About

Rodrigo Almeida is a Professor and the Hildebrand-Laumeister Chair in Plant Pathology at the Center for Computational Biology. He is part of the DE Faculty and is associated with the Department of Plant Pathology. His contact email is rodrigoalmeida@berkeley.edu, and he is involved in research related to computational biology, with a focus on plant pathology. Almeida's work is integrated within the Center for Computational Biology at UC Berkeley, where he contributes to advancing research in computational and systems biology, particularly in areas relevant to plant health and disease.

Research topics

• Biology
• Genetics
• Ecology
• Botany
• Biotechnology
• Computational biology
• Virology
• Horticulture
• Evolutionary biology

Selected publications

• Unreliable evidence to support a vector regulation hypothesis for <i>Xylella fastidiosa</i> –leafhopper interactions

  Applied and Environmental Microbiology · 2025-07-31 · 1 citations

  letterOpen access1st authorCorresponding
  PublisherDOI

• Isolation, Phylogenetic Inferences, and Early Diversification of <i>Xylella fastidiosa</i> subsp. <i>fastidiosa</i> in Cova da Beira Region, Portugal

  Phytopathology · 2025-05-15 · 2 citations

  articleOpen access

  The introduction of Xylella fastidiosa, a plant pathogen with a broad host range, poses a significant threat to agriculture and natural ecosystems. We analyzed six X. fastidiosa subsp. fastidiosa strains obtained from the Beira Interior region of Portugal, an area known for fruit production. Whole-genome sequencing and phylogenetic analyses were performed to genetically characterize these strains and determine their origin. The results suggest that these outbreak-demarcated areas originated from a single introduction event traced back to California, United States. All six strains belong to subspecies fastidiosa, sequence type 1, which has been reported to infect a variety of economically important crops, including cherry, plum, almond, and grapevine. A molecular clock analysis estimated that the introduction occurred between 2010 and 2020 (95% highest posterior density 1999 to 2022), with the strains forming a clade that diverged circa 2020. The findings underscore the importance of continued surveillance in both agricultural and unmanaged ecosystems, as the presence and potential impact of X. fastidiosa on Portuguese landscapes remain largely unknown.

  PublisherOA PDFDOI

• A pathogen of good taste: genetics of a bacterial host jump of the plant pathogen <i>Xylella fastidiosa</i> from coffee to wine grapes.

  PubMed · 2025-07-01

  articleOpen accessSenior author

  whole-genome sequences, 15 from the source region of Costa Rica and 289 from the introduced clade, we tested for traces of adaptation to grapevines. We found both genes and SNPs that are associated with the host shift to grapevines. These results support the hypothesis that a host jump with genetic adaptation occurred following the introduction of the pathogen into the USA.

  PublisherOA PDFDOI

• A Mobile-First Decision Support System for Real-Time Workforce Management in Industrial IoT Environments

  Advances in intelligent systems and computing · 2025-01-01

  book-chapter
  PublisherDOI

• Natural competence in the bacterial pathogen Xylella fastidiosa varies across genotypes and is associated with adhesins

  PLoS Pathogens · 2025-12-08

  articleOpen accessCorresponding

  Natural competence is one of the mechanisms of horizontal gene transfer, an important process that contributes to host-use evolution and other types of environmental adaptation in bacteria. Recently, the plant pathogen Xylella fastidiosa has undergone expansion of its host and geographic ranges. Natural competence has been empirically documented for a few strains of X. fastidiosa, but its prevalence across genotypes and populations is largely unknown. In this study, we characterized the natural competence in vitro of 142 X. fastidiosa strains from diverse hosts and geographic origins, and revealed substantial variability among strains, particularly across subspecies. X. fastidiosa subsp. fastidiosa strains were largely naturally competent, while only 15% of studied subsp. multiplex strains showed recombination, and none of the strains classified in other subspecies were competent. While recombination rates in vitro were associated with subspecies classification, host and climatic variables from the area of isolation did not explain differences in recombination across strains. A genome-wide association study identified several genes linked to variation in natural competence, including a heretofore unknown role for xadA2, which codes for a surface afimbrial adhesin, and the already known fimbrial adhesin type IV pili genes pilY1-1 and pilY1-3. Overall, this study highlights the variability of natural competence among X. fastidiosa strains, that could have an impact on their potential for adaptation to the environment.

  PublisherDOI

• A biophysical approach to the design of networks of communication systems

  ArXiv.org · 2025-06-25

  preprintOpen access1st authorCorresponding

  Inspired by the growth dynamics of the protist \textit{Physarum polycephalum}, we employ a formalism that describes adaptive, incompressible Hagen-Poiseuille flows on channel networks to identify graphs connecting different nodes within Euclidean space. These graphs are either suboptimal or optimal with respect to their length. Occasionally, we derive graph tree configurations that are topologically equivalent to Steiner trees. This methodology can be utilised to assist in making decisions regarding the design of communication networks, such as fibre webs, motorways, or railway networks. As a demonstration of the practicality of this approach, we explicitly apply this framework to the Portuguese railway network.

  PublisherOA PDFDOI

• Artificial Intelligence in the Identification of Germinated Soybean Seeds

  AgriEngineering · 2025-06-02 · 1 citations

  articleOpen access

  This study resulted from the demand for seeds with physiological qualities and studies in germination tests applied for seed improvement aimed at productive and homogeneous harvests. The objective of this study was to improve the classification of seeds in germination tests by introducing YOLO as a classification tool for germinated or nongerminated seeds to specify the results and optimize the analysis period. Germination tests were performed for Glycine max (soybean) seeds, and the capture of images from the tests and conventional categorization was performed by uncorrelated individuals, for the processing of these images and application to YOLO. Subsequently, graphical analyses of the YOLO results and comparison metrics with conventional categorization were performed to determine the accuracy of YOLO as a seed categorization tool. The results derived from the analysis of the graphs and comparisons to the conventional methodology of seed classification showed the effectiveness of YOLO for classifying seeds as germinated or nongerminated, reaching 95% accuracy in seed classification, beyond the range of 0–0.110 of the prediction errors, determined by the application of the methodology of mean square error, highlighting the efficiency of YOLO.

  PublisherOA PDFDOI

• Do stylet‐borne aphid‐transmitted viruses share the same binding sites?

  Annals of Applied Biology · 2025-07-14 · 1 citations

  articleOpen access

  Abstract Specific binding sites for non‐circulative viruses within the mouthparts of aphid vectors have been investigated with limited success. Such sites have been described more precisely for cauliflower mosaic virus (CaMV, Caulimovirus ), and shown to be restricted to the acrostyle, a specific anatomical structure located in the common duct of the aphid stylets. However, the nature and precise location of binding sites of other non‐circulative viruses (e.g., cucumoviruses and potyviruses), and whether distinct viral species compete for the same sites remains unknown. In this study, competition between non‐circulative viruses for binding sites was assessed for viruses that differ in their transmission mode: cucumber mosaic virus (CMV, Cucumovirus ), transmitted by the capsid strategy, and three viruses using the helper strategy for their transmission—turnip mosaic virus (TuMV, Potyvirus ), zucchini yellow mosaic virus (ZYMV, Potyvirus ), and CaMV. In this work, we performed competition and sequential acquisition experiments, with contrasting results obtained depending on the virus species used and the sequence of acquisition/inoculation of the potentially competing viruses. Our results showed that potyviruses and caulimoviruses do not appear to compete for the same binding sites and/or receptors within aphid stylets, as no modifications in their transmission rates were observed regardless of their acquisition sequence. However, a decrease of CMV transmission rate when ZYMV was previously acquired, suggests that potyviruses and cucumoviruses might compete for binding sites in their aphid vectors. Moreover, we observed that potyviruses and cucumoviruses can be co‐acquired and co‐inoculated in the same plant cell during a single intracellular puncture, demonstrating co‐infection of individual cells by more than a single virus species.

  PublisherOA PDFDOI

• A biophysical approach to the design of networks of communication systems

  2025-07-16

  preprintOpen access1st authorCorresponding

  Inspired by the growth dynamics of the protist Physarum polycephalum , we apply the formalism describing adaptive incompressible Hagen-Poiseuilly flows on channel networks to find graphs connecting different nodes distributed on an Euclidean space. These graphs are suboptimal or optimal relative to the graph length. We sometimes obtain graph tree configurations topologically equivalent to Steiner trees. This approach is applied to design communication systems, such as railway systems, highways, or fibre webs. As a proof of concept, we explicitly apply this framework to the Portuguese railway systems.

  PublisherOA PDFDOI

• Multiple genotypes of a quarantine plant pathogen detected in New Zealand indigenous plants located in a botanical garden overseas

  Plant Pathology · 2024-10-27 · 2 citations

  articleOpen accessSenior author

  Abstract Xylella fastidiosa is a xylem‐limited bacterial plant pathogen transmitted by insect vectors. It infects a wide range of plant species and causes devastating diseases. Botanical gardens are global repositories of plant diversity exposed to local biotic and abiotic stresses. We used molecular diagnostic tools for the detection of X . fastidiosa in a collection of New Zealand indigenous plants grown in a X . fastidiosa ‐infected Californian area to determine if any species were infected with this bacterial pathogen and to help inform biosecurity responses. To this end, 130 New Zealand indigenous plant species comprising 72 genera, growing in the University of California Botanical Garden at Berkeley, California, were screened for X . fastidiosa . Multiple PCR‐based methods were used to detect the pathogen at the subspecies and sequence‐type levels directly from plant material; nine plant species tested positive by at least two PCR‐based methods. All nine infections were identified as X . fastidiosa subsp. multiplex sequence types 6 or 7 by the amplification of seven housekeeping genes. Three strains were cultured in vitro and their whole genome sequences were obtained; these strains belonged to three distinct clades within subspecies multiplex , indicating that the infections were not transmitted among these New Zealand indigenous plant species. The information gathered in this study will help to assess the risk of X . fastidiosa to New Zealand indigenous flora and the potential spillover to crops of agricultural importance. The work also shows the applied value of botanical garden collections as sentinels for international plant pathogen biosecurity risk assessment.

  PublisherOA PDFDOI

Frequent coauthors

• Matthew P. Daugherty

  University of California, Riverside

  32 shared

• Helvécio Della Coletta-Filho

  Agronomical Institute of Campinas

  31 shared

• Nabil Killiny

  Florida Department of Citrus

  30 shared

• Anne Sicard

  Centre de Coopération Internationale en Recherche Agronomique pour le Développement

  27 shared

• João Roberto Spotti Lopes

  Universidade Brasil

  26 shared

• María Saponari

  Institute for Sustainable Plant Protection

  22 shared

• Alexander H. Purcell

  University of California, Berkeley

  21 shared

• Michael Ionescu

  University of California, Berkeley

  19 shared

Labs

• Center for Computational BiologyPI