Table 1.

P. freudenreichii strains included in this study. Summary of the genome sequences

Strain	Sequence name	Accession number	Genome size (bp)	Genome coverage	GC%	No. of predicted genes	Note
JS	PFREUDJS001	LN997841	2,675,045	691	67%	2382	Sequenced previously [26]; 261 a
JS2	PFRJS2	LT576032	2,655,351	317	67%	2310	257 a
JS4	PFRJS4	LT576033	2,654,663	158	67%	2366	259 a
JS7	PFRJS7–1	LT618776	2,738,418	300	67%	2412	Genome with prophage; 263 a
	PFRJS7–2	LT618777	2,700,482	50	67%	2355	Genome without phage
	PFRJS7-ph	LT618778	37,936	60	65%	59	Circular phage
JS8	PFRJS8	LT576042	2,655,373	392	67%	2324	264 a
JS9	PFRJS9–1	LT618785	2,720,049	219	67%	2405	Additional transposase gene; 265 a
	PFRJS9–2	LT618786	2,718,592	219	67%	2401
JS10	PFRJS10	LT576035	2,626,110	208	67%	2329	266 a
JS11	PFRJS11	LT576038	2,537,402	501	67%	2200	274 a
JS12	PFRJS12–1	LT604998	2,615,181	250	67%	2275	Additional transposase gene; 275 a
	PFRJS12–2	LT576787	2,613,734	250	67%	2274
	PFRJS12–3	LT604882	24,909	400	64%	32	Putative conjugative plasmid
JS13	PFRJS13–1	LT618779	2,537,370	210	67%	2201	11-gene insertion; 276 a
	PFRJS13–2	LT618780	2,520,651	90	67%	2189
JS14	PFRJS14	LT593929	2,507,188	330	67%	2180	277 a
JS15	PFRJS15–1	LT618787	2,621,081	94	67%	2322	3 additional transposase genes; 281 a
	PFRJS15–2	LT618788	2,616,005	94	67%	2320	Transposase gene disrupting a Type III RM methylase
JS16	RM25	CP010341	2,649,163	190	67%	2321	Sequenced previously [25]; 282 a
JS17	PFRJS17–1	LT618789	2,755,516	192	67%	2455	Duplicated transposase gene; 283 a
	PFRJS17–2	LT618790	2,754,069	192	67%	2454
JS18	PFRJS18	LT576034	2,661,974	190	67%	2358	284 a
JS20	PFRJS20–1	LT618791	2,678,207	106	67%	2384	286 a
	PFRJS20–2	LT618792	2,682,327	106	67%	2376	3 additional transposase genes; one disrupting another transposase gene
JS21	PFRJS21–1	LT618781	2,659,993	222	67%	2330	Additional transposase genes; 287 a
	PFRJS21–2	LT618782	2,658,550	222	67%	2329
JS22	PFRJS22–1	LT599498	2,633,661	190	67%	2326	Genome with prophage; 288 a
	PFRJS22-ph	LT615138	39,309	102	66%	61	Circular phage
JS23	PFRJS-23	LT618793	2,630,698	210	67%	2335	Genome with prophage; 289 a
	PFRJS-23-ph	LT618794	42,723	25	65%	66	Circular phage
JS25	PFRJS25–1	LT618783	2,666,517	400	67%	2336	291 a
	PFRJS25–2 pl	LT618784	35,640	800	64%	46	Putative conjugative plasmid

^a Strain number in the previous study [48]