS ^d	CRISPR ^e		Max. DR ^f
11A	26	II ^h	II	6		3	14
13_1	17	II ^h	I	19		5	93
15_9	18	IV	II	15		6	22
381	90	I ^h	I ^b	14		3	120
3A1	34	II	I	15		5	67
3_3	20	I ^h	I	15		5	52
7BTORR	21	II ^h	II	6		4	15
84_3	25	I ^h	II	6		2	82
A7436	103	IV ^h	I	15		5	17
A7A1-28	28	II ^h	II ^h	14		4	64
A7A1_28	17	II ^h	II	15		4	64
AFR5B1	18	I ^h	II	6		3	67
AJW4	87	II ^h	II ^h	1		2	12
ATCC_33277	96	I	I ^h	14		3	120
ATCC_49417	28	III ^h	II	16		3	8
Ando	8	II ^h	II ^h	2		3	16
F0185	8	II	I ^h	6		15	13
F0566	17	I	I ^h	12		7	19
F0568	14	II	I ^h	6		7	35
F0569	15	II	I ^h	14		22	13
F0570	11	I	I ^h	7		3	9
HG66	81	I ^h	I ^h	14		3	97
JCVI_SC001	23	II	II ^h	0		3	6
KCOM_2797	32	II ^h	I ^h	17		3	74
MP4-504	35	I ^h		6		3	37
SJD11	14	II ^j	I ^h	13		3	46
SJD12	12	I ^b	I ^h	16		5	20
SJD2	10	I ^b	II ^h	4		3	22
SJD4	10	II ^i	II ^h	15		6	72
SJD5	8	I ^b	II ^h	4		3	22
SU60	23	IV	I	15		3	82
TDC60	40	II	I ^h	15		5	66
W4087	13	II	I ^h	6		4	19
W50	25	IV	I ^g,h	15		5	24
W83	59	IV ^h		15		4	24

^a To identify more transposases, sequences of P. gingivalis transposases that were annotated in the 35 genomes, as well as additional ones found in the NCBI protein database, were used to search against all the proteins annotated in the 35 genomes. Proteins that were not previously annotated as transposases but had ≥90% identity and ≥90% length coverage to the queries were considered additional transposases.

^b To identify more FimA proteins, sequences of P. gingivalis FimA that were annotated in the 35 genomes, as well as additional ones found in the NCBI protein database, were used to search against all the proteins annotated in the 35 genomes. Proteins that were not previously annotated as FimA but with ≥90% identity and ≥90% length coverage to the queries were considered additional FimA.

^c To identify more Mfa1 proteins, sequences of P. gingivalis Mfa1 that were annotated in the 35 genomes, as well as additional ones found in the NCBI protein database, were used to search against all the proteins annotated in the 35 genomes. Proteins that were not previously annotated as Mfa1 but with ≥90% identity and ≥90% length coverage to the queries were considered additional Mfa1.

^d CAS: CRISPR Associated System proteins. To identify more CAS proteins, sequences of P. gingivalis CAS that were annotated in the 35 genomes, as well as additional ones found in the NCBI protein database, were used to search against all the proteins annotated in the 35 genomes. Proteins that were not previously annotated as Mfa1 but with ≥90% identity and ≥90% length coverage to the queries were considered additional CRISPR-CAS proteins.

^e CRISPR: these are the number of CRISPR DNA sequences identified by the online CRISPRfinder programme (http://crispr.i2bc.paris-saclay.fr/Server/) [57].

^f Max. DR: Maximal number of direct repeats among the CRISPR identified.

^g A full version of Type I Mfa1 in W50 was 451 a.a. in Figure 1.

^h These annotations were inferred based on the phylogenetic tree in Figure 1; the original NCBI annotation was not associated with fimbrilin or no fimbrilin type inferred.

ⁱ FimA protein of SJD4 was annotated as Type Ib in Figure 1.

^j FimA protein SJD11 was annotated as Type Ib in Figure 1.

Figure 1. Major and minor fimbrilin proteins encoded in the 35 P. gingivalis genomic sequences. All the fimbrilin proteins were detected in the following manner: The keyword FimA/Mfa1/fimbrilin were used to select from the proteins predicted in the 35 genomes, which were annotated by the NCBI prokaryotic genome annotation pipeline [54]. The keywords were also used to search for P. gingivalis FimA from the NCBI protein databases. These “seed” proteins were then searched against all the proteins in the 35 genomes to identify additional fimbrilin candidates. These potential candidates matched with the seed proteins at ≥ 90% sequence identity and ≥ 90% length coverage. The additional candidates were combined with other annotated fimbrilin proteins and aligned with the “mafftℍ program [55]. The aligned sequences were used to build a phylogenetic tree with the “FastTree” program [56]. For each fimbrilin shown in the tree, the Genbank accession number was printed first, followed with the strain label (in blue), the original functional annotation (by NCBI), and the size of the protein sequences in amino acids (red)

Figure 2. Syntenic analysis of 9 P. gingivalis genomic sequences. Of the 35 currently available P. gingivalis genomics sequences, eight are considered finished with one final successfully assembled contig. The sequence of JCVI SC001 appears to have a one-contig circular sequence under the Genbank Accession number CM001843, however it is a pseudo-contig generated by ordering the 284 unassembled contigs using the sequence of strain TDC60 as the template. Thus, the syntenies, illustrated as the same color across different genomes, of JCVI SC001 appear to be in similar order of those in TDC60 and may not be the true order in this genome. Syntenies were detected with the “MUAVE” program (version 2.4.0) [57] and were illustrated as rectangles of the same colors across all genomes. Two groups of syntenies were indicated with blue and red arrows underneath to exemplify the different rearrangement and inversion events in different genomes for this species

Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172.

 PubMed Web of Science ®Google Scholar

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780.

 PubMed Web of Science ®Google Scholar

Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490.

 PubMed Web of Science ®Google Scholar

Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5(6): e11147. DOI:10.1371/journal.pone.0011147.

 PubMed Web of Science ®Google Scholar