Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

Anamitra Bhattacharyya; Stephanie Stilwagen; Gary Reznik; Helene Feil; William S. Feil; Iain Anderson; Axel Bernal; Mark D'Souza; Natalia Ivanova; Vinayak Kapatral; Niels Larsen; Tamara Los; Athanasios Lykidis; Eugene Selkov; Theresa L. Walunas; Alexander Purcell; Rob A. Edwards; Trevor Hawkins; Robert Haselkorn; Ross Overbeek; Nikos C. Kyrpides; Paul F. Predki

doi:10.1101/gr.370702

Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

Anamitra Bhattacharyya, Stephanie Stilwagen, Gary Reznik, Helene Feil, William S. Feil, Iain Anderson, Axel Bernal, Mark D'Souza, Natalia Ivanova, Vinayak Kapatral, Niels Larsen, Tamara Los, Athanasios Lykidis, Eugene Selkov, Theresa L. Walunas, Alexander Purcell, Rob A. Edwards, Trevor Hawkins, Robert Haselkorn, Ross OverbeekNikos C. Kyrpides, Paul F. Predki

Research output: Contribution to journal › Letter › peer-review

66 Citations (Scopus)

Abstract

Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight all unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium for Xylella.

Original language	English
Pages (from-to)	1556-1563
Number of pages	8
Journal	Genome Research
Volume	12
Issue number	10
DOIs	https://doi.org/10.1101/gr.370702
Publication status	Published - 1 Oct 2002
Externally published	Yes

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1101/gr.370702Licence: In Copyright

Cite this

Bhattacharyya, A., Stilwagen, S., Reznik, G., Feil, H., Feil, W. S., Anderson, I., Bernal, A., D'Souza, M., Ivanova, N., Kapatral, V., Larsen, N., Los, T., Lykidis, A., Selkov, E., Walunas, T. L., Purcell, A., Edwards, R. A., Hawkins, T., Haselkorn, R., ... Predki, P. F. (2002). Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Research, 12(10), 1556-1563. https://doi.org/10.1101/gr.370702

@article{189a4a10580a46e58b2ae3d379cc5bff,

title = "Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights",

abstract = "Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight all unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium for Xylella.",

author = "Anamitra Bhattacharyya and Stephanie Stilwagen and Gary Reznik and Helene Feil and Feil, {William S.} and Iain Anderson and Axel Bernal and Mark D'Souza and Natalia Ivanova and Vinayak Kapatral and Niels Larsen and Tamara Los and Athanasios Lykidis and Eugene Selkov and Walunas, {Theresa L.} and Alexander Purcell and Edwards, {Rob A.} and Trevor Hawkins and Robert Haselkorn and Ross Overbeek and Kyrpides, {Nikos C.} and Predki, {Paul F.}",

year = "2002",

month = oct,

day = "1",

doi = "10.1101/gr.370702",

language = "English",

volume = "12",

pages = "1556--1563",

journal = "Genome Research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

number = "10",

}

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 Research, vol. 12, no. 10, pp. 1556-1563. https://doi.org/10.1101/gr.370702

TY - JOUR

T1 - Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

AU - Bhattacharyya, Anamitra

AU - Stilwagen, Stephanie

AU - Reznik, Gary

AU - Feil, Helene

AU - Feil, William S.

AU - Anderson, Iain

AU - Bernal, Axel

AU - D'Souza, Mark

AU - Ivanova, Natalia

AU - Kapatral, Vinayak

AU - Larsen, Niels

AU - Los, Tamara

AU - Lykidis, Athanasios

AU - Selkov, Eugene

AU - Walunas, Theresa L.

AU - Purcell, Alexander

AU - Edwards, Rob A.

AU - Hawkins, Trevor

AU - Haselkorn, Robert

AU - Overbeek, Ross

AU - Kyrpides, Nikos C.

AU - Predki, Paul F.

PY - 2002/10/1

Y1 - 2002/10/1

N2 - Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight all unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium for Xylella.

AB - Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Here we report a comparative analysis of one complete and two draft genome sequences of the phytopathogenic bacterium, Xylella fastidiosa, which causes serious disease in plants, including citrus, almond, and oleander. We present highlights of an in silico analysis based on a comparison of reconstructions of core biological subsystems. Cellular pathway reconstructions have been used to identify a small number of genes, which are likely to reside within the draft genomes but are not captured in the draft assembly. These represented only a small fraction of all genes and were predominantly large and small ribosomal subunit protein components. By using this approach, some of the inherent limitations of draft sequence can be significantly reduced. Despite the incomplete nature of the draft genomes, it is possible to identify several phage-related genes, which appear to be absent from the draft genomes and not the result of insufficient sequence sampling. This region may therefore identify potential host-specific functions. Based on this first functional reconstruction of a phytopathogenic microbe, we spotlight all unusual respiration machinery as a potential target for biological control. We also predicted and developed a new defined growth medium for Xylella.

UR - http://www.scopus.com/inward/record.url?scp=0036798237&partnerID=8YFLogxK

U2 - 10.1101/gr.370702

DO - 10.1101/gr.370702

M3 - Letter

C2 - 12368248

AN - SCOPUS:0036798237

SN - 1088-9051

VL - 12

SP - 1556

EP - 1563

JO - Genome Research

JF - Genome Research

IS - 10

ER -

Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights

Abstract

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this