Identification of genetic relationships and subspecies signatures in Xylella fastidiosa

Denancé, Nicolas; Briand, Martial; Gaborieau, Romain; Gaillard, Sylvain; Jacques, Marie-Agnès

doi:10.1186/s12864-019-5565-9

BMC Genomics

Table 6 Main features related to the specific mers identified in X. fastidiosa subspecies

From: Identification of genetic relationships and subspecies signatures in Xylella fastidiosa

A. X. fastidiosa subspecies	FAS¹	FAS2¹	SAN¹	SAN2¹	MOR¹	MUL¹	PAU¹
number of mers	2905	1978	9808	5765	3094	4906	11,365
number of unique mers	2836	1957	9431	5636	2995	4813	11,162
total mer size (bp)	133,179	85,038	518,683	292,740	142,614	258,228	627,685
number of mers in CDS	2172	1411	7783	4161	2341	3603	9088
number of unique CDS	1142	811	2406	1646	1115	1119	1711
total mer size in CDS (bp)	100,015	60,092	414,736	215,901	108,336	189,973	504,054
number of mers in intergenic regions	733	567	2025	1604	753	1303	2277
total mer size in intergenic regions (bp)	33,164	24,946	103,947	76,839	34,278	68,255	123,631
B. Combination morus + other subspecies	MOR-FAS¹	MOR-FAS2¹	MOR-SAN¹	MOR-SAN2¹	MOR-SAN-SAN2¹	MOR-SAN-SAN2-FAS2¹	MOR-MUL¹	MOR-PAU¹
number of mers	495	1236	352	371	237	3389	2131	71
number of unique mers	491	1222	347	358	235	3369	2072	71
total mer size (bp)	20,058	53,052	13,123	14,066	8019	136,470	98,450	2377
number of mers in CDS	331	825	258	243	116	2367	1638	58
number of unique CDS	216	430	192	178	103	806	572	41
total mer size in CDS (bp)	13,428	36,147	9816	9275	4249	96,946	76,167	2018
number of mers in intergenic regions	164	411	94	128	121	1022	493	13
total mer size in intergenic regions (bp)	6630	16,905	3307	4791	3770	39,524	22,283	359
C. Within subspecies pauca	pauca I.1¹	pauca I.2¹	pauca I.3¹	CFBP 8072¹	Hib4¹
number of mers	1266	2360	3885	4775	4694
number of unique mers	1238	2323	3644	4663	4596
total mer size (bp)	59,733	121,367	207,098	283,540	341,563
number of mers in CDS	1003	1776	3194	3150	3338
number of unique CDS	486	716	1147	1205	1324
total mer size in CDS (bp)	47,655	92,528	173,936	194,240	269,888
number of mers in intergenic regions	263	584	690	1625	1356
total mer size in intergenic regions (bp)	12,078	28,839	33,162	89,300	71,675

¹Composition of the groups:
MOR (subsp. morus): Mul-MD and Mul0034 (Reference: 2,666,577 bp). FAS (subsp. fastidiosa): ATCC 35879, DSM 10026, CFBP 7969, CFBP 7970, CFBP 8071, CFBP 8082, CFBP 8351, EB92–1, GB514, M23, Stag’s Leap and Temecula1 (Reference: 2,521,148 bp). FAS2 (subsp. fastidiosa): All the members of the group FAS (with Temecula1 as reference), plus CFBP 8073. MUL (subsp. multiplex): ATCC 35871, BB01, CFBP 8078, CFBP 8416, CFBP 8417, CFBP 8418, Dixon, Griffin-1, Sy-VA and M12 (Reference: 2,475,130 bp). SAN (subsp. sandyi): Ann-1 (Reference: 2,780,908 bp). SAN2 (subsp. sandyi-like): CFBP 8356 and CO33 (Reference: 2,416,985 bp). PAU (subsp. pauca): 32, 3124, 11,399, 6c, CFBP 8072, CoDiRO, COF0324, COF0407, CVC0251, CVC0256, Fb7, Hib4, J1a12, OLS0478, OLS0479, Pr8x, U24D and 9a5c (Reference: 2,731,750 bp). pauca I.1 (subsp. pauca): U24D, Fb7, CVC0251, CVC0256, J1a12, 11,399, 3124, 32 and 9a5c (Reference: 2,731,750 bp). pauca I.2 (subsp. pauca): 6c, COF0324 and Pr8x (Reference: 2,666,242 bp). pauca I.3 (subsp. pauca): COF0407, OLS0478, OLS0479 and CoDiRO (Reference: 2,542,932 bp). CFBP 8072 (subsp. pauca; 2,496,662 bp). Hib4 (subsp. pauca; 2,877,548 bp)

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ISSN: 1471-2164

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