Abstract
Xylella fastidiosa causes bacterial leaf scorch in landscape trees including sycamore. We determined the draft genome of X. fastidiosa strain Sy-Va, isolated in Virginia from a sycamore tree displaying leaf scorch symptoms. The Sy-VA genome contains 2,477,829 bp, and has a G+C content of 51.64 mol%.
GENOME ANNOUNCEMENT
Xylella fastidiosa is a Gram-negative, nutritionally fastidious, insect-transmitted and xylem-inhabiting bacterium that causes a wide range of plant diseases, including Pierce’s disease of grapevine and bacterial leaf scorch in landscape trees such as sycamore. At present, five complete genomes of X. fastidiosa have been reported, including those of the citrus variegated chlorosis strain 9a5c (1), Pierce’s disease strains Temecula 1 (2) and GB514 (3), and almond leaf scorch strains M12 and M23 (4). Draft genomes have also been published for the oleander strain Ann1, the almond strain Dixon (5), the elderberry strain EB92-1 (6), and very recently for the mulberry strain Mul-MD (7) and the oak strain griffin-1 (8) of X. fastidiosa. We announce here determination of the draft genome of the sycamore strain of X. fastidiosa, Sy-VA, which was isolated in October of 2002 from a sycamore tree displaying leaf scorch symptoms in Virginia.
Genomic DNA was extracted, from a pure culture of X. fastidiosa strain Sy-VA grown in periwinkle wilt medium (9), using the Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s instructions. Random shotgun and 3-kb mate-pair libraries of Sy-VA were generated and sequenced using Roche 454 GS (FLX titanium) pyrosequencing, resulting in 360,445 shotgun reads and 727,509 mate-pair and single reads totaling 351,334,881 bases having a read length average of ca. 300 bases. After processing by the Newbler gsAssembler v2.7, the total number of reads from all libraries was 1,073,162 aligned reads, with 349,185,278 bases aligned. The genome was assembled into 139 contigs and 25 scaffolds using the Newbler Assembler. The average length of all the contigs was 17,826 bases. The largest contig was 342,206 bases. Among the large contigs that are greater than 600 bases, the N50 contig size was 119,240 bases. All the contigs were run through an annotation pipeline using GeneMark.hmm to predict coding regions based on prior Xylella fastidiosa gene models. To determine endpoints of putative protein coding genes >149 bases, BLASTx was carried out using the contigs as queries against the non-redundant protein sequences (nr). Selected open reading frames that were not consistent with annotated Xylella genes were manually annotated. Predictions of regions encoding tRNAs and rRNAs were made using tRNAscan-SE and RNAmmer programs, respectively.
The depth of sequencing read coverage per base position was 141× for this draft genome of the X. fastidiosa strain Sy-VA; the genome contains 2,477,829 bp and has a G+C content of 51.64 mol%. A total of 2,231 protein-encoding regions or putative genes were predicted, 2,168 of which were tentatively assigned a function. In addition, a ~26-kb plasmid sequence was found that is most similar to the plasmid of the grapevine-infecting GB514 strain (3) of X. fastidiosa.
Nucleotide sequence accession numbers.
This whole-genome shotgun sequence has been deposited at DDBJ/EMBL/GenBank under the accession no. JMHP00000000. The version described in this paper is version JMHP01000000.
ACKNOWLEDGMENTS
This research was supported by the U.S. Department of Agriculture, Agricultural Research Service.
Footnotes
Citation Guan W, Shao J, Davis RE, Zhao T, Huang Q. 2014. Genome sequence of a Xylella fastidiosa strain causing sycamore leaf scorch disease in Virginia. Genome Announc. 2(4):e00773-14. doi:10.1128/genomeA.00773-14.
REFERENCES
- 1. Simpson AJ, Relnac FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LM, Araya JE, Baia GS, Baptista CS, Barros MH, Bonaccorsi ED, Bordin S, Bové JM, Briones MR, Bueno MR, Camargo AA, Camargo LE, Carraro DM, Carrer H, Colauto NB, Colombo C, Costa FF, Costa MC, Costa-Neto CM, Coutinho LL, Cristofani M, Dias-Neto E, Docena C, El-Dorry H, Facincani AP, Ferreira AJ, Ferreira VC, Ferro JA, Fraga JS, França SC, Franco MC, Frohme M, Furlan LR, Garnier M, Goldman GH, Goldman MH, Gomes SL, Gruber A, Ho PL, Hoheisel JD, Junqueira ML, Kemper EL, Kitajima JP, Krieger JE, Kuramae EE, Laigret F, Lambais MR, Leite LC, Lemos EG, Lemos MV, Lopes SA, Lopes CR, Machado JA, Machado MA, Madeira AM, Madeira HM, Marino CL, Marques MV, Martins EA, Martins EM, Matsukuma AY, Menck CF, Miracca EC, Miyaki CY, Monteriro-Vitorello CB, Moon DH, Nagai MA, Nascimento AL, Netto LE, Nhani A, Nobrega FG, Nunes LR, Oliveira MA, de Oliveira MC, de Oliveira RC, Palmieri DA, Paris A, Peixoto BR, Pereira GA, Pereira HA, Pesquero JB, Quaggio RB, Roberto PG, Rodrigues V, de M Rosa AJ, de Rosa VE, de Sá RG, Santelli RV, Sawasaki HE, da Silva AC, da Silva AM, da Silva FR, da Silva WA, da Silveira JF, Silvestri ML, Siqueira WJ, de Souza AA, de Souza AP, Terenzi MF, Truffi D, Tsai SM, Tsuhako MH, Vallada H, Van Sluys MA, Verjovski-Almeida S, Vettore AL, Zago MA, Zatz M, Meidanis J, Setubal JC. 2000. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 406:151–159 [DOI] [PubMed] [Google Scholar]
- 2. Van Sluys MA, De Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LE, da Silva AC, Moon DH, Takita MA, Lemos EG, Machado MA, Ferro MI, da Silva FR, Goldman MH, Goldman GH, Lemos MV, El-Dorry H, Tsai SM, Carrer H, Carraro DM, de Oliveira RC, Nunes LR, Siqueira WJ, Coutinho LL, Kimura ET, Ferro ES, Harakava R, Kuramae EE, Marino CL, Giglioti E, Abreu IL, Alves LM, do Amaral AM, Baia GS, Blanco SR, Brito MS, Cannavan FS, Celestino AV, da Cunha AF, Fenille RC, Ferro JA, Formighieri EF, Kishi LT, Leoni SG, Oliveira AR, Rosa VE, Sassaki FT, Sena JA, de Souza AA, Truffi D, Tsukumo F, Yanai GM, Zaros LG, Civerolo EL, Simpson AJ, Almeida NF, Setubal JC, Kitajima JP. 2003. Comparative analyses of the complete genome sequences of Pierce’s disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriol. 185:1018–1026. 10.1128/JB.185.3.1018-1026.2003 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Schreiber IV, Koiral H, Lara M, Ojeda A, Dowd M, Bextin SE, Moran L. 2010. Unraveling the first Xylella fastidiosa subsp. Fastidiosa genome from Texas. Southwest Entomol. 35:479–483. 10.3958/059.035.0336 [DOI] [Google Scholar]
- 4. Chen J, Xie G, Han S, Chertkov O, Sims D, Civerolo EL. 2010. Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California. J. Bacteriol. 192:4534. 10.1128/JB.00651-10 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Bhattacharyya A, Stilwagen S, Reznik G, Feil H, Feil WS, Anderson I, Bernal A, D’Souza M, Ivanova N, Kapatral V, Larsen N, Los T, Lykidis A, Selkov E, Walunas TL, Purcell A, Edwards RA, Hawkins T, Haselkorn R, Overbeek R, Kyrpides NC, Predki PF. 2002. Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res. 12:1556–1563. 10.1101/gr.370702 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Zhang S, Flores-Cruz Z, Kumar D, Chakrabarty P, Hopkins DL, Gabriel DW. 2011. The Xylella fastidiosa biocontrol strain EB92-1 genome is very similar and syntenic to Pierce’s disease strains. J. Bacteriol. 193:5576–5577. 10.1128/JB.05430-11 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Guan W, Shao J, Zhao T, Huang Q. 2014. Genome sequence of a Xylella fastidiosa strain causing mulberry leaf scorch disease in Maryland. Genome Announc. 2(2):e00916-13. 10.1128/genomeA.00916-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Chen J, Huang H, Chang C-J, Stenger DC. 2013. Draft genome sequence of Xylella fastidiosa subsp. multiplex strain griffin-1 from Quercus rubra in Georgia. Genome Announc. 1(5):e00756-13. 10.1128/genomeA.00756-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Davis MJ, Raju BC, Brlansky RH, Lee RF, Timmer LW, Norris RC, McCoy RE. 1983. Periwinkle wilt bacterium: axenic culture, pathogenicity, and relationships to other gram-negative, xylem-inhabiting bacteria. Phytopathology 73:1510–1515. 10.1094/Phyto-73-1510 [DOI] [Google Scholar]