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Budimir I, Giampieri E, Saccenti E, Suarez-Diez M, Tarozzi M, Dall'Olio D, Merlotti A, Curti N, Remondini D, Castellani G, Sala C. Intraspecies characterization of bacteria via evolutionary modeling of protein domains. Sci Rep 2022; 12:16595. [PMID: 36198716 PMCID: PMC9534902 DOI: 10.1038/s41598-022-21036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.
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Affiliation(s)
- Iva Budimir
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Martina Tarozzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniele Dall'Olio
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Alessandra Merlotti
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
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Patané JSL, Martins J, Rangel LT, Belasque J, Digiampietri LA, Facincani AP, Ferreira RM, Jaciani FJ, Zhang Y, Varani AM, Almeida NF, Wang N, Ferro JA, Moreira LM, Setubal JC. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics 2019; 20:700. [PMID: 31500575 PMCID: PMC6734499 DOI: 10.1186/s12864-019-6007-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. RESULTS Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. CONCLUSIONS Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.
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Affiliation(s)
- José S L Patané
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz Thiberio Rangel
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Luciano A Digiampietri
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Agda Paula Facincani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Rafael Marini Ferreira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Fabrício José Jaciani
- Departamento de Pesquisa e Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, SP, Brazil
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Alessandro M Varani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Jesus A Ferro
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Leandro M Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.
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Gong X, Hung KH, Ting YW, Hsu TW, Malikova L, Tran HT, Huang CL, Liu SH, Chiang TY. Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). PLoS One 2017; 12:e0183209. [PMID: 28841664 PMCID: PMC5571923 DOI: 10.1371/journal.pone.0183209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.
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Affiliation(s)
- Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yu-Wei Ting
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, Taiwan
| | - Lenka Malikova
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Botany CAS, Třeboň, Czech Republic
| | - Huyen Trang Tran
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Natural Science Education, Vinh University, Vinh, Nghe An, Vietnam
| | - Chao-Li Huang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (SHL); (CLH)
| | - Shih-Hui Liu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, United States of America
- Missouri Botanical Garden, Saint Louis, Missouri, United States of America
- * E-mail: (TYC); (SHL); (CLH)
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (SHL); (CLH)
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Knöppel A, Lind PA, Lustig U, Näsvall J, Andersson DI. Minor fitness costs in an experimental model of horizontal gene transfer in bacteria. Mol Biol Evol 2014; 31:1220-7. [PMID: 24536043 DOI: 10.1093/molbev/msu076] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genes introduced by horizontal gene transfer (HGT) from other species constitute a significant portion of many bacterial genomes, and the evolutionary dynamics of HGTs are important for understanding the spread of antibiotic resistance and the emergence of new pathogenic strains of bacteria. The fitness effects of the transferred genes largely determine the fixation rates and the amount of neutral diversity of newly acquired genes in bacterial populations. Comparative analysis of bacterial genomes provides insight into what genes are commonly transferred, but direct experimental tests of the fitness constraints on HGT are scarce. Here, we address this paucity of experimental studies by introducing 98 random DNA fragments varying in size from 0.45 to 5 kb from Bacteroides, Proteus, and human intestinal phage into a defined position in the Salmonella chromosome and measuring the effects on fitness. Using highly sensitive competition assays, we found that eight inserts were deleterious with selection coefficients (s) ranging from ≈ -0.007 to -0.02 and 90 did not have significant fitness effects. When inducing transcription from a PBAD promoter located at one end of the insert, 16 transfers were deleterious and 82 were not significantly different from the control. In conclusion, a major fraction of the inserts had minor effects on fitness implying that extra DNA transferred by HGT, even though it does not confer an immediate selective advantage, could be maintained at selection-transfer balance and serve as raw material for the evolution of novel beneficial functions.
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Affiliation(s)
- Anna Knöppel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Blank CE. Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time. Archaea 2012; 2012:843539. [PMID: 23226971 DOI: 10.1155/2012/843539] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/02/2012] [Accepted: 10/02/2012] [Indexed: 01/26/2023]
Abstract
Phylogenomic analyses of archaeal genome sequences are providing windows into the group's evolutionary past, even though most archaeal taxa lack a conventional fossil record. Here, phylogenetic analyses were performed using key metabolic genes that define the metabolic niche of microorganisms. Such genes are generally considered to have undergone high rates of lateral gene transfer. Many gene sequences formed clades that were identical, or similar, to the tree constructed using large numbers of genes from the stable core of the genome. Surprisingly, such lateral transfer events were readily identified and quantifiable, occurring only a relatively small number of times in the archaeal domain of life. By placing gene acquisition events into a temporal framework, the rates by which new metabolic genes were acquired can be quantified. The highest lateral transfer rates were among cytochrome oxidase genes that use oxygen as a terminal electron acceptor (with a total of 12–14 lateral transfer events, or 3.4–4.0 events per billion years, across the entire archaeal domain). Genes involved in sulfur or nitrogen metabolism had much lower rates, on the order of one lateral transfer event per billion years. This suggests that lateral transfer rates of key metabolic proteins are rare and not rampant.
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Francino MP. The ecology of bacterial genes and the survival of the new. Int J Evol Biol 2012; 2012:394026. [PMID: 22900231 DOI: 10.1155/2012/394026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.
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Karpowicz SJ, Prochnik SE, Grossman AR, Merchant SS. The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem 2011; 286:21427-39. [PMID: 21515685 PMCID: PMC3122202 DOI: 10.1074/jbc.m111.233734] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 04/11/2011] [Indexed: 11/06/2022] Open
Abstract
The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.
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Affiliation(s)
| | - Simon E. Prochnik
- the United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598, and
| | - Arthur R. Grossman
- the Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Sabeeha S. Merchant
- From the Department of Chemistry and Biochemistry and
- Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
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Abstract
Background Microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. Assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem. Results We have developed a new approach that uses linear programming to find between-genome relationships, by treating tables of genetic affinities (here, represented by transformed BLAST e-values) as an optimization problem. Validation trials on simulated data demonstrate the effectiveness of the approach in recovering and representing vertical and lateral relationships among genomes. Application of the technique to a set comprising Aquifex aeolicus and 75 other thermophiles showed an important role for large genomes as 'hubs' in the gene sharing network, and suggested that genes are preferentially shared between organisms with similar optimal growth temperatures. We were also able to discover distinct and common genetic contributors to each sequenced representative of genus Pseudomonas. Conclusions The linear programming approach we have developed can serve as an effective inference tool in its own right, and can be an efficient first step in a more-intensive phylogenomic analysis.
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Affiliation(s)
- Catherine Holloway
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia B3 H 1W5, Canada
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10
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Abstract
The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. Here, we give an introduction to the field and provide an overview of the articles presented in this issue.
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Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de Biochimie, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, Québec, H3T 1J4, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics, McGill University, 3775 University Steet, Montréal, Québec, H3A 2B4, Canada
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