34 results on '"Conrad, Roth E."'
Search Results
2. Towards estimating the number of strains that make up a natural bacterial population
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Viver, Tomeu, Conrad, Roth E., Rodriguez-R, Luis M., Ramírez, Ana S., Venter, Stephanus N., Rocha-Cárdenas, Jairo, Llabrés, Mercè, Amann, Rudolf, Konstantinidis, Konstantinos T., and Rossello-Mora, Ramon
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- 2024
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- View/download PDF
3. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development
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Carey, Sarah B, Jenkins, Jerry, Lovell, John T, Maumus, Florian, Sreedasyam, Avinash, Payton, Adam C, Shu, Shengqiang, Tiley, George P, Fernandez-Pozo, Noe, Healey, Adam, Barry, Kerrie, Chen, Cindy, Wang, Mei, Lipzen, Anna, Daum, Chris, Saski, Christopher A, McBreen, Jordan C, Conrad, Roth E, Kollar, Leslie M, Olsson, Sanna, Huttunen, Sanna, Landis, Jacob B, Burleigh, J Gordon, Wickett, Norman J, Johnson, Matthew G, Rensing, Stefan A, Grimwood, Jane, Schmutz, Jeremy, and McDaniel, Stuart F
- Subjects
Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,1.1 Normal biological development and functioning ,Animals ,DNA Transposable Elements ,Evolution ,Molecular ,Female ,Male ,Mammals ,Sex Chromosomes ,Sexual Development - Abstract
Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.
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- 2021
4. Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
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Conrad, Roth E., Viver, Tomeu, Gago, Juan F., Hatt, Janet K., Venter, Stephanus N., Rossello-Mora, Ramon, and Konstantinidis, Konstantinos T.
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- 2022
- Full Text
- View/download PDF
5. Towards estimating the number of strains that make up a natural bacterial population
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Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, National Science Foundation (US), Georgia Institute of Technology (US), Max Planck Society, Universidad de Las Islas Baleares, Projekt DEAL, Viver, Tomeu [0000-0001-8868-9292], Rosselló-Mora, Ramón [0000-0001-8253-3107], Viver, Tomeu, Conrad, Roth E., Rodriguez-R, Luis M., Ramírez, Ana S., Venter, Stephanus N., Rocha-Cárdenas, Jairo, Llabrés, Mercè, Amann, Rudolf, Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, National Science Foundation (US), Georgia Institute of Technology (US), Max Planck Society, Universidad de Las Islas Baleares, Projekt DEAL, Viver, Tomeu [0000-0001-8868-9292], Rosselló-Mora, Ramón [0000-0001-8253-3107], Viver, Tomeu, Conrad, Roth E., Rodriguez-R, Luis M., Ramírez, Ana S., Venter, Stephanus N., Rocha-Cárdenas, Jairo, Llabrés, Mercè, Amann, Rudolf, Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón
- Abstract
What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural “gap” in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that –although our 138 isolates represented about 80% of the Sal. ruber population– the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
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- 2024
6. An ANI gap within bacterial species that advances the definitions of intra-species units
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National Science Foundation (US), Max Planck Society, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), University of Innsbruck, Viver, Tomeu [0000-0001-8868-9292], Rosselló-Mora, Ramón [0000-0001-8253-3107], Rodriguez-R, Luis M., Conrad, Roth E., Viver, Tomeu, Feistel, Dorian J., Lindner, Blake G., Venter, Stephanus N., Orellana, Luis H., Amann, Rudolf, Rosselló-Mora, Ramón, Konstantinidis, Konstantinos T., National Science Foundation (US), Max Planck Society, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), University of Innsbruck, Viver, Tomeu [0000-0001-8868-9292], Rosselló-Mora, Ramón [0000-0001-8253-3107], Rodriguez-R, Luis M., Conrad, Roth E., Viver, Tomeu, Feistel, Dorian J., Lindner, Blake G., Venter, Stephanus N., Orellana, Luis H., Amann, Rudolf, Rosselló-Mora, Ramón, and Konstantinidis, Konstantinos T.
- Abstract
Large-scale surveys of prokaryotic communities (metagenomes), as well as isolate genomes, have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90%–95% are comparatively rare. However, it remains unclear if such “discontinuities” or gaps in ANI values can be observed within species and thus used to advance and standardize intra-species units. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least 10 genome representatives each and available long-read metagenomes, we show that another discontinuity exists between 99.2% and 99.8% (midpoint 99.5%) ANI in most of these species. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with ~20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity., With funding from the Spanish government through the ‘María de Maeztu Unit of Excelence’ accreditation (CEX2021-001198-M).
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- 2024
7. A natural ANI gap that can define intra-species units of bacteriophages and other viruses
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National Science Foundation (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Aldeguer-Riquelme, Borja, Conrad, Roth E., Antón, Josefa, Rosselló-Mora, Ramón, Konstantinidis, Konstantinos T., National Science Foundation (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Aldeguer-Riquelme, Borja, Conrad, Roth E., Antón, Josefa, Rosselló-Mora, Ramón, and Konstantinidis, Konstantinos T.
- Abstract
Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A 95% whole-genome average nucleotide identity (ANI) gap is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage species revealed a region of low frequency of pairs around 99.2-99.8% ANI, showing 3-fold or fewer pairs than expected for an even or normal distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts, and from a variety of environments, although a few exceptions to this pattern were also observed (∼3.7% of the total species evaluated) and are likely attributed to cultivation biases. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled including SARS-CoV-2, whose ANI-based clusters matched well the WHO-defined Variants of Concern, indicating that they represent functionally and/or ecologically distinct units. The existence of sequence-discrete units appears to be predominantly driven by (high) ecological cohesiveness coupled to either recombination frequency for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2. These results indicate that fundamentally different underlying mechanisms could lead to similar diversity patterns. Based on these results, we propose the 99.5% ANI as a practical, standardized, and data-supported threshold for defining viral intra-species units of bacteriophages, for which we propose the term genomovars.
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- 2024
8. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps
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Viver, Tomeu, Conrad, Roth E., Orellana, Luis H., Urdiain, Mercedes, González-Pastor, José E., Hatt, Janet K., Amann, Rudolf, Antón, Josefa, Konstantinidis, Konstantinos T., and Rosselló-Móra, Ramon
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- 2021
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9. An ANI gap within bacterial species that advances the definitions of intra-species units
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Rodriguez-R, Luis M., primary, Conrad, Roth E., additional, Viver, Tomeu, additional, Feistel, Dorian J., additional, Lindner, Blake G., additional, Venter, Stephanus N., additional, Orellana, Luis H., additional, Amann, Rudolf, additional, Rossello-Mora, Ramon, additional, and Konstantinidis, Konstantinos T., additional
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- 2023
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10. MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes
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Ruiz-Perez, Carlos A., Conrad, Roth E., and Konstantinidis, Konstantinos T.
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- 2021
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11. Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”
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Rodriguez-R, Luis M., Jain, Chirag, Conrad, Roth E., Aluru, Srinivas, and Konstantinidis, Konstantinos T.
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- 2021
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12. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.
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Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos-Caparros, Esteban, Sanchez-Martinez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Gridan, Ionuț Mădălin, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., Rossello-Mora, Ramon, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos-Caparros, Esteban, Sanchez-Martinez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Gridan, Ionuț Mădălin, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., and Rossello-Mora, Ramon
- Abstract
Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
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- 2023
13. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov
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Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, National Science Foundation (US), Ministry of Research, Innovation and Digitization (Romania), Consejo Federal de Ciencia y Tecnología (Argentina), Ministerio de Universidades (España), Govern de les Illes Balears, Viver, Tomeu [0000-0001-8868-], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L, Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, National Science Foundation (US), Ministry of Research, Innovation and Digitization (Romania), Consejo Federal de Ciencia y Tecnología (Argentina), Ministerio de Universidades (España), Govern de les Illes Balears, Viver, Tomeu [0000-0001-8868-], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L, Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón
- Abstract
Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
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- 2023
14. Description of four new Salinibacter species, two cultivated and named following the rules of the bacteriological code: Salinibacter pepae sp. nov., Salinibacter grassmerensis sp. nov.; and two uncultivated and named following the rules of the SeqCode: Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. [Dataset]
- Author
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Viver, Tomeu [0000-0001-8868-9292], Urdiain, Mercedes [0000-0001-6834-0237], Viver, Tomeu [tviver@imedea.uib-csic.es], Rosselló-Mora, Ramón [ramon@imedea.uib-csic.es], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Viver, Tomeu [0000-0001-8868-9292], Urdiain, Mercedes [0000-0001-6834-0237], Viver, Tomeu [tviver@imedea.uib-csic.es], Rosselló-Mora, Ramón [ramon@imedea.uib-csic.es], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón
- Abstract
Figure S1. Geographical distribution of the six locations studied here and their inter-location distances (given in the table). The distances given in each location refer to Mallorca. The hypersaline here are: Mallorca (Es Trenc and S’Avall and separated by 3.5 km) and Santa Pola in Spain, Fără Fund in Romania, Great Salt Lake (USA), Pampa (Laguna Colorada Chica and Laguna Colorada Grande, separated by 23 Km), and Lake Grassmere (New Zealand). Table S1. Statistics of Salinibacter MAGs recovered using different bioinformatic tools. MAGs selected for further analysis and taxonomic classification are marked in red. Text S1: In addition to the taxonomic study, here we assessed the different tools SPADES and MegaHIT assemblers, and MetaBAT binning tools selecting contigs with length > 2,000 pbs or > 5,000 pbs to retrieve the best quality MAG (Sup. Table S1). We observed that different tools and combinations rendered different qualities of the MAGs. The selection of contigs with length > 5,000 pbs binning rendered MAGs with a lower genome size, lower completeness and similar contamination. From the FF metagenome (Romania), the highest quality MAG was retrieved using the assembler SPADES and MetaBAT binning tool using a minimum contig length of 2,000 pbs. From CCH and CG metagenomes (Argentina), the highest quality MAGs were retrieved using the assembler MegaHIT and MetaBAT binning tool using a minimum contig length of 2,000 pbs (Sup. Table S1). Figure S2. Genomic clustering based on Average Amino-acid Identity (AAI) of genomes included in the study. Figure S3. Pangenome hierarchical clustering based on the presence (grey) or absence (black) of orthologous genes. Table S2. Pangenome statistics between genomes belonging to the same species. Table S3: CRISPR-Cas systems found in the Salinibacter pepae and Salinibacter grassmerensis genomes. Table S4. Cell morphologies of the new isolates. All cells have been cultivated onto MA agar. for 10 days at 12ºC. The morphology was ob
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- 2023
15. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development
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Society for the Study of Evolution (US), Emil Aaltonen Foundation, University of Turku, Carey, Sarah B.[0000-0002-6431-0660], Jenkins, Jerry [0000-0002-7943-3997], Lovell, John T. [0000-0002-8938-1166], Maumus, Florian [0000-0001-7325-0527], Sreedasyam, Avinash [0000-0001-7336-7012], Shu, Shengqiang [0000-0002-4336-8994], Tiley, George P. [0000-0003-0053-0207], Fernandez-Pozo, Noe [0000-0002-6489-5566], Healey, Adam [0000-0002-3088-6856], Barry, Kerrie [0000-0002-8999-6785], Chen, Cindy [0000-0002-7539-103X], Lipzen, Anna [0000-0003-2293-9329], Daum, Chris [0000-0003-3895-5892], Saski, Christopher A.[0000-0002-2780-4274], McBreen, Jordan C.[0000-0001-8867-6483], Conrad, Roth E.[Conrad, Roth E.], Kollar, Leslie M.[0000-0001-8726-9085], Olsson, Sanna [0000-0002-1199-4499], Huttunen, Sanna [0000-0003-1374-9857], Landis, Jacob B.[0000-0002-5631-5365], Burleigh, J. Gordon [0000-0001-8120-5136], Wickett, Norman [0000-0003-0944-1956], Johnson, Matthew [0000-0002-1958-6334], Rensing, Stefan A. [0000-0002-0225-873X], Carey, Sarah B., Jenkins, Jerry, Lovell, John T., Maumus, Florian, Sreedasyam, Avinash, Payton, Adam C., Shu, Shengqiang, Tiley, George P., Fernández-Pozo, Noé, Healey, Adam, Barry, Kerrie W., Chen, Cindy, Wang, Mei, Lipzen, Anna, Daum, Christopher, Saski, Christopher, McBreen, Jordan C., Conrad, Roth E., Kollar, Leslie M., Olsson, Sanna, Huttunen, Sanna, Landis, Jacob B., Burleigh, J. Gordon, Wickett, Norman, Johnson, Matthew, Rensing, Stefan A., Grimwood, Jane, Schmutz, Jeremy, McDaniel, Stuart F., Society for the Study of Evolution (US), Emil Aaltonen Foundation, University of Turku, Carey, Sarah B.[0000-0002-6431-0660], Jenkins, Jerry [0000-0002-7943-3997], Lovell, John T. [0000-0002-8938-1166], Maumus, Florian [0000-0001-7325-0527], Sreedasyam, Avinash [0000-0001-7336-7012], Shu, Shengqiang [0000-0002-4336-8994], Tiley, George P. [0000-0003-0053-0207], Fernandez-Pozo, Noe [0000-0002-6489-5566], Healey, Adam [0000-0002-3088-6856], Barry, Kerrie [0000-0002-8999-6785], Chen, Cindy [0000-0002-7539-103X], Lipzen, Anna [0000-0003-2293-9329], Daum, Chris [0000-0003-3895-5892], Saski, Christopher A.[0000-0002-2780-4274], McBreen, Jordan C.[0000-0001-8867-6483], Conrad, Roth E.[Conrad, Roth E.], Kollar, Leslie M.[0000-0001-8726-9085], Olsson, Sanna [0000-0002-1199-4499], Huttunen, Sanna [0000-0003-1374-9857], Landis, Jacob B.[0000-0002-5631-5365], Burleigh, J. Gordon [0000-0001-8120-5136], Wickett, Norman [0000-0003-0944-1956], Johnson, Matthew [0000-0002-1958-6334], Rensing, Stefan A. [0000-0002-0225-873X], Carey, Sarah B., Jenkins, Jerry, Lovell, John T., Maumus, Florian, Sreedasyam, Avinash, Payton, Adam C., Shu, Shengqiang, Tiley, George P., Fernández-Pozo, Noé, Healey, Adam, Barry, Kerrie W., Chen, Cindy, Wang, Mei, Lipzen, Anna, Daum, Christopher, Saski, Christopher, McBreen, Jordan C., Conrad, Roth E., Kollar, Leslie M., Olsson, Sanna, Huttunen, Sanna, Landis, Jacob B., Burleigh, J. Gordon, Wickett, Norman, Johnson, Matthew, Rensing, Stefan A., Grimwood, Jane, Schmutz, Jeremy, and McDaniel, Stuart F.
- Abstract
Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable ele ments, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.
- Published
- 2021
16. ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes
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Zhang, Si-Yu, primary, Suttner, Brittany, additional, Rodriguez-R, Luis M., additional, Orellana, Luis H., additional, Conrad, Roth E., additional, Liu, Fang, additional, Rowell, Jessica L., additional, Webb, Hattie E., additional, Williams-Newkirk, Amanda J., additional, Huang, Andrew, additional, and Konstantinidis, Konstantinos T., additional
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- 2022
- Full Text
- View/download PDF
17. Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning
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National Science Foundation (US), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Konstantinidis, Konstantinos T., Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Rosselló-Mora, Ramón, National Science Foundation (US), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Konstantinidis, Konstantinos T., Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., and Rosselló-Mora, Ramón
- Abstract
Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial and archaeal taxa to show that these taxa form persistent, sequence-discrete, species-like populations. While these populations harbor extensive intra-population gene diversity, even within a single saltern site, only a small minority of these genes appear to be functionally important during environmental perturbations. We outline an approach to detect and track such populations and their ecologically important genes that should be broadly applicable.
- Published
- 2022
18. Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
- Author
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National Science Foundation (US), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Conrad, Roth E., Viver, Tomeu, Gago, Juan F., Hatt, Janet K., Venter, Stephanus N., Roselló Mora, Ramón A., Konstantinidis, Konstantinos T., National Science Foundation (US), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Conrad, Roth E., Viver, Tomeu, Gago, Juan F., Hatt, Janet K., Venter, Stephanus N., Roselló Mora, Ramón A., and Konstantinidis, Konstantinos T.
- Abstract
Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.
- Published
- 2022
19. Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning
- Author
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Konstantinidis, Konstantinos T, primary, Viver, Tomeu, additional, Conrad, Roth E, additional, Venter, Stephanus N, additional, and Rossello-Mora, Ramon, additional
- Published
- 2022
- Full Text
- View/download PDF
20. RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity
- Author
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Gerhardt, Kenji, primary, Ruiz-Perez, Carlos A., additional, Rodriguez-R, Luis M., additional, Conrad, Roth E., additional, and Konstantinidis, Konstantinos T., additional
- Published
- 2022
- Full Text
- View/download PDF
21. Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
- Author
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Conrad, Roth E, primary, Viver, Tomeu, additional, Gago, Juan F, additional, Hatt, Janet K, additional, Venter, Stephanus N, additional, Rossello-Mora, Ramon, additional, and Konstantinidis, Konstantinos T, additional
- Published
- 2021
- Full Text
- View/download PDF
22. Importancia ecológica del pangenoma para la adaptación de las especies a cambios ambientales: genómica comparada de Salinibacter ruber
- Author
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Viver, Tomeu, Conrad, Roth E., Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and European Commission
- Abstract
Resumen del trabajo presentado a la XVI Reunión de la Red Nacional de Microorganismos Extremófilos, celebrada en sesiones telemáticas del 17 de diciembre 2020 al 25 febrero 2021., Ministerio de ciencia e innovación Gobierno de España (MICROMATES PGC2018-096956-B-C44 y MARBIOM RTC-2017-6405-1), incluyendo fondos (FEDER).
- Published
- 2021
23. ¿Qué es una 'cepa' y cuántas de la misma especie coexistirían en un sistema natural?
- Author
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Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and European Commission
- Abstract
Resumen del trabajo presentado al XXVIII Congreso Nacional de Microbiología, celebrado virtualmente del 28 de junio al 2 de julio de 2021., Ministerio de ciencia e innovación Gobierno de España (MICROMATES PGC2018-096956- B-C44 y MARBIOM RTC-2017-6405-1), incluyendo fondos FEDER.
- Published
- 2021
24. Dinámica y selección de comunidades halófilas extremas sometidas a estrés osmótico cíclico
- Author
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Bustos, Esteban, Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Konstantinidis, Konstantinos T., Bosch, Rafael, Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and European Commission
- Abstract
Resumen del trabajo presentado al XXVIII Congreso Nacional de Microbiología, celebrado virtualmente del 28 de junio al 2 de julio de 2021., Ministerio de ciencia e innovación Gobierno de España (MICROMATES PGC2018-096956- B-C44; MARBIOM RTC-2017-6405-1), incluyendo fondos (FEDER). Contrato predoctoral FPI 2019 (PRE2019-088016).
- Published
- 2021
25. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps
- Author
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Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Viver, Tomeu, Conrad, Roth E., Orellana, Luis H., Urdiain, Mercedes, González-Pastor, José E., Hatt, Janet K., Amann, Rudolf, Anton, Josefa, Konstantinidis, Konstantinos T., Rosselló Móra, Ramon, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Viver, Tomeu, Conrad, Roth E., Orellana, Luis H., Urdiain, Mercedes, González-Pastor, José E., Hatt, Janet K., Amann, Rudolf, Anton, Josefa, Konstantinidis, Konstantinos T., and Rosselló Móra, Ramon
- Abstract
Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations.
- Published
- 2021
26. Importancia ecológica del pangenoma para la adaptación de las especies a cambios ambientales: genómica comparada de Salinibacter ruber
- Author
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Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Viver, Tomeu, Conrad, Roth E., Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Viver, Tomeu, Conrad, Roth E., Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón
- Published
- 2021
27. Dinámica y selección de comunidades halófilas extremas sometidas a estrés osmótico cíclico
- Author
-
Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Bustos, Esteban, Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Konstantinidis, Konstantinos T., Bosch, Rafael, Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Bustos, Esteban, Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Konstantinidis, Konstantinos T., Bosch, Rafael, and Rosselló-Mora, Ramón
- Published
- 2021
28. ¿Qué es una “cepa” y cuántas de la misma especie coexistirían en un sistema natural?
- Author
-
Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Viver, Tomeu, Conrad, Roth E., Venter, Stephanus N., Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón
- Published
- 2021
29. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps
- Author
-
Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Max Planck Society, National Science Foundation (US), Viver, Tomeu, Conrad, Roth E., Orellana, Luis H., Urdiain, Mercedes, González-Pastor, José Eduardo, Hatt, Janet K., Amann, Rudolf, Antón, Josefa, Konstantinidis, Konstantinos T., Roselló Mora, Ramón A., Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Max Planck Society, National Science Foundation (US), Viver, Tomeu, Conrad, Roth E., Orellana, Luis H., Urdiain, Mercedes, González-Pastor, José Eduardo, Hatt, Janet K., Amann, Rudolf, Antón, Josefa, Konstantinidis, Konstantinos T., and Roselló Mora, Ramón A.
- Abstract
Microbial communities thriving in hypersaline brines of solar salterns are highly resistant and resilient to environmental changes, and salinity is a major factor that deterministically influences community structure. Here, we demonstrate that this resilience occurs even after rapid osmotic shocks caused by a threefold change in salinity (a reduction from 34 to 12% salts) leading to massive amounts of archaeal cell lysis. Specifically, our temporal metagenomic datasets identified two co-occurring ecotypes within the most dominant archaeal population of the brines Haloquadratum walsbyi that exhibited different salt concentration preferences. The dominant ecotype was generally more abundant and occurred in high-salt conditions (34%); the low abundance ecotype always co-occurred but was enriched at salinities around 20% or lower and carried unique gene content related to solute transport and gene regulation. Despite their apparent distinct ecological preferences, the ecotypes did not outcompete each other presumably due to weak functional differentiation between them. Further, the osmotic shock selected for a temporal increase in taxonomic and functional diversity at both the Hqr. walsbyi population and whole-community levels supporting the specialization-disturbance hypothesis, that is, the expectation that disturbance favors generalists. Altogether, our results provide new insights into how intraspecies diversity is maintained in light of substantial gene-content differences and major environmental perturbations.
- Published
- 2021
30. ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes.
- Author
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Si-Yu Zhang, Suttner, Brittany, Rodriguez-R, Luis M., Orellana, Luis H., Conrad, Roth E., Fang Liu, Rowell, Jessica L., Webb, Hattie E., Williams-Newkirk, Amanda J., Huang, Andrew, and Konstantinidis, Konstantinos T.
- Published
- 2022
- Full Text
- View/download PDF
31. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps
- Author
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Viver, Tomeu, primary, Conrad, Roth E., additional, Orellana, Luis H., additional, Urdiain, Mercedes, additional, González-Pastor, José E., additional, Hatt, Janet K., additional, Amann, Rudolf, additional, Antón, Josefa, additional, Konstantinidis, Konstantinos T., additional, and Rosselló-Móra, Ramon, additional
- Published
- 2020
- Full Text
- View/download PDF
32. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development
- Author
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Avinash Sreedasyam, Jerry Jenkins, Jacob B. Landis, Kerrie Barry, Stuart F. McDaniel, Sanna Olsson, Stefan A. Rensing, Jordan C. McBreen, Noe Fernandez-Pozo, J. Gordon Burleigh, Chris Daum, Matthew G. Johnson, Leslie M. Kollar, Christopher A. Saski, Adam Healey, Adam C. Payton, John T. Lovell, Jane Grimwood, Sanna Huttunen, Florian Maumus, Sarah B. Carey, Jeremy Schmutz, Anna Lipzen, Shengqiang Shu, Cindy Chen, Roth E. Conrad, Mei Wang, George P. Tiley, Norman J. Wickett, Society for the Study of Evolution (US), Emil Aaltonen Foundation, University of Turku, Carey, Sarah B., Jenkins, Jerry, Lovell, John T., Maumus, Florian, Sreedasyam, Avinash, Shu, Shengqiang, Tiley, George P., Fernandez-Pozo, Noe, Healey, Adam, Barry, Kerrie, Chen, Cindy, Lipzen, Anna, Daum, Chris, Saski, Christopher A., McBreen, Jordan C., Conrad, Roth E., Kollar, Leslie M., Olsson, Sanna, Huttunen, Sanna, Landis, Jacob B., Burleigh, J. Gordon, Wickett, Norman J., Matthew G Johnson, Rensing, Stefan A., Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Carey, Sarah B.[0000-0002-6431-0660], Jenkins, Jerry [0000-0002-7943-3997], Lovell, John T. [0000-0002-8938-1166], Maumus, Florian [0000-0001-7325-0527], Sreedasyam, Avinash [0000-0001-7336-7012], Shu, Shengqiang [0000-0002-4336-8994], Tiley, George P. [0000-0003-0053-0207], Fernandez-Pozo, Noe [0000-0002-6489-5566], Healey, Adam [0000-0002-3088-6856], Barry, Kerrie [0000-0002-8999-6785], Chen, Cindy [0000-0002-7539-103X], Lipzen, Anna [0000-0003-2293-9329], Daum, Chris [0000-0003-3895-5892], Saski, Christopher A.[0000-0002-2780-4274], McBreen, Jordan C.[0000-0001-8867-6483], Conrad, Roth E.[Conrad, Roth E.], Kollar, Leslie M.[0000-0001-8726-9085], Olsson, Sanna [0000-0002-1199-4499], Huttunen, Sanna [0000-0003-1374-9857], Landis, Jacob B.[0000-0002-5631-5365], Burleigh, J. Gordon [0000-0001-8120-5136], Wickett, Norman J.[0000-0003-0944-1956], Matthew G Johnson [0000-0002-1958-6334, and Rensing, Stefan A. [0000-0002-0225-873X]
- Subjects
0106 biological sciences ,Male ,[SDV]Life Sciences [q-bio] ,01 natural sciences ,Genome ,R Package ,Negative selection ,Research Articles ,Genetics ,Mammals ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Ceratodon purpureus ,Sex Chromosomes ,Phylogenetic analysis ,biology ,Sexual Development ,Reveals ,SciAdv r-articles ,tool ,3. Good health ,CD-Hit ,Female ,Recombination ,Research Article ,Biotechnology ,Transposable element ,Evolution ,1.1 Normal biological development and functioning ,Population ,Evolution, Molecular ,03 medical and health sciences ,Underpinning research ,Complex ,Sequence ,Animals ,education ,Gene ,030304 developmental biology ,Evolutionary Biology ,Autosome ,Protein ,Plant Sciences ,Molecular ,biology.organism_classification ,DNA Transposable Elements ,010606 plant biology & botany ,Genome annotation - Abstract
Centro de Investigación Forestal (CIFOR), Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable ele ments, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants., This work was supported by NSF DEB-1541005 and 1542609 and start-up funds from UF to S.F.M.; microMORPH Cross-Disciplinary Training Grant, Sigma-Xi Grant-In-Aid of Research, and Society for the Study of Evolution Rosemary Grant Award to S.B.C.; NSF DEB-1239992 to N.J.W.; the Emil Aaltonen Foundation and the University of Turku to S.O.; and NSF DEB-1541506 to J.G.B. and S.F.M. The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231., 12 Pág. Supplementary material for this article is available at http://advances.sciencemag.org/cgi/ content/full/7/27/eabh2488/DC1
- Published
- 2021
33. A natural ANI gap that can define intra-species units of bacteriophages and other viruses.
- Author
-
Aldeguer-Riquelme B, Conrad RE, Antón J, Rossello-Mora R, and Konstantinidis KT
- Subjects
- Phylogeny, SARS-CoV-2 genetics, SARS-CoV-2 classification, Humans, Viruses genetics, Viruses classification, Genetic Variation, Bacteriophages genetics, Bacteriophages classification, Bacteriophages isolation & purification, Genome, Viral
- Abstract
Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage ( Caudoviricetes ) species revealed a region of low frequency of ANI values around 99.2%-99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars., Importance: Viral species are composed of an ensemble of intra-species variants whose individual dynamics may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of mostly bacteriophage genomes, we show that there is a widely distributed natural gap in whole-genome average nucleotide identity values in most, but not all, of these species that can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
34. An ANI gap within bacterial species that advances the definitions of intra-species units.
- Author
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Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, and Konstantinidis KT
- Subjects
- Prokaryotic Cells, Phylogeny, Sequence Analysis, DNA, Genome, Bacterial, Bacteria genetics
- Abstract
Importance: Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings., Competing Interests: The authors declare no conflict of interest.
- Published
- 2024
- Full Text
- View/download PDF
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