Genome sequencing of four strains of Phylotype I, II and IV of <i>Ralstonia solanacearum</i> that cause potato bacterial wilt in India

Patil, Virupaksh U.; Girimalla, Vanishree; Sagar, Vinay; Chauhan, Rajinder Singh; Chakrabarti, Swarup Kumar

doi:10.1016/j.bjm.2016.10.016

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Genome Announcements • Braz. J. Microbiol. 48 (2) • Apr-Jun 2017 • https://doi.org/10.1016/j.bjm.2016.10.016 copy

Genome sequencing of four strains of Phylotype I, II and IV of Ralstonia solanacearum that cause potato bacterial wilt in India

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Ralstonia solanacearum is a heterogeneous species complex causing bacterial wilts in more than 450 plant species distributed in 54 families. The complexity of the genome and the wide diversity existing within the species has led to the concept of R. solanacearum species complex (RsSC). Here we report the genome sequence of the four strains (RS2, RS25, RS48 and RS75) belonging to three of the four phylotypes of R. solanacearum that cause potato bacterial wilt in India. The genome sequence data would be a valuable resource for the evolutionary, epidemiological studies and quarantine of this phytopathogen.

Keywords:
Potato wilt; Ralstonia; Species Complex; Phylotype; Bipartite; Genome

Strain	Origin	Isolated from	Phylotype^a a Sequevar numbers are in parenthesis.	Sequence status	Genome size (Kb)^b b CHR - chromosome, MLP - Megaplsmid, ND - not available.			GC%^c c G + C content in percent.	CDS^d d CDS - number of coding sequences.	rRNA^e e Number of genes coding for ribosomal RNAs.	tRNA^f f Number of genes coding for transfer RNAs.	T3E^g g Number of predicted type III effectors.	Reference
					CHR	MPL	Total
Grenada9-1	Grenada	Banana	IIA(6)	Draft	NA	NA	5479	66.60	5365	3^h h ARAGON tRNA detection.	56^h h ARAGON tRNA detection.	NA	⁹9 Ailloud F, Lowe T, Cellier G, Roche D, Allen C, Prior P. Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity. BMC Genomics. 2015;16:270.
IBSBF1503	Peru	Cucumber	II(4)NPB	Draft	NA	NA	5514	66.70	5452	3^h h ARAGON tRNA detection.	54^h h ARAGON tRNA detection.	NA
CBF1416	Costa Rica	Plantain	IIB(3)	Draft	NA	NA	5744	66.60	5722	3^h h ARAGON tRNA detection.	59^h h ARAGON tRNA detection.	NA
Rs-09-161	India	Eggplant	I/R1b3	Complete	3741	1985	5726	66.82	5213	3^h h ARAGON tRNA detection.	66^h h ARAGON tRNA detection.	71	¹⁰10 Raman R, Gaitonde S, Achari G, et al. Genome sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, strains Rs-09-161 and Rs-10-244, isolated from eggplant and Chili in India. Genome Announc. 2014;2(3):e00323-e414.
Rs-10-244	India	Chilli	I/R1b3	Complete	3716	2025	5741	66.98	5202	3^h h ARAGON tRNA detection.	63^h h ARAGON tRNA detection.	76
RS-2 ⁱ i Isolated from the infected stem.	Indore (MP), India	Potato	IIB(1)	Draft	3481	1608	4768	57.36	4590	2	53	63	This study
RS-25 ^j j Isolated from infected tubers.	Shimla (HP), India	Potato	I(45)	Draft	3065	1950	5232	60.11	4732	3	57	91
RS-48 ^j j Isolated from infected tubers.	Shimla (HP), India	Potato	I(30)	Draft	3065	1727	5300	60.10	4817	3	57	89
RS-75 ⁱ i Isolated from the infected stem.	Shillong (Meghalaya), India	Potato	IV(8)	Draft	2903	1720	5045	60.06	4867	2	54	73
GMI1000	Fr. Guyana	Tomato	I (18)	Complete	3716	2094	5811	67.00	5120	4	57	74	¹¹11 Salanoubat M, Genin S, Artiguenave F, et al. Genome sequencing of the plant pathogen Ralstonia solanacearum. Nature. 2002;415:497-502.
Y45	China	Tomato	IB	Draft	3726	1986	5712	NA	5496	5	53	ND	¹²12 Li Z, Wu S, Bai X, et al. Genome sequence of the tobacco bacterial wilt pathogen Ralstonia solanacearum. J Bacteriol. 2011;193(21):6088-6089.
FYQ_4	China	Tomato	I	Complete	3715	2089	5805	66.82	5153	9	62	ND	¹³13 Cao Y, Tian B, Liu Y, et al. Genome sequencing of Ralstonia solanacearum FQY_4, isolated from a bacterial wilt nursery used for breeding crop resistance. Genome Announc. 2013;1(3):e00125-e213.
K60	USA	Tomato	IIA(7)	Draft	3717	1773	5490	66.70	5213	3^h h ARAGON tRNA detection.	51^h h ARAGON tRNA detection.	ND	¹⁴14 Remenant B, Babujee L, Lajus A, Médigue C, Prior P, Allen C. Sequencing of K60, type strain of the major plant pathogen Ralstonia solanacearum. J Bacteriol. 2012;194(10):2742-2743.
CFBP2957	Fr. West Indies	Tomato	IIA(36)	Complete	3539	2144	5683	69.90	5310	1	56	72	¹⁵15 Remenant B, Goutaland BC, Guidot A, et al. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics. 2010;11:379.
Molk2	Phillippines	Banana	IIB(3)	Draft	NA	NA	5961	66.70	5061	1	34	75
CMR15	Cameroon	Tomato	III(29)	Complete	3594	1963	5593	69.90	5149	3	59	67
Psi07	Indonesia	Tomato	IV(10)	Complete	3508	2085	5606	66.30	5247	1	49	74
Po82	Mexico	Potato	IIB(4)	Complete	3481	1949	5430	66.65	5019	3	54	75	¹⁶16 Xu J, Zheng HJ, Liu L, et al. Complete genome sequence of the plant pathogen Ralstonia solanacearum strain Po82. J Bacteriol. 2011;193(16):4261-4262.
BDB R229	Indonesia	Banana	IV	Draft	3574	1585	5159	66.50	4629	1	45	57	¹⁷17 Remenant B, de Cambiaire J-C, Cellier G, et al. Ralstonia syzygii, the blood disease bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles. PLoS ONE. 2011;6(9):e24356.
R. syzygii R24	Indonesia	Clove	IV	Draft	3681	1743	5424	65.90	4867	2	50	48

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E-mail: bjm@sbmicrobiologia.org.br

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[1] *Corresponding author at: Division of Crop Improvement, Central Potato Research Institute, Shimla 171 001, Himachal Pradesh, India. E-mails: veerubt@gmail.com virupakshagouda.patil@icar.gov.in (V.U. Patil).