Ricardo I. Alcalá Briseño

I am a Ph.D. candidate at the Plant Pathology Department at the University of Florida. I am investigating viral communities assemblage in landscape agroecology (Virome Network Analysis ViNA). Also, I am interested in the identification of ecological patterns of viruses.
The goal of my research is to asses the viral ecological dynamics in crop systems.


News and coming events:

  • COVID-19 working from home – Since March 2020

Aug 2020

  • Attending to Plant Health 2020 ::APS:: online. Presentation of a digital poster about the sweetpotato virome, and network analysis applications link.

  • Webinar speaker at Solaria Biodata link. Presenting about ““‘Virome studies in agroecological systems applying epidemiological tools and network analysis”. Aug, 11 2020.

Feb – Mar 2020

  • A CABANA workshop in association with EMBL-EBI, was held a workshop about NGS analysis applied to virome sequencing in agricultural systems at the University of Costa Rica, from Feb 24 to 28th and March 2 to 4th, in San Jose, Costa Rica.

Feb 2020

  • Participation in the Roots, tubers and banana (RTB). Annual Pest Risk Assessment Meetings. CC2.1. International Potato Center (CCAFS, CGIAR). Entebbe, Uganda.

May 2019

  • Participated in the Roots, tubers and banana (RTB). Annual Pest Risk Assessment Meetings. CC3.1. Virome networks analysis and its application to agriculture: sweetpotato and potato. (Seoul National University). Seoul, South Korea.

March 2019

  • Invited to present a Master lecture at the Symposium of the Peru Potato Virome: Project results and closure. Presenting the work on “Papaya Virome in Southeast Mexico: Discovery of associations of viruses using viral metagenomics and network analysis”. International Potato Center (CIP, CGIAR). Lima, Peru.
  • Participation in the Roots, tubers and banana (RTB), Annual Seed Systems Meeting. CC2.1. Presenting virome network analysis and its application for seed systems. International Institute of Tropical Agriculture (IITA, CGIAR). Ibadan, Nigeria.

Awards

November 2018

  • Award at the 25th annual International Student Achievement Awards in the IFAS College of Agricultural and Life Sciences (CALS), University of Florida

Reviews and discussions

August 2020

  • A manuscript in collaboration with my friend and colleague Dr. Saad. A data mining approach for the identification of Blueberry red ringspot virus genomes from blueberry root transcriptomes in Florida. Published in Scientific Reports.

June 2020

February 2020

  • A discussion paper on Effective altruism as an ethical lens on research priorities. A live document coming soon. Led by Garrett KA open access in Phytopathology

October 2019

  • A manuscript on the cross-protection in the form of antagonism: the case of Papaya mosaic virus protecting papaya plants against Papaya ringspot virus. Led by Laura Silva-Rosales, is now online in ISHS Acta Horticulturae

September 2018

  • A white paper, from a contribution at the Symposium at University Park, June 2018, on the perspective and futures scenarios of phytobiome management, in Phytobiome Journal

August 2018

  • New paper, led by Karen A. Garrett, on network analysis to address grand challenges in Annual Review of Phytopathology

Novel viruses

August 2020

  • A novel endornavirus identification in Geranium carolinianum and the occurrence within three agroecosystems. Virus Research, led by Rodrigo Valverde

October 2019

  • A new comovirus species from tabasco pepper (Capsicum frutescens) online in Virus Genes, led by Rodrigo A. Valverde.

August 2018

  • A new virus species, Phaseolus vulgaris endornavirus 3 (PvEV3), in the family Endornaviridae was described in Cyamopsis tetragonoloba online in Virus Research, led by Rodrigo A. Valverde.

July 2017

  • A new mastrevirus species, Sugarcane striate virus (SCStV), reported in Florida, Guadeloupe and Reunion infecting Saccharum spp online in Virology Journal, led by Philippe C. Rott.

Mixed infections

September 2018

  • New paper, led by Rodrigo A. Valverde describing a mixed infection of Endornavirus infecting Phaseolus vulgaris is now online in Virus Research

May 2018

  • New report, led by Rodrigo A. Valverde describing a mixed infection of two tobamovirus infecting Capsicum annuum is now online in Plant Disease

April 2015

  • New report on a emerging disease in St. Augustinegrass cv. Floratam in Florida, is now online in Plant Desease

Book chapters

June 2020

December 2015

  • Book chapter, led by Laura Silva-Rosales on Sugarcane mosaic virus a potyvirus distributed worldwide infecting sugarcane, maize and other grasses, edited by Tennant P and Fermin G in CABI
Research

Virome Network Analysis

I am developing a network framework for the analysis of complex viromes in the agroecological landscape, by applying concepts of island biogeography, network analysis and metagenomics. The bipartite network structure explains very intuitively the association of virus and plant–hosts, describing ecological patterns of interactions such as nested and modular. Understanding community structure of viruses, we can translate that knowledge into management strategies and apply other plant disease ecology. A long-term goal of this work is to create a more quantitative approach for understanding community assembly rules and for predicting future emerging pathogens.

Virome dynamics respond to the distribution of plants, changes in the landscape for agricultural usage and climate change alter the patterns of distribution of hosts, and vectors, therefore the landscape connectivity allow emerging pathogens to establish in new niches. We are comparing host and location combinations to determine ecological patterns, viral positive and negative interactions, and spatial relationships.

Diversity of viruses: Viral discovery

Viral metagenomics is a useful tool for assessing the diversity of viruses. Using high-throughput sequencing (HTS) has become the standard tool for virus diagnosis, and the to go tool for revealing associations of viruses within the plant host. Viruses interactions occur at different levels within plant-host, causing necrosis, mosaics, stunting symptoms and some times, asymptomatic. Another interesting feature is that this technique reveals multiple interactions that otherwise would have been difficult to identify, in most cases when an unknown virus is present within the same plant.

publication

– prepints & recent publications –

    -2020-

    1. Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes
      Saad N, Alcalá-Briseño RI, Polston JE, Olmstead JW, Varsani A, and Harmon PF.
      Scientific Reports 2020
    2. Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems
      Herschlag R, Okada R, Alcalá-Briseño RI, de Souto ER, and Valverde RA.
      Virus Research 2020
      https://doi.org/10.1016/j.virusres.2020.198116
    3. Network Analysis of the Papaya Orchard Virome from Two Agroecological Regions of Chiapas, Mexico
      Alcalá-Briseño RI, Casarrubias-Castillo K, López-Ley D, Garrett KA, Silva-Rosales L, and Heck M.
      mSystems 2020

    -2019-

    1. Revisiting cross-protection in the form of antagonism: the case of Papaya mosaic virus protecting papaya plants against Papaya ringspot virus
      Silva-Rosales L, Vargas P, Alcalá-Briseño R, and Casarrubias K.
      Acta Horticulturae 2019
      10.17660/ActaHortic.2019.1250.9
    2. Genome sequence and phylogenetic analysis of a novel comovirus from tabasco pepper (Capsicum frutescens)
      Alcalá-Briseño RI, Lotrakul P, and Valverde RA.
      Virus Genes 2019
    3. Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities
      Phytobiomes 2019
      10.1094/PBIOMES-01-19-0006-W

    -2018-

    1. Genomic sequence of a novel endornavirus from Phaseolus vulgaris and occurrence in mixed infections with two other endornaviruses
      Okada R, Alcalá-Briseño RI, Escalante C, Sabanadzovic S, and Valverde RA.
      Virus Research 2018
      10.1016/j.virusres.2018.09.005
    2. A novel endornavirus isolated from cluster bean (Cyamopsis tetragonoloba)
      Alcalá-Briseño RI, Okada R, Herrera F, and Valverde RA.
      Archives of Virology 2018
      10.1007/s00705-018-3831-9
    3. First Report of a Mixed Infection of Pepper mild mottle virus and Tobacco mild green mosaic virus in Pepper (Capsicum annuum) in the United States
      Escalante C, Alcalá-Briseño RI, and Valverde RA.
      Am Phytopath Society 2018
      10.1111/j.1744-7348.2001.tb00097.x
    software

    plot_from_SDT

    The An R script to plot the output of SDT that allows to plot the identities generated by the Species Demarcation Tool (SDT) [Written by Brejnev Muhire ( SDT package ). Link to Github

    Virome Network Analysis (ViNA)

    I am developing a software that analyze viral metagenomics identification to to qualitative and quantitative network analysis of virome data . This software is part of the development of a virome network analysis framework aiming to understand virome communities in the agroecological landscape ( SDT package ). Link to Github

    experience

    Education

    202X Ph.D candidate Plant Pathology, Plant Pathology, University of Florida

    2013 M.S. Plant Biotechnology, CINVESTAV Irapuato

    2009 B.S. Biology, University of Guadalajara

    Conferences and meetings

    2019 Oral presentation at the 14th International Plant Virus Epidemiology. Seoul, South Korea. “Bipartite network analysis for understanding associations in plant virome: the sweet potato virome in Africa”, May 13-18.

    2019 Roots, tubers and banana (RTB), CGIAR. Annual Pest Risk Assessment Meetings. CC3.1. Seoul National University. Seoul, South Korea, May 20-21.

    2019 Roots, tubers and banana (RTB), CGIAR. Annual Seed Systems Meeting. CC2.1. International Institute of Tropical Agriculture (IITA). Ibadan, Nigeria, March 13-14.

    Professional experience

    2014-2016 Research Scholar, Department of Plant Pathology, University of Florida, USA

    2012-2013 Research Assistant, Department of Genetic Engineering, CINVESTAV Irapuato, Mexico

    2016 Teaching assistant, Introduction to applied bioinformatics, Department of Plant Pathology, UF

    2012 Instructor, Training in molecular techniques for the diagnosis of plant viruses in papaya plants, AGROMOD, Mexico

    post
    contact

    Laboratory of Agricultural Networks Garret_lab

    Department of Plant Pathology University of Florida Gainesville, Fl, 32611

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