Genetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing

Bridel, Sébastien; Bourgeon, Frédéric; Marie, Arnaud; Saulnier, Denis; Pasek, Sophie; Nicolas, Pierre; Bernardet, Jean-François; Duchaud, Eric

doi:10.1186/s13567-020-00782-0

Veterinary Research

Table 1 General genome features.

From: Genetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing

Strain	Country	Host	Tissue	Date of isolation	Technology	Reads (post-trimming)	Contigs (> 2000pb)	Total length	GC %	Coverage	Number of predicted genomic islands	SNPs vs. NCIMB 2154^T	Predicted CDS	Genbank Assembly
NCIMB 2154T	Japan	Pagrus major	Skin	1977	[20]	n/a	1	3453 971	32.01	1734	29	0	2774	GCA_900119795.1
TM-KORJJ	Korea	Paralichthys olivaceus	n/a	n/a	PacBio	n/a	1	3333 272	31.98	300	24	15 049	2735	GCA_004803875.1
NBRC 15946	Japan	n/a	n/a	n/a	HiSeq	n/a	96	3 240 791	31.80	123	20	10 084	2692	GCA_000509405.1
P1-39	France	Dicentrarchus labrax	Liver	2010	HiSeq (2 × 100 bp)	56 562 140	104	3 337 690	31.79	93	23	15 401	2788	GCA_902705535
P4-45	France	Dicentrarchus labrax	Skin	2010	HiSeq (2 × 100 bp)	54 681 392	73	3 349 546	31.81	70	27	15 707	2843	GCA_902705495
902	France	Dicentrarchus labrax	Skin	2013	HiSeq (2 × 100 bp)	88 844 854	68	3 372 337	31.80	85	24	15 521	2851	GCA_902705365
Aq16-85	French Polynesia	Platax orbicularis	Skin	2016	MiSeq (2 × 300 bp)	2 174 369	43	3 198 696	31.88	220	21	14 929	2664	GCA_902705305
Aq16-88	French Polynesia	Platax orbicularis	Skin	2016	MiSeq (2 × 300 bp)	3 434 486	45	3 196 671	31.88	301	21	14 966	2665	GCA_902705275
Aq16-89	French Polynesia	Platax orbicularis	Skin	2016	MiSeq (2 × 300 bp)	2 156 781	45	3 196 642	31.89	171	21	14 914	2666	GCA_902705375
TFA4	French Polynesia	Platax orbicularis	Skin	2013	MiSeq (2 × 300 bp)	2 369 550	66	3 356 632	31.82	226	33	14 961	2865	GCA_902705565
FS08(1)	Italy	Sparus aurata	Skin	2006	MiSeq (2 × 300 bp)	1 256 466	54	3 399 437	31.81	87	30	4424	2866	GCA_902705395
NAC SLCC MFF	Malta	Dicentrarchus labrax	Skin	1995	MiSeq (2 × 300 bp)	1 091 150	80	3 352 671	31.81	76	29	40 598	2795	GCA_902705345
USC SP9.1	Spain	Salmo salar	Skin	1993	MiSeq (2 × 300 bp)	727 120	80	3 395 385	31.84	46	30	31 252	2779	GCA_902705515
DPIF 89/3001-6.2	Tasmania	Latris lineata	Skin	1989	MiSeq ( 2 × 300 bp)	1 019 320	129	3 448 890	31.77	66	33	26 962	2788	GCA_902705315
DPIF 89/0239-1	Tasmania	Salmo salar	Skin	1989	MiSeq (2 × 300 bp)	1 496 188	55	3 353 931	31.90	92	28	17 743	2773	GCA_902705355
USC SE30.1	Spain	Oncorhynchus kisutch	Mouth	1993	MiSeq (2 × 300 bp)	749 406	111	3 544 405	31.75	52	30	31 928	2928	GCA_902705525
UCD SB2	California	Atractoscion nobilis	n/a	1995	MiSeq (2 × 300 bp)	1 323 140	50	3 308 376	31.91	85	23	17 064	2715	GCA_902705445
JIP 32/91-4	France	Dicentrarchus labrax	Skin	1991	MiSeq (2 × 300 bp)	1 031 822	59	3 447 003	31.80	59	31	17 265	2872	GCA_902705385
CVI1001048	Holland	Solea solea	Skin	2010	MiSeq (2 × 300 bp)	1 242 180	42	3224 047	31.94	90	16	1659	2670	GCA_902705265
FC	Chile	Scophthalmus maximus	Eye	1998	MiSeq (2 × 300 bp)	1086 816	57	3 505 634	32.01	70	27	16 571	2921	GCA_902705415
P2-48	France	Solea senegalensis	Skin	2010	MiSeq (2 × 300 bp)	1 349 672	55	3 418 994	31.86	90	34	43 607	2910	GCA_902705555
P2-27	Spain	Scophthalmus maximus	Skin	2011	MiSeq (2 × 300 bp)	1 087 036	88	3 371 677	31.82	76	24	19 639	2821	GCA_902705465
JIP 46/00	France	Scophthalmus maximus	Skin	2000	MiSeq (2 × 300 bp)	1 155 334	56	3 371 335	31.89	73	25	17 215	2781	GCA_902705435
JIP 10/97	France	Scophthalmus maximus	Skin	1997	MiSeq (2 × 300 bp)	1 345 346	52	3 333 073	31.86	86	22	17 441	2746	GCA_902705285
NCIMB 2158	Scotland	Solea solea	Skin	1981	MiSeq (2 × 300 bp)	1 138 826	74	3 369 590	31.87	79	28	17 387	2797	GCA_902705425

The list of contributors is available in Additional file 1.

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