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Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea. Proc Natl Acad Sci U S A 2017; 114:3198-3203. [PMID: 28265051 DOI: 10.1073/pnas.1618556114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria are major sources of oxygen, nitrogen, and carbon in nature. In addition to the importance of their primary metabolism, some cyanobacteria are prolific producers of unique and bioactive secondary metabolites. Chemical investigations of the cyanobacterial genus Moorea have resulted in the isolation of over 190 compounds in the last two decades. However, preliminary genomic analysis has suggested that genome-guided approaches can enable the discovery of novel compounds from even well-studied Moorea strains, highlighting the importance of obtaining complete genomes. We report a complete genome of a filamentous tropical marine cyanobacterium, Moorea producens PAL, which reveals that about one-fifth of its genome is devoted to production of secondary metabolites, an impressive four times the cyanobacterial average. Moreover, possession of the complete PAL genome has allowed improvement to the assembly of three other Moorea draft genomes. Comparative genomics revealed that they are remarkably similar to one another, despite their differences in geography, morphology, and secondary metabolite profiles. Gene cluster networking highlights that this genus is distinctive among cyanobacteria, not only in the number of secondary metabolite pathways but also in the content of many pathways, which are potentially distinct from all other bacterial gene clusters to date. These findings portend that future genome-guided secondary metabolite discovery and isolation efforts should be highly productive.
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52
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Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction. Mol Phylogenet Evol 2016; 107:338-344. [PMID: 27894995 DOI: 10.1016/j.ympev.2016.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 11/09/2016] [Accepted: 11/25/2016] [Indexed: 11/24/2022]
Abstract
Long Branch Attraction (LBA) is a well-known artifact in phylogenetic reconstruction when dealing with branch length heterogeneity. Here we show another phenomenon, Short Branch Attraction (SBA), which occurs when BLAST searches, a phenetic analysis, are used as a surrogate method for phylogenetic analysis. This error also results from branch length heterogeneity, but this time it is the short branches that are attracting. The SBA artifact is reciprocal and can be returned 100% of the time when multiple branches differ in length by a factor of more than two. SBA is an intended feature of BLAST searches, but becomes an issue, when top scoring BLAST hit analyses are used to infer Horizontal Gene Transfers (HGTs), assign taxonomic category with environmental sequence data in phylotyping, or gather homologous sequences for building gene families. SBA can lead researchers to believe that there has been a HGT event when only vertical descent has occurred, cause slowly evolving taxa to be over-represented and quickly evolving taxa to be under-represented in phylotyping, or systematically exclude quickly evolving taxa from analyses. SBA also contributes to the changing results of top scoring BLAST hit analyses as the database grows, because more slowly evolving taxa, or short branches, are added over time, introducing more potential for SBA. SBA can be detected by examining reciprocal best BLAST hits among a larger group of taxa, including the known closest phylogenetic neighbors. Therefore, one should look for this phenomenon when conducting best BLAST hit analyses as a surrogate method to identify HGTs, in phylotyping, or when using BLAST to gather homologous sequences.
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53
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Schorn MA, Alanjary MM, Aguinaldo K, Korobeynikov A, Podell S, Patin N, Lincecum T, Jensen PR, Ziemert N, Moore BS. Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters. MICROBIOLOGY-SGM 2016; 162:2075-2086. [PMID: 27902408 DOI: 10.1099/mic.0.000386] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.
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Affiliation(s)
- Michelle A Schorn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Mohammad M Alanjary
- German Centre for Infection Research (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), University of Tuebingen, Tuebingen, Germany
| | | | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Department of Statistical Modeling, St. Petersburg State University, St. Petersburg, Russia
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Nastassia Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | | | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.,Center for Microbiome Innovation, University of California, San Diego, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), University of Tuebingen, Tuebingen, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA.,Center for Microbiome Innovation, University of California, San Diego, USA
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54
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Yin Z, Zhu B, Feng H, Huang L. Horizontal gene transfer drives adaptive colonization of apple trees by the fungal pathogen Valsa mali. Sci Rep 2016; 6:33129. [PMID: 27634406 PMCID: PMC5025739 DOI: 10.1038/srep33129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/22/2016] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer (HGT) often has strong benefits for fungi. In a study of samples from apple canker in Shaanxi Province, China, diverse microbes, along with the necrotrophic pathogen Valsa mali, were found to colonize the apple bark, thus providing ample opportunity for HGT to occur. In the present study, we identified 32 HGT events in V. mali by combining phyletic distribution-based methods with phylogenetic analyses. Most of these HGTs were from bacteria, whereas several others were from eukaryotes. Three HGTs putatively functioned in competition with actinomycetes, some of which showed a significant inhibitory effect on V. mali. Three HGTs that were probably involved in nitrogen uptake were also identified. Ten HGTs were thought to be involved in pathogenicity because they were related to known virulence factors, including cell wall-degrading enzymes and candidate effector proteins. HGT14, together with HGT32, was shown to contribute to bleomycin resistance of V. mali.These results suggest that HGT drives the adaptive evolution of V. mali. The HGTs identified here provide new clues for unveiling the adaptation mechanisms and virulence determinants of V. mali.
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Affiliation(s)
- Zhiyuan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Baitao Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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55
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Cummings ME, Barbé D, Leao TF, Korobeynikov A, Engene N, Glukhov E, Gerwick WH, Gerwick L. A novel uncultured heterotrophic bacterial associate of the cyanobacterium Moorea producens JHB. BMC Microbiol 2016; 16:198. [PMID: 27577966 PMCID: PMC5006271 DOI: 10.1186/s12866-016-0817-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 08/19/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Filamentous tropical marine cyanobacteria such as Moorea producens strain JHB possess a rich community of heterotrophic bacteria on their polysaccharide sheaths; however, these bacterial communities have not yet been adequately studied or characterized. RESULTS AND DISCUSSION Through efforts to sequence the genome of this cyanobacterial strain, the 5.99 MB genome of an unknown bacterium emerged from the metagenomic information, named here as Mor1. Analysis of its genome revealed that the bacterium is heterotrophic and belongs to the phylum Acidobacteria, subgroup 22; however, it is only 85 % identical to the nearest cultured representative. Comparative genomics further revealed that Mor1 has a large number of genes involved in transcriptional regulation, is completely devoid of transposases, is not able to synthesize the full complement of proteogenic amino acids and appears to lack genes for nitrate uptake. Mor1 was found to be present in lab cultures of M. producens collected from various locations, but not other cyanobacterial species. Diverse efforts failed to culture the bacterium separately from filaments of M. producens JHB. Additionally, a co-culturing experiment between M. producens JHB possessing Mor1 and cultures of other genera of cyanobacteria indicated that the bacterium was not transferable. CONCLUSION The data presented support a specific relationship between this novel uncultured bacterium and M. producens, however, verification of this proposed relationship cannot be done until the "uncultured" bacterium can be cultured.
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Affiliation(s)
- Milo E Cummings
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Debby Barbé
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tiago Ferreira Leao
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anton Korobeynikov
- Department of Statistical Modelling, St. Petersburg State University, Saint Petersburg, Russia
- Center for Algorithmic Biotechnology, St. Petersburg State University, Saint Petersburg, Russia
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
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56
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Browne P, Tamaki H, Kyrpides N, Woyke T, Goodwin L, Imachi H, Bräuer S, Yavitt JB, Liu WT, Zinder S, Cadillo-Quiroz H. Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments. ISME JOURNAL 2016; 11:87-99. [PMID: 27552639 DOI: 10.1038/ismej.2016.104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 11/09/2022]
Abstract
Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H+ rather than Na+ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na+ and H+ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.
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Affiliation(s)
- Patrick Browne
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephen Zinder
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Swette Center for Environmental Biotechnology at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
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57
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Xu F, Jerlström-Hultqvist J, Kolisko M, Simpson AGB, Roger AJ, Svärd SG, Andersson JO. On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. BMC Biol 2016; 14:62. [PMID: 27480115 PMCID: PMC4967989 DOI: 10.1186/s12915-016-0284-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/13/2016] [Indexed: 01/08/2023] Open
Abstract
Background It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the genomic basis for evolutionary transitions between lifestyles in diplomonads, a group of anaerobic eukaryotes. Most described diplomonads are intestinal parasites or commensals of various animals, but there are also free-living diplomonads found in oxygen-poor environments such as marine and freshwater sediments. All these nest well within groups of parasitic diplomonads in phylogenetic trees, suggesting that they could be secondarily free-living. Results We present a transcriptome study of Trepomonas sp. PC1, a diplomonad isolated from marine sediment. Analysis of the metabolic genes revealed a number of proteins involved in degradation of the bacterial membrane and cell wall, as well as an extended set of enzymes involved in carbohydrate degradation and nucleotide metabolism. Phylogenetic analyses showed that most of the differences in metabolic capacity between free-living Trepomonas and the parasitic diplomonads are due to recent acquisitions of bacterial genes via gene transfer. Interestingly, one of the acquired genes encodes a ribonucleotide reductase, which frees Trepomonas from the need to scavenge deoxyribonucleosides. The transcriptome included a gene encoding squalene-tetrahymanol cyclase. This enzyme synthesizes the sterol substitute tetrahymanol in the absence of oxygen, potentially allowing Trepomonas to thrive under anaerobic conditions as a free-living bacterivore, without depending on sterols from other eukaryotes. Conclusions Our findings are consistent with the phylogenetic evidence that the last common ancestor of diplomonads was dependent on a host and that Trepomonas has adapted secondarily to a free-living lifestyle. We believe that similar studies of other groups where free-living taxa are nested within parasites could reveal more examples of secondarily free-living eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0284-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Feifei Xu
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Present address: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Martin Kolisko
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Present address: Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, ON, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto, ON, Canada
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan O Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Bennke CM, Krüger K, Kappelmann L, Huang S, Gobet A, Schüler M, Barbe V, Fuchs BM, Michel G, Teeling H, Amann RI. Polysaccharide utilisation loci ofBacteroidetesfrom two contrasting open ocean sites in the North Atlantic. Environ Microbiol 2016; 18:4456-4470. [DOI: 10.1111/1462-2920.13429] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christin M. Bennke
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Karen Krüger
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Lennart Kappelmann
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Sixing Huang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Inhoffenstraße 7B 38124 Braunschweig Germany
| | - Angélique Gobet
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models; Station Biologique de Roscoff, CS 90074 F-29688 Roscoff cedex Bretagne France
| | - Margarete Schüler
- University of Bayreuth; Biologie / Elektronenmikroskopie B1, Universitätsstraße 30 95447 Bayreuth Germany
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Étude des Génomes, C.E.A, Institut de Génomique - Genoscope; 2 rue Gaston Crémieux 91057 Évry cedex France
| | - Bernhard M. Fuchs
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Gurvan Michel
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models; Station Biologique de Roscoff, CS 90074 F-29688 Roscoff cedex Bretagne France
| | - Hanno Teeling
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
| | - Rudolf I. Amann
- Max-Planck-Institute for Marine Microbiology, Department of Molecular Ecology; Celsiusstraße 1 28359 Bremen Germany
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Asenjo F, Olmos A, Henríquez-Piskulich P, Polanco V, Aldea P, Ugalde JA, Trombert AN. Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate. PeerJ 2016; 4:e1950. [PMID: 27114887 PMCID: PMC4841242 DOI: 10.7717/peerj.1950] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/29/2016] [Indexed: 01/23/2023] Open
Abstract
Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2) from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other Lactobacillus species, identified several unique genes of L. kunkeei MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs). Discussion. The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in L. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments. L. kunkeei could be a new source of Lactobacillus with beneficial properties. Indeed, L. kunkeei MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.
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Affiliation(s)
- Freddy Asenjo
- Centro de Genética y Genómica, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo , Santiago , Chile
| | - Alejandro Olmos
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor , Santiago , Chile
| | | | - Victor Polanco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile; Centro de Estudios Apícolas CEAPI Mayor, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Patricia Aldea
- Centro de Estudios Apícolas CEAPI Mayor, Facultad de Ciencias, Universidad Mayor , Santiago , Chile
| | - Juan A Ugalde
- Centro de Genética y Genómica, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo , Santiago , Chile
| | - Annette N Trombert
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor , Santiago , Chile
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Abstract
Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe2+/Pb2+ permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co2+/Zn2+/Cd2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.
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Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis. Sci Rep 2016; 6:23971. [PMID: 27035119 PMCID: PMC4817515 DOI: 10.1038/srep23971] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022] Open
Abstract
Bifidobacteria are members of the human gut microbiota, being numerically dominant in the colon of infants, while also being prevalent in the large intestine of adults. In this study, we determined and analyzed the pan-genome of Bifidobacterium adolescentis, which is one of many bacteria found in the human adult gut microbiota. In silico analysis of the genome sequences of eighteen B. adolescentis strains isolated from various environments, such as human milk, human feces and bovine rumen, revealed a high level of genetic variability, resulting in an open pan-genome. Compared to other bifidobacterial taxa such as Bifidobacterium bifidum and Bifidobacterium breve, the more extensive B. adolescentis pan-genome supports the hypothesis that the genetic arsenal of this taxon expanded so as to become more adaptable to the variable and changing ecological niche of the gut. These increased genetic capabilities are particularly evident for genes required for dietary glycan-breakdown.
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62
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Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis 2016. [DOI: 10.1007/s13199-016-0390-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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63
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Modulation of theeps-ome transcription of bifidobacteria through simulation of human intestinal environment. FEMS Microbiol Ecol 2016; 92:fiw056. [DOI: 10.1093/femsec/fiw056] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 11/14/2022] Open
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Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:258. [PMID: 27933100 PMCID: PMC5124317 DOI: 10.1186/s13068-016-0670-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. CONCLUSIONS Functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.
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Affiliation(s)
- Jesse C. Traller
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Shawn J. Cokus
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - David A. Lopez
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Olga Gaidarenko
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Sarah R. Smith
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - John P. McCrow
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sean D. Gallaher
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Michael Thompson
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Orna Cook
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Marco Morselli
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Artur Jaroszewicz
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Eric E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
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Nguyen M, Ekstrom A, Li X, Yin Y. HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes. Toxins (Basel) 2015; 7:4035-53. [PMID: 26473921 PMCID: PMC4626719 DOI: 10.3390/toxins7104035] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 11/16/2022] Open
Abstract
Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share genes with HTGCs, and that HTGs are significantly enriched in SMGCs. Our genome-wide analysis thus presented very strong evidence to support the hypothesis that HGT has played a very critical role in the evolution of SMGCs. The program is freely available at http://cys.bios.niu.edu/HGTFinder/ HGTFinder.tar.gz.
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Affiliation(s)
- Marcus Nguyen
- Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA.
| | - Alex Ekstrom
- Department of Computer Science, Northern Illinois University, DeKalb, IL 60115-2857, USA.
| | - Xueqiong Li
- Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA.
- College of Life Sciences, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, Inner Mongolia, China.
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA.
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Adato O, Ninyo N, Gophna U, Snir S. Detecting Horizontal Gene Transfer between Closely Related Taxa. PLoS Comput Biol 2015; 11:e1004408. [PMID: 26439115 PMCID: PMC4595140 DOI: 10.1371/journal.pcbi.1004408] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 06/20/2015] [Indexed: 01/12/2023] Open
Abstract
Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive. We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set. When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain. The transfer of genetic material between organisms, usually denoted as horizontal (or lateral) gene transfer (HGT or LGT), is a prime mechanism in microbial evolution and responsible for genetic innovation and the evolution of genome architecture. Detecting HGT between closely related species or strains is imperative as drug-resistant pathogenic strains most often acquire their virulence from closely related bacteria. The proposed method combines two evolutionary signals that were not employed in the past for this task. One is the synteny index (SI), measuring the loss of synteny in an organism, and the other is a novel concept—constant relative mutability (CRM), maintaining that genes preserve their relative evolution rate along linages (although the latter ones may each change). We show both in simulation and real biological data that the method is sound and, in the cases examined, provides stronger sensitivity than existing methods. We therefore believe this novel approach represents a significant advance, for the first time enabling the detection of previously ignored HGT events that will bring us closer to the goal of detecting all newly acquired genes in a particular strain. Availability: The method is publicly available at http://research.haifa.ac.il/~ssagi/software/nearHGT.zip
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Affiliation(s)
- Orit Adato
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Noga Ninyo
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology Tel Aviv University, Tel-Aviv, Israel
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
- * E-mail:
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Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages. Appl Environ Microbiol 2015; 81:8265-76. [PMID: 26386059 DOI: 10.1128/aem.01659-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/12/2015] [Indexed: 11/20/2022] Open
Abstract
Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments.
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68
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Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proc Natl Acad Sci U S A 2015. [PMID: 26221022 DOI: 10.1073/pnas.1501615112] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton-bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore- related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton-bacterial interactions in both positive and negative feedback loops.
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69
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Álvarez-Canales G, Arellano-Álvarez G, González-Domenech CM, de la Cruz F, Moya A, Delaye L. Identification of Xenologs and Their Characteristic Low Expression Levels in the Cyanobacterium Synechococcus elongatus. J Mol Evol 2015; 80:292-304. [PMID: 26040248 DOI: 10.1007/s00239-015-9684-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 05/28/2015] [Indexed: 02/07/2023]
Abstract
Horizontal gene transfer (HGT) is a central process in prokaryotic evolution. Once a gene is introduced into a genome by HGT, its contribution to the fitness of the recipient cell depends in part on its expression level. Here we show that in Synechococcus elongatus PCC 7942, xenologs derived from non-cyanobacterial sources exhibited lower expression levels than native genes in the genome. In accord with our observation, xenolog codon adaptation indexes also displayed relatively low expression values. These results are in agreement with previous reports that suggested the relative neutrality of most xenologs. However, we also demonstrated that some of the xenologs detected participated in cellular functions, including iron starvation acclimation and nitrate reduction, which corroborate the role of HGT in bacterial adaptation. For example, the expression levels of some of the xenologs detected are known to increase under iron-limiting conditions. We interpreted the overall pattern as an indication that there is a selection pressure against high expression levels of xenologs. However, when a xenolog protein product confers a selective advantage, natural selection can further modulate its expression level to meet the requirements of the recipient cell. In addition, we show that ORFans did not exhibit significantly lower expression levels than native genes in the genome, which suggested an origin other than xenology.
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Affiliation(s)
- Gilberto Álvarez-Canales
- Departamento de Ingeniería Genética, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
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70
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Bräuer S, Cadillo-Quiroz H, Kyrpides N, Woyke T, Goodwin L, Detter C, Podell S, Yavitt JB, Zinder SH. Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. MICROBIOLOGY-SGM 2015; 161:1572-1581. [PMID: 25998264 DOI: 10.1099/mic.0.000117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.
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Affiliation(s)
- Suzanna Bräuer
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | - Hinsby Cadillo-Quiroz
- Swette Center for Environmental Biotechnology at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Chris Detter
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY 14853, USA
| | - Stephen H Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Modolo L, Picard F, Lerat E. A new genome-wide method to track horizontally transferred sequences: application to Drosophila. Genome Biol Evol 2015; 6:416-32. [PMID: 24497602 PMCID: PMC3942030 DOI: 10.1093/gbe/evu026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Because of methodological breakthroughs and the availability of an increasing amount of whole-genome sequence data, horizontal transfers (HTs) in eukaryotes have received much attention recently. Contrary to similar analyses in prokaryotes, most studies in eukaryotes usually investigate particular sequences corresponding to transposable elements (TEs), neglecting the other components of the genome. We present a new methodological framework for the genome-wide detection of all putative horizontally transferred sequences between two species that requires no prior knowledge of the transferred sequences. This method provides a broader picture of HTs in eukaryotes by fully exploiting complete-genome sequence data. In contrast to previous genome-wide approaches, we used a well-defined statistical framework to control for the number of false positives in the results, and we propose two new validation procedures to control for confounding factors. The first validation procedure relies on a comparative analysis with other species of the phylogeny to validate HTs for the nonrepeated sequences detected, whereas the second one built upon the study of the dynamics of the detected TEs. We applied our method to two closely related Drosophila species, Drosophila melanogaster and D. simulans, in which we discovered 10 new HTs in addition to all the HTs previously detected in different studies, which underscores our method’s high sensitivity and specificity. Our results favor the hypothesis of multiple independent HTs of TEs while unraveling a small portion of the network of HTs in the Drosophila phylogeny.
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Affiliation(s)
- Laurent Modolo
- Université de Lyon, France, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, VIlleurbanne, France
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Xiang H, Zhang R, De Koeyer D, Pan G, Li T, Liu T, Zhou Z. New evidence on the relationship between Microsporidia and Fungi: a genome-wide analysis by DarkHorse software. Can J Microbiol 2014; 60:557-68. [DOI: 10.1139/cjm-2014-0209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microsporidia are a group of obligate intracellular eukaryotic parasites that infect a wide variety of species, including humans. Phylogenetic analysis indicates a relationship between the Microsporidia and the Fungi. However, most results are based on the analysis of relatively few genes. DarkHorse analysis involves the transformation of BLAST results into a lineage probability index (LPI) value and allows for the comparison of genes for an entire genome with those of other genomes. Thus, we can see which genes from the microsporidia score most closely based on the LPI with other eukaryotic organisms. In this analysis, we calculated the LPI for each gene from the genomes of 7 Microsporidia, Antonospora locustae, Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis, Nosema bombycis, Nosema ceranae, and Nematocida parisii, to analyze the genetic relationships between Microsporidia and other species. It was found that many (91%) genes were most closely correlated with genes from other microsporidial genomes and had the highest mean LPI (0.985), indicating a monophyletic origin of the Microsporidia. In a subsequent analysis, we excluded the other Microsporidia from the analysis to look for relationships before the divergence of Microsporidia, and found that 43% of the microsporidial genes scored highest with fungal genes, and a higher mean LPI was found with Fungi than with other kingdoms, suggesting that Microsporidia is closely related to Fungi at the genomic level. Microsporidial genes were functionally clustered based on the KOG (Eukaryotic COG) database, and the possible lineages for each gene family were discussed in concert with the DarkHorse results.
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Affiliation(s)
- Heng Xiang
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, People’s Republic of China
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Ruizhi Zhang
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400715, People’s Republic of China
| | - David De Koeyer
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing 400715, People’s Republic of China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing 400715, People’s Republic of China
| | - Tie Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing 400715, People’s Republic of China
| | - Zeyang Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing 400715, People’s Republic of China
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Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics 2014; 15:717. [PMID: 25159222 PMCID: PMC4155097 DOI: 10.1186/1471-2164-15-717] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 08/20/2014] [Indexed: 11/23/2022] Open
Abstract
Background First pass methods based on BLAST match are commonly used as an initial step to separate the different phylogenetic histories of genes in microbial genomes, and target putative horizontal gene transfer (HGT) events. This will continue to be necessary given the rapid growth of genomic data and the technical difficulties in conducting large-scale explicit phylogenetic analyses. However, these methods often produce misleading results due to their inability to resolve indirect phylogenetic links and their vulnerability to stochastic events. Results A new computational method of rapid, exhaustive and genome-wide detection of HGT was developed, featuring the systematic analysis of BLAST hit distribution patterns in the context of a priori defined hierarchical evolutionary categories. Genes that fall beyond a series of statistically determined thresholds are identified as not adhering to the typical vertical history of the organisms in question, but instead having a putative horizontal origin. Tests on simulated genomic data suggest that this approach effectively targets atypically distributed genes that are highly likely to be HGT-derived, and exhibits robust performance compared to conventional BLAST-based approaches. This method was further tested on real genomic datasets, including Rickettsia genomes, and was compared to previous studies. Results show consistency with currently employed categories of HGT prediction methods. In-depth analysis of both simulated and real genomic data suggests that the method is notably insensitive to stochastic events such as gene loss, rate variation and database error, which are common challenges to the current methodology. An automated pipeline was created to implement this approach and was made publicly available at: https://github.com/DittmarLab/HGTector. The program is versatile, easily deployed, has a low requirement for computational resources. Conclusions HGTector is an effective tool for initial or standalone large-scale discovery of candidate HGT-derived genes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-717) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiyun Zhu
- Department of Biological Sciences, University at Buffalo, State University of New York, 109 Cooke Hall, Buffalo, NY 14260, USA.
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74
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Genomic encyclopedia of type strains of the genus Bifidobacterium. Appl Environ Microbiol 2014; 80:6290-302. [PMID: 25085493 DOI: 10.1128/aem.02308-14] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bifidobacteria represent one of the dominant microbial groups that are present in the gut of various animals, being particularly prevalent during the suckling stage of life of humans and other mammals. However, the overall genome structure of this group of microorganisms remains largely unexplored. Here, we sequenced the genomes of 42 representative (sub)species across the Bifidobacterium genus and used this information to explore the overall genetic picture of this bacterial group. Furthermore, the genomic data described here were used to reconstruct the evolutionary development of the Bifidobacterium genus. This reconstruction suggests that its evolution was substantially influenced by genetic adaptations to obtain access to glycans, thereby representing a common and potent evolutionary force in shaping bifidobacterial genomes.
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Grilli J, Romano M, Bassetti F, Cosentino Lagomarsino M. Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers. Nucleic Acids Res 2014; 42:6850-60. [PMID: 24829449 PMCID: PMC4066789 DOI: 10.1093/nar/gku378] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome ‘flux’. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection.
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Affiliation(s)
- Jacopo Grilli
- Dipartimento di Fisica e Astronomia "G. Galilei", Università di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Mariacristina Romano
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria, 16, 20133 Milano, Italy
| | - Federico Bassetti
- Università di Pavia, Dipartimento di Matematica, via Ferrata 1, 27100 Pavia, Italy
| | - Marco Cosentino Lagomarsino
- CNRS, UMR 7238, Paris, France Sorbonne Universités, UPMC Université Paris 06, UMR 7238 Computational and Quantitative Biology, Genomic Physics Group, 15 rue de l'École de Médecine, Paris, France
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Guo L, Han L, Yang L, Zeng H, Fan D, Zhu Y, Feng Y, Wang G, Peng C, Jiang X, Zhou D, Ni P, Liang C, Liu L, Wang J, Mao C, Fang X, Peng M, Huang J. Genome and transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. cubense causing banana vascular wilt disease. PLoS One 2014; 9:e95543. [PMID: 24743270 PMCID: PMC3990668 DOI: 10.1371/journal.pone.0095543] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 03/28/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The asexual fungus Fusarium oxysporum f. sp. cubense (Foc) causing vascular wilt disease is one of the most devastating pathogens of banana (Musa spp.). To understand the molecular underpinning of pathogenicity in Foc, the genomes and transcriptomes of two Foc isolates were sequenced. METHODOLOGY/PRINCIPAL FINDINGS Genome analysis revealed that the genome structures of race 1 and race 4 isolates were highly syntenic with those of F. oxysporum f. sp. lycopersici strain Fol4287. A large number of putative virulence associated genes were identified in both Foc genomes, including genes putatively involved in root attachment, cell degradation, detoxification of toxin, transport, secondary metabolites biosynthesis and signal transductions. Importantly, relative to the Foc race 1 isolate (Foc1), the Foc race 4 isolate (Foc4) has evolved with some expanded gene families of transporters and transcription factors for transport of toxins and nutrients that may facilitate its ability to adapt to host environments and contribute to pathogenicity to banana. Transcriptome analysis disclosed a significant difference in transcriptional responses between Foc1 and Foc4 at 48 h post inoculation to the banana 'Brazil' in comparison with the vegetative growth stage. Of particular note, more virulence-associated genes were up regulated in Foc4 than in Foc1. Several signaling pathways like the mitogen-activated protein kinase Fmk1 mediated invasion growth pathway, the FGA1-mediated G protein signaling pathway and a pathogenicity associated two-component system were activated in Foc4 rather than in Foc1. Together, these differences in gene content and transcription response between Foc1 and Foc4 might account for variation in their virulence during infection of the banana variety 'Brazil'. CONCLUSIONS/SIGNIFICANCE Foc genome sequences will facilitate us to identify pathogenicity mechanism involved in the banana vascular wilt disease development. These will thus advance us develop effective methods for managing the banana vascular wilt disease, including improvement of disease resistance in banana.
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Affiliation(s)
- Lijia Guo
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Laying Yang
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huicai Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | | | | | - Guofen Wang
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | | | | | | | - Changcong Liang
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lei Liu
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jun Wang
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chao Mao
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Junsheng Huang
- Key Laboratory of Monitoring and Control of Tropical Agricultural and Forest Invasive Alien Pests, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Jaron KS, Moravec JC, Martínková N. SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. Bioinformatics 2013; 30:1081-1086. [PMID: 24371153 DOI: 10.1093/bioinformatics/btt727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/09/2013] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead. RESULTS We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition. AVAILABILITY AND IMPLEMENTATION Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research-data-analysis-tools-sighunt are implemented in C and R and are platform-independent. CONTACT 376090@mail.muni.cz or martinkova@ivb.cz.
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Affiliation(s)
- Kamil S Jaron
- Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jiří C Moravec
- Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Natália Martínková
- Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME JOURNAL 2013; 8:979-90. [PMID: 24335829 DOI: 10.1038/ismej.2013.221] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/05/2013] [Accepted: 11/10/2013] [Indexed: 02/01/2023]
Abstract
Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate, but not sodium, chloride or calcium ions, while relative abundances of Halorubrum, Haloarcula, Halonotius, Halobaculum and Salinibacter-related sequences correlated negatively with Haloquadratum and these same ionic factors. Nanohaloarchaea and Halorhabdus-related sequence abundances were inversely correlated with each other, but not other taxonomic groups. These data, along with predicted gene functions from nearly-complete assembled population metagenomes, suggest different ecological phenotypes for Nanohaloarchaea and Halorhabdus-related strains versus other community members. Nucleotide percent G+C compositions were consistently lower in community metagenomic reads from summer versus winter samples. The same seasonal G+C trends were observed within taxonomically binned read subsets from each of seven different genus-level archaeal groups. Relative seasonal abundances were also linked to percent G+C for assembled population genomes. Together, these data suggest that extreme ionic conditions may exert selective pressure on archaeal populations at the level of genomic nucleotide composition, thus contributing to seasonal successional processes. Despite the unavailability of cultured representatives for most of the organisms identified in this study, effective coordination of physical and biological measurements has enabled discovery and quantification of unexpected taxon-specific, environmentally mediated factors influencing microbial community structure.
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79
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Yue J, Sun G, Hu X, Huang J. The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis. BMC Genomics 2013; 14:729. [PMID: 24156600 PMCID: PMC4046809 DOI: 10.1186/1471-2164-14-729] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 10/17/2013] [Indexed: 12/29/2022] Open
Abstract
Background It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. Results Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids. Conclusions Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-729) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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80
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Swithers KS, Soucy SM, Lasek-Nesselquist E, Lapierre P, Gogarten JP. Distribution and Evolution of the Mobile vma-1b Intein. Mol Biol Evol 2013; 30:2676-87. [DOI: 10.1093/molbev/mst164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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81
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Wei W, Zhang T, Lin D, Yang ZJ, Guo FB. Transcriptional abundance is not the single force driving the evolution of bacterial proteins. BMC Evol Biol 2013; 13:162. [PMID: 23914835 PMCID: PMC3734234 DOI: 10.1186/1471-2148-13-162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/01/2013] [Indexed: 11/20/2022] Open
Abstract
Background Despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated. In this study, we have assessed the effects of 16 different biological features on the evolutionary rates (ERs) of protein-coding sequences in bacterial genomes. Results Our analysis of 18 bacterial species revealed new correlations between ERs and constraining factors. Previous studies have suggested that transcriptional abundance overwhelmingly constrains the evolution of yeast protein sequences. This transcriptional abundance leads to selection against misfolding or misinteractions. In this study we found that there was no single factor in determining the evolution of bacterial proteins. Not only transcriptional abundance (codon adaptation index and expression level), but also protein-protein associations (PPAs), essentiality (ESS), subcellular localization of cytoplasmic membrane (SLM), transmembrane helices (TMH) and hydropathicity score (HS) independently and significantly affected the ERs of bacterial proteins. In some species, PPA and ESS demonstrate higher correlations with ER than transcriptional abundance. Conclusions Different forces drive the evolution of protein sequences in yeast and bacteria. In bacteria, the constraints are involved in avoiding a build-up of toxic molecules caused by misfolding/misinteraction (transcriptional abundance), while retaining important functions (ESS, PPA) and maintaining the cell membrane (SLM, TMH and HS). Each of these independently contributes to the variation in protein evolution.
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Affiliation(s)
- Wen Wei
- Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054 Chengdu, China
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Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One 2013; 8:e61692. [PMID: 23637883 PMCID: PMC3630111 DOI: 10.1371/journal.pone.0061692] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/13/2013] [Indexed: 01/10/2023] Open
Abstract
Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Juan A. Ugalde
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Priya Narasingarao
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
| | - Karla B. Heidelberg
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Pan G, Xu J, Li T, Xia Q, Liu SL, Zhang G, Li S, Li C, Liu H, Yang L, Liu T, Zhang X, Wu Z, Fan W, Dang X, Xiang H, Tao M, Li Y, Hu J, Li Z, Lin L, Luo J, Geng L, Wang L, Long M, Wan Y, He N, Zhang Z, Lu C, Keeling PJ, Wang J, Xiang Z, Zhou Z. Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation. BMC Genomics 2013; 14:186. [PMID: 23496955 PMCID: PMC3614468 DOI: 10.1186/1471-2164-14-186] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/26/2013] [Indexed: 01/05/2023] Open
Abstract
Background Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees). Results Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability. Conclusions Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms such as gene duplication, horizontal gene transfer, and transposable element expansion. We also showed that the duplicated genes can serve as raw materials for evolutionary innovations possibly contributing to the increase of pathologenic ability. Based on our research, we propose that duplicated genes of N. bombycis should be treated as primary targets for treatment designs against pébrine.
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Affiliation(s)
- Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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de Carvalho MO, Loreto ELS. Methods for detection of horizontal transfer of transposable elements in complete genomes. Genet Mol Biol 2012; 35:1078-84. [PMID: 23411916 PMCID: PMC3571429 DOI: 10.1590/s1415-47572012000600024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent advances in nucleic acid sequencing technology are creating a diverse landscape for the analysis of horizontal transfer in complete genomes. Previously limited to prokaryotes, the availability of complete genomes from close eukaryotic species presents an opportunity to validate hypotheses about the patterns of evolution and mechanisms that drive horizontal transfer. Many of those methods can be transported from methods previously used in prokaryotic genomes, as the assumptions for horizontal transfer can be interpreted as the same. Some methods, however, require a complete adaptation, while others need refinements in sensitivity and specificity to deal with the huge datasets generated from next-generation sequencing technologies. Here we list the types of methods used for horizontal transfer detection, as well as theirs strengths and weakness.
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Affiliation(s)
- Marcos Oliveira de Carvalho
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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85
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Liu L, Chen X, Skogerbø G, Zhang P, Chen R, He S, Huang DW. The human microbiome: A hot spot of microbial horizontal gene transfer. Genomics 2012; 100:265-70. [DOI: 10.1016/j.ygeno.2012.07.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 07/06/2012] [Accepted: 07/16/2012] [Indexed: 12/19/2022]
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86
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Teeling H, Glöckner FO. Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform 2012; 13:728-42. [PMID: 22966151 PMCID: PMC3504927 DOI: 10.1093/bib/bbs039] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/09/2012] [Indexed: 12/21/2022] Open
Abstract
Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space. Recently, a new type of holistic ecosystem study has emerged that seeks to combine metagenomics with biodiversity, meta-expression and contextual data. Such 'ecosystems biology' approaches bear the potential to not only advance our understanding of environmental microbes to a new level but also impose challenges due to increasing data complexities, in particular with respect to bioinformatic post-processing. This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and bioinformaticians alike.
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87
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Xiong D, Xiao F, Liu L, Hu K, Tan Y, He S, Gao X. Towards a better detection of horizontally transferred genes by combining unusual properties effectively. PLoS One 2012; 7:e43126. [PMID: 22905214 PMCID: PMC3419211 DOI: 10.1371/journal.pone.0043126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/16/2012] [Indexed: 02/01/2023] Open
Abstract
Background Horizontal gene transfer (HGT) is one of the major mechanisms contributing to microbial genome diversification. A number of computational methods for finding horizontally transferred genes have been proposed in the past decades; however none of them has provided a reliable detector yet. In existing parametric approaches, only one single compositional property can participate in the detection process, or the results obtained through each single property are just simply combined. It’s known that different properties may mean different information, so the single property can’t sufficiently contain the information encoded by gene sequences. In addition, the class imbalance problem in the datasets, which also results in great errors for the gene detection, hasn’t been considered by the published methods. Here we developed an effective classifier system (Hgtident) that used support vector machine (SVM) by combining unusual properties effectively for HGT detection. Results Our approach Hgtident includes the introduction of more representative datasets, optimization of SVM model, feature selection, handling of imbalance problem in the datasets and extensive performance evaluation via systematic cross-validation methods. Through feature selection, we found that JS-DN and JS-CB have higher discriminating power for HGT detection, while GC1–GC3 and k-mer (k = 1, 2, …, 7) make the least contribution. Extensive experiments indicated the new classifier could reduce Mean error dramatically, and also improve Recall by a certain level. For the testing genomes, compared with the existing popular multiple-threshold approach, on average, our Recall and Mean error was respectively improved by 2.81% and reduced by 26.32%, which means that numerous false positives were identified correctly. Conclusions Hgtident introduced here is an effective approach for better detecting HGT. Combining multiple features of HGT is also essential for a wider range of HGT events detection.
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Affiliation(s)
- Dapeng Xiong
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Fen Xiao
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Li Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Kai Hu
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Yanping Tan
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
| | - Shunmin He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People’s Republic of China
- * E-mail: (SH); (XG)
| | - Xieping Gao
- Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, People’s Republic of China
- * E-mail: (SH); (XG)
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Zhaxybayeva O, Swithers KS, Foght J, Green AG, Bruce D, Detter C, Han S, Teshima H, Han J, Woyke T, Pitluck S, Nolan M, Ivanova N, Pati A, Land ML, Dlutek M, Doolittle WF, Noll KM, Nesbø CL. Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date. Genome Biol Evol 2012; 4:700-8. [PMID: 22798451 PMCID: PMC3516359 DOI: 10.1093/gbe/evs059] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Here we describe the genome of Mesotoga prima MesG1.Ag4.2, the first genome of a mesophilic Thermotogales bacterium. Mesotoga prima was isolated from a polychlorinated biphenyl (PCB)-dechlorinating enrichment culture from Baltimore Harbor sediments. Its 2.97 Mb genome is considerably larger than any previously sequenced Thermotogales genomes, which range between 1.86 and 2.30 Mb. This larger size is due to both higher numbers of protein-coding genes and larger intergenic regions. In particular, the M. prima genome contains more genes for proteins involved in regulatory functions, for instance those involved in regulation of transcription. Together with its closest relative, Kosmotoga olearia, it also encodes different types of proteins involved in environmental and cell-cell interactions as compared with other Thermotogales bacteria. Amino acid composition analysis of M. prima proteins implies that this lineage has inhabited low-temperature environments for a long time. A large fraction of the M. prima genome has been acquired by lateral gene transfer (LGT): a DarkHorse analysis suggests that 766 (32%) of predicted protein-coding genes have been involved in LGT after Mesotoga diverged from the other Thermotogales lineages. A notable example of a lineage-specific LGT event is a reductive dehalogenase gene-a key enzyme in dehalorespiration, indicating M. prima may have a more active role in PCB dechlorination than was previously assumed.
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Affiliation(s)
- Olga Zhaxybayeva
- Department of Biology, West Virginia University
- Department of Biological Sciences, Dartmouth College
| | | | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Anna G. Green
- Department of Molecular and Cell Biology, University of Connecticut
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Shunsheng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - Marlena Dlutek
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - W. Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Kenneth M. Noll
- Department of Molecular and Cell Biology, University of Connecticut
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
- *Corresponding author: E-mail:
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Puigbò P, Mekhedov S, Wolf YI, Koonin EV. A comprehensive census of horizontal gene transfers from prokaryotes to unikonts. Genome Biol 2011. [DOI: 10.1186/1465-6906-12-s1-p20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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90
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Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME JOURNAL 2011; 6:81-93. [PMID: 21716304 DOI: 10.1038/ismej.2011.78] [Citation(s) in RCA: 233] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1-0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named 'Nanohaloarchaea'. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.
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Affiliation(s)
- Priya Narasingarao
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
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91
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Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups. Antonie van Leeuwenhoek 2011; 100:1-34. [DOI: 10.1007/s10482-011-9576-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 03/11/2011] [Indexed: 11/25/2022]
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92
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Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. ISME JOURNAL 2010; 5:918-28. [PMID: 21160538 DOI: 10.1038/ismej.2010.180] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.
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93
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Snir S, Trifonov E. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. J Comput Biol 2010; 17:1535-48. [DOI: 10.1089/cmb.2010.0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sagi Snir
- Department of Evolutionary Biology and the Institute of Evolution, Haifa University, Haifa, Israel
| | - Edward Trifonov
- Genome Diversity Center, Institute of Evolution, Haifa University, Haifa, Israel
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94
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Sun G, Yang Z, Ishwar A, Huang J. Algal genes in the closest relatives of animals. Mol Biol Evol 2010; 27:2879-89. [PMID: 20627874 DOI: 10.1093/molbev/msq175] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The spread of photosynthesis is one of the most important but controversial topics in eukaryotic evolution. Because of massive gene transfer from plastids to the nucleus and because of the possibility that plastids have been lost in evolution, algal genes in aplastidic organisms often are interpreted as footprints of photosynthetic ancestors. These putative plastid losses, in turn, have been cited as support for scenarios involving the spread of plastids in broadscale eukaryotic evolution. Phylogenomic analyses identified more than 100 genes of possible algal origin in Monosiga, a unicellular species from choanoflagellates, a group considered to be the closest protozoan relatives of animals and to be primitively heterotrophic. The vast majority of these algal genes appear to be derived from haptophytes, diatoms, or green plants. Furthermore, more than 25% of these algal genes are ultimately of prokaryotic origin and were spread secondarily to Monosiga. Our results show that the presence of algal genes may be expected in many phagotrophs or taxa of phagotrophic ancestry and therefore does not necessarily represent evidence of plastid losses. The ultimate prokaryotic origin of some algal genes and their simultaneous presence in both primary and secondary photosynthetic eukaryotes either suggest recurrent gene transfer events under specific environments or support a more ancient origin of primary plastids.
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Affiliation(s)
- Guiling Sun
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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95
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Koonin EV, Yutin N. Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology 2010; 53:284-92. [PMID: 20551680 DOI: 10.1159/000312913] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS The nucleo-cytoplasmic large DNA viruses (NCLDV) constitute an apparently monophyletic group that consists of 6 families of viruses infecting a broad variety of eukaryotes. A comprehensive genome comparison and maximum-likelihood reconstruction of NCLDV evolution reveal a set of approximately 50 conserved genes that can be tentatively mapped to the genome of the common ancestor of this class of eukaryotic viruses. We address the origins and evolution of NCLDV. RESULTS Phylogenetic analysis indicates that some of the major clades of NCLDV infect diverse animals and protists, suggestive of early radiation of the NCLDV, possibly concomitant with eukaryogenesis. The core NCLDV genes seem to have originated from different sources including homologous genes of bacteriophages, bacteria and eukaryotes. These observations are compatible with a scenario of the origin of the NCLDV at an early stage of the evolution of eukaryotes through extensive mixing of genes from widely different genomes. CONCLUSIONS The common ancestor of the NCLDV probably evolved from a bacteriophage as a result of recruitment of numerous eukaryotic and some bacterial genes, and concomitant loss of the majority of phage genes except for a small core of genes coding for proteins essential for virus genome replication and virion formation.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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96
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Mallet LV, Becq J, Deschavanne P. Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus. BMC Genomics 2010; 11:171. [PMID: 20226043 PMCID: PMC2848249 DOI: 10.1186/1471-2164-11-171] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/12/2010] [Indexed: 12/14/2022] Open
Abstract
Background Numerous cases of horizontal transfers (HTs) have been described for eukaryote genomes, but in contrast to prokaryote genomes, no whole genome evaluation of HTs has been carried out. This is mainly due to a lack of parametric methods specially designed to take the intrinsic heterogeneity of eukaryote genomes into account. We applied a simple and tested method based on local variations of genomic signatures to analyze the genome of the pathogenic fungus Aspergillus fumigatus. Results We detected 189 atypical regions containing 214 genes, accounting for about 1 Mb of DNA sequences. However, the fraction of atypical DNA detected was smaller than the average amount detected in the same conditions in prokaryote genomes (3.1% vs 5.6%). It appeared that about one third of these regions contained no annotated genes, a proportion far greater than in prokaryote genomes. When analyzing the origin of these HTs by comparing their signatures to a home made database of species signatures, 3 groups of donor species emerged: bacteria (40%), fungi (25%), and viruses (22%). It is to be noticed that though inter-domain exchanges are confirmed, we only put in evidence very few exchanges between eukaryotic kingdoms. Conclusions In conclusion, we demonstrated that HTs are not negligible in eukaryote genomes, bearing in mind that in our stringent conditions this amount is a floor value, though of a lesser extent than in prokaryote genomes. The biological mechanisms underlying those transfers remain to be elucidated as well as the biological functions of the transferred genes.
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Affiliation(s)
- Ludovic V Mallet
- Molécules thérapeutiques in silico (MTI), INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
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97
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Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 2010; 5:e8926. [PMID: 20126622 PMCID: PMC2812497 DOI: 10.1371/journal.pone.0008926] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 12/07/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed. METHODOLOGY/PRINCIPAL FINDINGS The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species. CONCLUSIONS/SIGNIFICANCE The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.
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Affiliation(s)
- Sinead C. Leahy
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - William J. Kelly
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Ron S. Ronimus
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Diana M. Pacheco
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Dong Li
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Zhanhao Kong
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Sharla McTavish
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carrie Sang
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Suzanne C. Lambie
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Debjit Dey
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T. Attwood
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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98
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Gao J, Chen LL. Theoretical methods for identifying important functional genes in bacterial genomes. Res Microbiol 2009; 161:1-8. [PMID: 19900539 DOI: 10.1016/j.resmic.2009.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 10/05/2009] [Accepted: 10/21/2009] [Indexed: 12/30/2022]
Abstract
Some functional genes, such as essential genes, highly expressed genes and horizontally transferred genes, play important roles in the survival and pathogenicity of bacteria. This review attempts to summarize current computational methods in identifying the above functional genes from bacterial genomes, which is of significant importance in exploring the bacterial genomes.
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Affiliation(s)
- Junxiang Gao
- School of Information and Communication Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, PR China
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99
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Freilich S, Goldovsky L, Gottlieb A, Blanc E, Tsoka S, Ouzounis CA. Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics 2009; 10:355. [PMID: 19860884 PMCID: PMC2775751 DOI: 10.1186/1471-2105-10-355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 10/27/2009] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. RESULTS The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples. CONCLUSION Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples.
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Affiliation(s)
- Shiri Freilich
- The Blavatnik School of Computer Sciences and School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.
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100
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Stiller JW, Huang J, Ding Q, Tian J, Goodwillie C. Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses? BMC Genomics 2009; 10:484. [PMID: 19843329 PMCID: PMC2770532 DOI: 10.1186/1471-2164-10-484] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 10/20/2009] [Indexed: 12/18/2022] Open
Abstract
Background How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, and two aplastidic sister taxa, Phytophthora ramorum and P. sojae. Results Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes. Conclusion Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different a priori assumptions inherent in competing evolutionary hypotheses.
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Affiliation(s)
- John W Stiller
- Department of Biology, East Carolina University, Greenville, USA.
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