A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

Alexis Criscuolo

doi:10.3897/rio.5.e36178

Doron Levin, Neta Raab, Yishay Pinto, Daphna Rothschild, Gal Zanir, Anastasia Godneva, Nadav Mellul, David Futorian, Doran Gal, Sigal Leviatan, David Zeevi, Ido Bachelet, Eran Segal (2021)
Diversity and functional landscapes in the microbiota of animals in the wild. Science 372: .

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Melanie Hennart, Julien Guglielmini, Sébastien Bridel, Martin C J Maiden, Keith A. Jolley, Alexis Criscuolo, Sylvain Brisse, Crystal Hepp (2022)
A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy ofKlebsiella pneumoniaeStrains. Molecular Biology and Evolution 39: .

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Sukriti Gujarati, Diptaraj Chaudhari, Ashwini Hagir, Mitesh Khairnar, Yogesh Shouche, Praveen Rahi (2020)
Klebsiella indica sp. nov., isolated from the surface of a tomato. International Journal of Systematic and Evolutionary Microbiology 70: 3278.

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Yuanyuan Huang, Yanfei Wu, Han Hu, Bangzhuo Tong, Jie Wang, Siyu Zhang, Yanyi Wang, Jicong Zhang, Yue Yin, Shengkun Dai, Wenjuan Zhao, Bolin An, Jiahua Pu, Yaomin Wang, Chao Peng, Nan Li, Jiahai Zhou, Yan Tan, Chao Zhong (2024)
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Stefan E. Heiden, Nils-Olaf Hübner, Jürgen A. Bohnert, Claus-Dieter Heidecke, Axel Kramer, Veronika Balau, Wolfgang Gierer, Stephan Schaefer, Tim Eckmanns, Sören Gatermann, Elias Eger, Sebastian Guenther, Karsten Becker, Katharina Schaufler (2020)
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition. Genome Medicine 12: .

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Jianke Yang, Yuanxin Ye, Ran Yi, De Bi, Sijia Zhang, Shiyun Han, Xianzhao Kan (2024)
A new perspective on codon usage, selective pressure, and phylogenetic implications of the plastomes in the Telephium clade (Crassulaceae). Gene 892: 147871.

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Inderjit S. Yadav, Nidhi Rawat, Parveen Chhuneja, Satinder Kaur, Christobal Uauy, Gerard Lazo, Yong Q. Gu, Jaroslav Doležel, Vijay K. Tiwari (2023)
Comparative genomic analysis of 5Mg chromosome of Aegilops geniculata and 5Uu chromosome of Aegilops umbellulata reveal genic diversity in the tertiary gene pool. Frontiers in Plant Science 14: .

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Peter Kämpfer, Hans-Jürgen Busse, John A. McInroy, Dominique Clermont, Alexis Criscuolo, Stefanie P. Glaeser (2021)
Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays . International Journal of Systematic and Evolutionary Microbiology 71: .

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Elena Requena, Lola Alonso-Guirado, Javier Veloso, María Villarino, Paloma Melgarejo, Eduardo Antonio Espeso, Inmaculada Larena (2023)
Comparative analysis of Penicillium genomes reveals the absence of a specific genetic basis for biocontrol in Penicillium rubens strain 212. Frontiers in Microbiology 13: .

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Peter Kämpfer, S. P. Glaeser, John A. McInroy, Dominique Clermont, Alexis Criscuolo, Hans-Jürgen Busse (2021)
Pseudomonas carbonaria sp. nov., isolated from charcoal. International Journal of Systematic and Evolutionary Microbiology 71: .

DOI: 10.1099/ijsem.0.004750

Budi Permana, Patrick N. A. Harris, Naomi Runnegar, Margaret Lindsay, Belinda C. Henderson, E. G. Playford, David L. Paterson, Scott A. Beatson, Brian M. Forde, Se-Ran Jun (2023)
Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland. Microbiology Spectrum 11: .

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Veronica Folliero, Carlo Ferravante, Valentina Iovane, Annamaria Salvati, Laura Crescenzo, Rossella Perna, Giusy Corvino, Maria T. Della Rocca, Vittorio Panetta, Alessandro Tranfa, Giuseppe Greco, Teresa Baldoni, Ugo Pagnini, Emiliana Finamore, Giorgio Giurato, Giovanni Nassa, Mariagrazia Coppola, Luigi Atripaldi, Rita Greco, Annamaria D’Argenio, Maria Grazia Foti, Rosamaria Abate, Annalisa Del Giudice, Bruno Sarnelli, Alessandro Weisz, Giuseppe Iovane, Renato Pinto, Gianluigi Franci, Massimiliano Galdiero (2024)
Whole Genome Sequence Dataset of Mycobacterium tuberculosis Strains from Patients of Campania Region. Scientific Data 11: .

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Peter Kämpfer, John A. McInroy, Dominique Clermont, Meina Neumann-Schaal, Alexis Criscuolo, Hans-Jürgen Busse, Stefanie P. Glaeser (2021)
Leucobacter soli sp. nov., from soil amended with humic acid. International Journal of Systematic and Evolutionary Microbiology 71: .

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Shekhar Nagar, Chandni Talwar, Shazia Haider, Akshita Puri, Kalaiarasan Ponnusamy, Madhuri Gupta, Utkarsh Sood, Abhay Bajaj, Rup Lal, Roshan Kumar (2020)
Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. Frontiers in Microbiology 11: .

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Peter Kämpfer, S. P. Glaeser, John A. McInroy, Jia Xu, Hans-Jürgen Busse, Dominique Clermont, Alexis Criscuolo (2020)
Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum . International Journal of Systematic and Evolutionary Microbiology 70: 5824.

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Daniel Mietchen, Lyubomir Penev, Teodor Georgiev, Boriana Ovcharova, Iva Kostadinova (2021)
Open science in practice: 300 published research ideas and outcomes illustrate how RIO Journal facilitates engagement with the research process. Research Ideas and Outcomes 7: .

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Sergey V Tarlachkov, Taras V Shevchuk, Maria del Carmen Montero-Calasanz, Irina P Starodumova, John Hancock (2020)
Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments. Bioinformatics 36: 1668.

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Elias Eger, Stefan E. Heiden, Katja Korolew, Claude Bayingana, Jules M. Ndoli, Augustin Sendegeya, Jean Bosco Gahutu, Mathis S. E. Kurz, Frank P. Mockenhaupt, Julia Müller, Stefan Simm, Katharina Schaufler (2021)
Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda. Frontiers in Microbiology 12: .

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Yinggai Song, Nickolas Menezes da Silva, Vania A. Vicente, Yu Quan, Marcus Teixeira, Jie Gong, Sybren de Hoog, Ruoyu Li (2021)
Comparative genomics of opportunistic Phialophora species involved in divergent disease types. Mycoses 64: 555.

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Marta Lourenço, Lisa Osbelt, Virginie Passet, François Gravey, Daniela Megrian, Till Strowig, Carla Rodrigues, Sylvain Brisse, Stefano Pagliara (2023)
Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance. Microbiology Spectrum 11: .

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Peter Kämpfer, Hans-Jürgen Busse, Dominique Clermont, Alexis Criscuolo, Stefanie P. Glaeser (2021)
Devosia equisanguinis sp. nov., isolated from horse blood. International Journal of Systematic and Evolutionary Microbiology 71: .

DOI: 10.1099/ijsem.0.005090

Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab (2022)
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling. Cell Systems 13: 817.

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Vladimir Smirnov, Tandy Warnow (2020)
Unblended disjoint tree merging using GTM improves species tree estimation. BMC Genomics 21: .

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Alexis Criscuolo (2020)
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Research 9: 1309.

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Javier E. Soto, Cecilia Hernández, Miguel Figueroa (2023)
JACC-FPGA: A hardware accelerator for Jaccard similarity estimation using FPGAs in the cloud. Future Generation Computer Systems 138: 26.

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Deangelo Wilson, John D. Rogers (2023)
Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting. Journal of Computational Biology 30: 250.

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Sathyanarayanan N. Aakur, Vishalini R. Laguduva, Priyadharsini Ramamurthy, Akhilesh Ramachandran (2024)
TEPI: Taxonomy-Aware Embedding and Pseudo-Imaging for Scarcely-Labeled Zero-Shot Genome Classification. IEEE Journal of Biomedical and Health Informatics 28: 2385.

DOI: 10.1109/JBHI.2024.3358842

Peter Kämpfer, André Lipski, Lucie Lamothe, Dominique Clermont, Alexis Criscuolo, John A. McInroy, Stefanie P. Glaeser (2022)
Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root. Archives of Microbiology 204: .

DOI: 10.1007/s00203-022-03225-w

Edgar Badell, Mélanie Hennart, Carla Rodrigues, Virginie Passet, Melody Dazas, Leonardo Panunzi, Valérie Bouchez, Annick Carmi–Leroy, Julie Toubiana, Sylvain Brisse (2020)
Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex. Research in Microbiology 171: 122.

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Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P. C. Rocha, David Vallenet, Christos A. Ouzounis (2020)
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLOS Computational Biology 16: e1007732.

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Martín R. Ide-Pérez, Ayixon Sánchez-Reyes, Jorge Luis Folch-Mallol, María del Rayo Sánchez-Carbente, Rajeev Singh (2024)
Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family. PLOS ONE 19: e0297232.

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Peter Kämpfer, André Lipski, Lucie Lamothe, Dominique Clermont, Alexis Criscuolo, John A. McInroy, Stefanie P. Glaeser (2023)
Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays. Antonie van Leeuwenhoek 116: 883.

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Loane Danès, Nicolas Tchitchek, Christophe Bécavin, Peter Robinson (2021)
Bacnet: a user-friendly platform for building multi-omics websites. Bioinformatics 37: 1335.

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Peter Kämpfer, André Lipski, John A. McInroy, Dominique Clermont, Lucie Lamothe, Stefanie P. Glaeser, Alexis Criscuolo (2023)
Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays . International Journal of Systematic and Evolutionary Microbiology 73: .

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Amanda Martirena-Ramírez, José Germán Serrano-Gamboa, Yordanis Pérez-Llano, Claribel Orquídea Zenteno-Alegría, Mario León Iza-Arteaga, María del Rayo Sánchez-Carbente, Ana María Fernández-Ocaña, Ramón Alberto Batista-García, Jorge Luis Folch-Mallol (2024)
Aspergillus brasiliensis E_15.1: A Novel Thermophilic Endophyte from a Volcanic Crater Unveiled through Comprehensive Genome-Wide, Phenotypic Analysis, and Plant Growth-Promoting Trails. Journal of Fungi 10: 517.

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Chiara Crestani, Gabriele Arcari, Annie Landier, Virginie Passet, Dorian Garnier, Sylvie Brémont, Nathalie Armatys, Annick Carmi-Leroy, Julie Toubiana, Edgar Badell, Sylvain Brisse (2023)
Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex. Research in Microbiology 174: 104113.

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Jingjing Huang, Pengjie Hu, Leixin Ye, Zhenghao Shen, Xinfei Chen, Fang Liu, Yuyan Xie, Jinhan Yu, Xin Fan, Meng Xiao, Clement K. M. Tsui, Weiping Wang, Yingxing Li, Ge Zhang, Koon Ho Wong, Lei Cai, Feng-yan Bai, Yingchun Xu, Linqi Wang (2024)
Pan-drug resistance and hypervirulence in a human fungal pathogen are enabled by mutagenesis induced by mammalian body temperature. Nature Microbiology 9: 1686.

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Elodie Barbier, Carla Rodrigues, Geraldine Depret, Virginie Passet, Laurent Gal, Pascal Piveteau, Sylvain Brisse, Edward G. Dudley (2020)
The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples . Applied and Environmental Microbiology 86: .

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Peter Kämpfer, Hans-Jürgen Busse, Stefanie P. Glaeser, Dominique Clermont, Alexis Criscuolo, Henriette Mietke (2019)
Jeotgalicoccus meleagridis sp. nov. isolated from bioaerosol from emissions of a turkey fattening plant and reclassification of Jeotgalicoccus halophilus Liu et al. 2011 as a later heterotypic synonym of Jeotgalicoccus aerolatus Martin et al. 2011. International Journal of Systematic and Evolutionary Microbiology 71: .

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Sergey V. Tarlachkov, Irina P. Starodumova, Lubov V. Dorofeeva, Natalia V. Prisyazhnaya, Semen A. Leyn, Jaime E. Zlamal, Sebastian Albu, Steven A. Nadler, Sergei A. Subbotin, Lyudmila I. Evtushenko, David A. Baltrus (2020)
Draft Genome Sequences of 13 Plant-Associated Actinobacteria of the Family Microbacteriaceae . Microbiology Resource Announcements 9: .

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Metin Balaban, Nishat Anjum Bristy, Ahnaf Faisal, Md Shamsuzzoha Bayzid, Siavash Mirarab, Thomas Lengauer (2022)
Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model. Bioinformatics Advances 2: .

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Ayixon Sánchez-Reyes, Itzel Gaytán, Julián Pulido-García, Manuel Burelo, Martín Vargas-Suárez, M. Javier Cruz-Gómez, Herminia Loza-Tavera (2023)
Genetic basis for the biodegradation of a polyether-polyurethane-acrylic copolymer by a landfill microbial community inferred by metagenomic deconvolution analysis. Science of The Total Environment 881: 163367.

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Arnaud Fichant, Rachelle Lanceleur, Salma Hachfi, Alexandra Brun-Barale, Anne-Louise Blier, Olivier Firmesse, Armel Gallet, Valérie Fessard, Mathilde Bonis (2024)
New Approach Methods to Assess the Enteropathogenic Potential of Strains of the Bacillus cereus Group, including Bacillus thuringiensis. Foods 13: 1140.

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Julien Guglielmini, Melanie Hennart, Edgar Badell, Julie Toubiana, Alexis Criscuolo, Sylvain Brisse, Daniel J. Diekema (2021)
Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae . Journal of Clinical Microbiology 59: .

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Sergey V. Tarlachkov, Irina P. Starodumova, Lubov V. Dorofeeva, Natalia V. Prisyazhnaya, Semen A. Leyn, Jaime E. Zlamal, Marinela L. Elane, Andrei L. Osterman, Steven A. Nadler, Sergei A. Subbotin, Lyudmila I. Evtushenko, David A. Baltrus (2020)
Complete and Draft Genome Sequences of 12 Plant-Associated Rathayibacter Strains of Known and Putative New Species . Microbiology Resource Announcements 9: .

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Estelle Mühle, Chloé Abry, Priscilla Leclerc, Gogoa-Marthe Goly, Alexis Criscuolo, Hans-Jürgen Busse, Peter Kämpfer, Jean-François Bernardet, Dominique Clermont, Olivier Chesneau (2021)
Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s. International Journal of Systematic and Evolutionary Microbiology 71: .

DOI: 10.1099/ijsem.0.004576