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This work was supported by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) grants projects RTA2011-00140-C03-02, RTA2014-00018-C02-01 and XAPDIAG EUPHRESCO II project. JGC held a PhD fellowship from the Spanish Government (Ministerio de Educacion, Cultura y Deporte fellowship FPU12/01000). We like to express our gratitude to Dr. James H. Graham from the University of Florida, Citrus Research and Education Center (CREC), for the scientific and English revision of this manuscript.

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Palacio-Bielsa, AnaAuthor

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September 17, 2019
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Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain

Publicated to:Standards In Genomic Sciences. 11 (12): 12- - 2016-01-28 11(12), DOI: 10.1186/s40793-016-0132-3

Authors: Garita-Cambronero, Jerson; Palacio-Bielsa, Ana; Lopez, Maria M; Cubero, Jaime

Affiliations

Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain. - Author
Ctr Invest & Tecnol Agroalimentaria Aragon, Zaragoza, Spain - Author
Inst Nacl Invest & Tecnol Agr & Alimentaria, Madrid, Spain - Author
Inst Valenciano Invest Agr, Valencia, Spain - Author
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain. - Author
Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain. - Author
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Abstract

Xanthomonas arboricola is a species in genus Xanthomonas which is mainly comprised of plant pathogens. Among the members of this taxon, X. arboricola pv. pruni, the causal agent of bacterial spot disease of stone fruits and almond, is distributed worldwide although it is considered a quarantine pathogen in the European Union. Herein, we report the draft genome sequence, the classification, the annotation and the sequence analyses of a virulent strain, IVIA 2626.1, and an avirulent strain, CITA 44, of X. arboricola associated with Prunus spp. The draft genome sequence of IVIA 2626.1 consists of 5,027,671 bp, 4,720 protein coding genes and 50 RNA encoding genes. The draft genome sequence of strain CITA 44 consists of 4,760,482 bp, 4,250 protein coding genes and 56 RNA coding genes. Initial comparative analyses reveals differences in the presence of structural and regulatory components of the type IV pilus, the type III secretion system, the type III effectors as well as variations in the number of the type IV secretion systems. The genome sequence data for these strains will facilitate the development of molecular diagnostics protocols that differentiate virulent and avirulent strains. In addition, comparative genome analysis will provide insights into the plant-pathogen interaction during the bacterial spot disease process.

Keywords

bacterial spot diseaseplant pathogenic bacteriaprunus spp.stone fruitsAnnotationBacteriaBacterial spot diseaseCog databaseGenusIdentificationIv secretionPlant pathogenic bacteriaProposalPrunus spp.Pv. pruniReclassificationStone fruitsSystemsXanthomonas arboricola

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Standards In Genomic Sciences, and although the journal is classified in the quartile Q4 (Agencia WoS (JCR)), its regional focus and specialization in Microbiology, give it significant recognition in a specific niche of scientific knowledge at an international level.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 1.83, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-26, the following number of citations:

  • WoS: 16
  • Scopus: 19
  • Europe PMC: 7

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-26:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 32.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 32 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 0.25.
  • The number of mentions on the social network Facebook: 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.