Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations

Michael Gétaz; Jochen Blom; Theo H. M. Smits; Joël F. Pothier

doi:10.1186/s42483-020-00061-y

Table 1 List of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae strains used in this study. The table provides geographic origin, host plant, year of isolation, CRISPR typing, genomic information such as genome length, contig number, GC content and number of CDS. The presence (+) or absence (−) of the pXf21 and pXf29 plasmids based on tBLASTn analysis of the origins of replication or based on BLASTn analysis of the complete plasmid sequences is also reported. Growth was assessed for each strain and the exponential time before stationary and generation time in hour are listed

From: Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations

Strain	Species	Geographic origin	Host plant	Year of isolation	(sub)group	Genome length	Contig number	GC content (%)	Sequencing technology	CDS	pXf21	pXf29	Exponential time before stationary (h)	Generation time (h)
PD 885^T	X. fragariae	US	Fragaria chiloensis var. ananassa	1960	Xf-CGr-IA	4,247,102	1 chr. + 2 plasmids	62.22	PacBio	4021	+	+	14	3.80
PD 4314	X. fragariae	US	Fragaria chiloensis var. ananassa	1960	Xf-CGr-IA	3,915,166	269	62.21	HiSeq	3526	+	+	28	4.52
PD 2659	X. fragariae	US	Fragaria sp.	1962	Xf-CGr-IA	3,906,466	307	62.22	HiSeq	3521	+	+	28	4.57
ICMP 659	X. fragariae	US	Fragaria sp.	1982	Xf-CGr-IA	4,261,751	430	62.22	MiSeq	4077	+	+	30	5.96
ICMP 661	X. fragariae	US	Fragaria sp.	1982	Xf-CGr-IA	4,237,456	439	62.25	MiSeq	4044	+	+	33	5.48
JVD-0051	X. fragariae	BE	NA	NA	Xf-CGr-IB	4,153,782	372	62.30	MiSeq	3931	+	–	25	4.37
Xf 61	X. fragariae	NL	var. Figaro	2010	Xf-CGr-IB	3,850,449	290	62.33	HiSeq	3428	+	–	26	4.57
PD 2905	X. fragariae	NL	Fragaria sp.	NA	Xf-CGr-IB	3,884,146	309	62.22	HiSeq	3466	+	–	20	4.29
LMG 25863^a	X. fragariae	BE	Fragaria × ananassa Elsanta	2011	Xf-CGr-IC	4,183,685	95	62.18	HiSeq	3920	+	+	28	4.59
GBBC 2087	X. fragariae	BE	NA	NA	Xf-CGr-IC	4,193,468	414	62.25	MiSeq	4024	–	+	20	4.31
JVD-0046	X. fragariae	BE	NA	NA	Xf-CGr-IC	4,189,841	296	62.24	MiSeq	3987	+	+	25	4.21
JVD-0047	X. fragariae	BE	NA	NA	Xf-CGr-IC	4,151,553	413	62.31	MiSeq	3936	–	–	22	3.68
GBBC 2088	X. fragariae	BE	NA	NA	Xf-CGr-IC	4,186,171	414	62.31	MiSeq	3984	+	–	26	4.62
CFBP 5253	X. fragariae	FR	Fragaria sp.	1999	Xf-CGr-IC	4,144,074	282	62.30	MiSeq	3899	+	–	17	4.07
CFBP 5257	X. fragariae	FR	Fragaria sp.	1999	Xf-CGr-IC	4,168,345	436	62.27	MiSeq	3977	–	+	26	3.98
CFBP 5260	X. fragariae	FR	Fragaria sp.	1999	Xf-CGr-IC	4,182,173	413	62.27	MiSeq	3995	+	+	15	3.95
ICMP 13779	X. fragariae	IT	Fragaria × ananassa Duchesne	1996	Xf-CGr-IC	4,214,022	416	62.27	MiSeq	4017	+	+	24	4.69
ICMP 13780	X. fragariae	IT	Fragaria × ananassa Duchesne	1996	Xf-CGr-IC	4,177,334	395	62.28	MiSeq	3978	+	+	24	4.13
PD 3160	X. fragariae	NL	NA	1996	Xf-CGr-IC	3,915,813	302	62.15	HiSeq	3533	+	+	18	4,28
PD 4634	X. fragariae	NL	Fragaria sp.	2003	Xf-CGr-IC	3,884,561	277	62.27	HiSeq	3493	+	+	24	4.41
PD 4932	X. fragariae	NL	Fragaria sp.	2004	Xf-CGr-IC	3,837,440	281	62.29	HiSeq	3540	+	+	28	5.21
PD 5205	X. fragariae	NL	Fragaria sp.	2005	Xf-CGr-IC	4,281,456	1 chr. + 2 plasmids	62.30	PacBio	4033	+	+	18	4.53
PD 5365	X. fragariae	NL	Fragaria sp.	2006	Xf-CGr-IC	3,877,123	298	62.27	HiSeq	3496	+	+	18	4.17
PD 5482	X. fragariae	NL	Fragaria sp.	2007	Xf-CGr-IC	3,888,298	286	62.27	HiSeq	3495	+	+	26	4.84
PD 6879	X. fragariae	NL	Fragaria sp.	2008	Xf-CGr-IC	3,869,542	296	62.27	HiSeq	3477	+	+	24	4.62
PD 6840	X. fragariae	NL	Fragaria sp.	2009	Xf-CGr-IC	3,870,901	288	62.28	HiSeq	3484	+	+	26	4.95
PD 6880	X. fragariae	NL	NA	2011	Xf-CGr-IC	3,868,438	279	62.28	HiSeq	3478	+	+	27	5.23
PD 6881	X. fragariae	NL	NA	2012	Xf-CGr-IC	3,883,071	287	62.27	HiSeq	3503	+	+	30	5.21
PD 6882	X. fragariae	NL	NA	2013	Xf-CGr-IC	3,884,412	274	62.28	HiSeq	3493	+	+	25	4.59
CFBP 4784	X. fragariae	PT	Fragaria sp. Thulda.	1995	Xf-CGr-IC	4,124,432	357	62.31	MiSeq	3904	+	–	24	4.64
CFBP 4785	X. fragariae	PT	Fragaria sp.	1998	Xf-CGr-IC	4,125,383	283	62.29	MiSeq	3868	+	–	18	4.43
CFBP 4786	X. fragariae	PT	Fragaria sp.	1998	Xf-CGr-IC	4,155,600	377	62.27	MiSeq	3924	+	+	NA	NA
FaP29^b	X. fragariae	US	Fragaria × ananassa Portola	2011	Xf-CGr-IC	4,282,602	1 chr. + 2 plasmids	62.30	PacBio	3983	+	+	NA	NA
FaP21^b	X. fragariae	US	Fragaria × ananassa Portola	2011	Xf-CGr-IC	4,282,698	1 chr. + 2 plasmids	62.30	PacBio	3986	+	+	NA	NA
ICMP 20572	X. fragariae	US	Fragaria × ananassa Duchesne	2014	Xf-CGr-IC	4,248,096	455	62.22	MiSeq	4119	+	+	27	5.21
ICMP 20573	X. fragariae	US	Fragaria × ananassa Duchesne	2014	Xf-CGr-IC	4,189,776	430	62.26	MiSeq	4000	+	–	25	4.85
ICMP 20574	X. fragariae	US	Fragaria × ananassa Duchesne	2014	Xf-CGr-IC	4,226,734	426	62.24	MiSeq	4068	+	+	23	4.52
ICMP 20575	X. fragariae	US	Fragaria × ananassa Duchesne	2014	Xf-CGr-IC	4,210,620	404	62.23	MiSeq	4041	+	+	28	4.40
CFBP 6767	X. fragariae	AU	Fragaria × ananassa	1975	Xf-CGr-II	4,129,734	293	62.31	MiSeq	3870	–	–	13	3.91
ICMP 6646	X. fragariae	AU	Fragaria × ananassa Duchesne	1975	Xf-CGr-II	4,137,939	370	62.32	MiSeq	3919	+	–	21	4.11
ICMP 6648	X. fragariae	AU	Fragaria × ananassa Duchesne	1975	Xf-CGr-II	4,153,233	396	62.31	MiSeq	3950	+	–	22	4.37
ICMP 5813	X. fragariae	BR	Fragaria × ananassa Duchesne	1977	Xf-CGr-II	4,147,663	395	62.30	MiSeq	3928	+	–	17	3.87
NCPPB 3743	X. fragariae	BR	Fragaria hybrid cv. Campinas	1990	Xf-CGr-II	4,121,221	257	62.30	MiSeq	3861	+	–	19	3.87
F1–80	X. fragariae	CH	Fragaria cv. Polka	1993	Xf-CGr-II	4,107,680	264	62.31	MiSeq	3829	–	–	22	3.61
F1–81	X. fragariae	CH	Fragaria sp.	1993	Xf-CGr-II	4,180,022	415	62.33	MiSeq	3959	+	–	23	4.05
F2–02	X. fragariae	CH	Fragaria sp.	1994	Xf-CGr-II	4,122,612	273	62.31	MiSeq	3875	+	–	27	4.70
CFBP 2510	X. fragariae	ES	Fragaria sp.	1982	Xf-CGr-II	4,136,197	280	62.29	MiSeq	3886	+	–	18	3.91
PD 3145	X. fragariae	ES	Fragaria sp.	1997	Xf-CGr-II	3,838,331	315	62.32	HiSeq	3431	+	–	16	4.14
NBC 2815	X. fragariae	ES	Fragaria sp.	1997	Xf-CGr-II	4,268,155	1 chr. + 1 plasmid	62.31	PacBio	3939	+	–	18	5.10
CFBP 1558	X. fragariae	FR	Fragaria sp.	1974	Xf-CGr-II	4,155,692	284	62.30	MiSeq	3909	+	–	18	3.80
PD 2662	X. fragariae	GR	Fragaria sp.	1979	Xf-CGr-II	3,825,417	276	62.31	HiSeq	3446	+	–	18	4.00
NCPPB 2473	X. fragariae	IT	Fragaria vesca	1972	Xf-CGr-II	4,169,971	319	62.30	MiSeq	3947	+	–	14	3.84
ICMP 6269	X. fragariae	NZ	Fragaria × ananassa Duchesne	1971	Xf-CGr-II	4,171,021	426	62.34	MiSeq	3954	+	–	17	4.61
ICMP 6277	X. fragariae	NZ	Fragaria × ananassa Duchesne	1972	Xf-CGr-II	4,178,618	426	62.33	MiSeq	3966	+	–	17	4.48
ICMP 6278	X. fragariae	NZ	Fragaria × ananassa Duchesne	1972	Xf-CGr-II	4,170,405	416	62.33	MiSeq	3984	–	–	19	4.14
PD 2660	X. fragariae	NZ	Fragaria ananassa var. tioga	1972	Xf-CGr-II	3,857,327	283	62.33	HiSeq	3453	+	–	20	4.21
ICMP 4019	X. fragariae	NZ	Fragaria × ananassa Duchesne	1974	Xf-CGr-II	4,160,354	405	62.31	MiSeq	3946	+	–	20	3.96
NCPPB 1822	X. fragariae	US	Fragaria chiloensis var. ananassa	1966	Xf-CGr-II	4,138,917	268	62.30	MiSeq	3877	–	–	24	3.92
LMG 19146	X. arboricola pv. fragariae	FR	NA	1986	NA	4,884,039	39	65.88	MiSeq	4020	NR	NR	8	1.56
CFBP 6773	X. arboricola pv. fragariae	NA	NA	NA	NA	4,692,498	39	65.95	MiSeq	3852	NR	NR	NA	NA
LMG 19145^PT	X. arboricola pv. fragariae	IT	Fragaria × ananassa	1993	NA	4,906,785	39	65.88	MiSeq	4019	NR	NR	8	1.56
LMG 19144	X. arboricola pv. fragariae	IT	Fragaria × ananassa	1993	NA	4,842,182	58	65.94	MiSeq	3954	NR	NR	7.4	1.50
CFBP 6762	X. arboricola pv. fragariae	IT	Fragaria × ananassa	1993	NA	4,889,284	38	65.75	MiSeq	4044	NR	NR	NA	NA

^a Genome sequence data obtained from GenBank assembly accession GCA_000376745.1 (Vandroemme et al. 2013a)
^b Genome sequence data obtained from GenBank assembly accessions GCA_001705565.1 and GCA_001705545.1 (Henry and Leveau 2016)
NA: not applicable, NR: not relevant, AU: Australia, BE: Belgium, BR: Brazil, CH: Switzerland, ES: Spain, FR: France, GR: Greece, IT: Italy, NL: Netherlands, NZ: New Zealand, PT: Portugal, US: United States

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