151
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Utter DR, Borisy GG, Eren AM, Cavanaugh CM, Mark Welch JL. Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. Genome Biol 2020; 21:293. [PMID: 33323129 PMCID: PMC7739467 DOI: 10.1186/s13059-020-02200-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. RESULTS Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous. CONCLUSIONS Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.
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Affiliation(s)
- Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | | | - A Murat Eren
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Jessica L Mark Welch
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
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152
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Verma DK, Chaudhary C, Singh L, Sidhu C, Siddhardha B, Prasad SE, Thakur KG. Isolation and Taxonomic Characterization of Novel Haloarchaeal Isolates From Indian Solar Saltern: A Brief Review on Distribution of Bacteriorhodopsins and V-Type ATPases in Haloarchaea. Front Microbiol 2020; 11:554927. [PMID: 33362726 PMCID: PMC7755889 DOI: 10.3389/fmicb.2020.554927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/17/2020] [Indexed: 01/10/2023] Open
Abstract
Haloarchaea inhabit high salinity environments worldwide. They are a potentially rich source of crucial biomolecules like carotenoids and industrially useful proteins. However, diversity in haloarchaea present in Indian high salinity environments is poorly studied. In the present study, we isolated 12 haloarchaeal strains from hypersaline Kottakuppam, Tamil Nadu solar saltern in India. 16S rRNA based taxonomic characterization of these isolates suggested that nine of them are novel strains that belong to genera Haloarcula, Halomicrobium, and Haloferax. Transmission electron microscopy suggests the polymorphic nature of these haloarchaeal isolates. Most of the haloarchaeal species are known to be high producers of carotenoids. We were able to isolate carotenoids from all these 12 isolates. The UV-Vis spectroscopy-based analysis suggests that bacterioruberin and lycopene are the major carotenoids produced by these isolates. Based on the visual inspection of the purified carotenoids, the isolates were classified into two broad categories i.e., yellow and orange, attributed to the differences in the ratio of bacterioruberin and lycopene as confirmed by the UV-Vis spectral analysis. Using a PCR-based screening assay, we were able to detect the presence of the bacteriorhodopsin gene (bop) in 11 isolates. We performed whole-genome sequencing for three bop positive and one bop negative haloarchaeal isolates. Whole-genome sequencing, followed by pan-genome analysis identified multiple unique genes involved in various biological functions. We also successfully cloned, expressed, and purified functional recombinant bacteriorhodopsin (BR) from one of the isolates using Escherichia coli as an expression host. BR has light-driven proton pumping activity resulting in the proton gradient across the membrane, which is utilized by V-Type ATPases to produce ATP. We analyzed the distribution of bop and other accessory genes involved in functional BR expression and ATP synthesis in all the representative haloarchaeal species. Our bioinformatics-based analysis of all the sequenced members of genus Haloarcula suggests that bop, if present, is usually inserted between the genes coding for B and D subunits of the V-type ATPases operon. This study provides new insights into the genomic variations in haloarchaea and reports expression of new BR variant having good expression in functional form in E. coli.
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Affiliation(s)
- Dipesh Kumar Verma
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Chetna Chaudhary
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Latika Singh
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Chandni Sidhu
- MTCC-Microbial Type Culture Collection & Gene Bank, Council of Scientific and Industrial Research Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Senthil E Prasad
- Biochemical Engineering Research and Process Development Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
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153
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Pangenome Analysis of Mycobacterium tuberculosis Reveals Core-Drug Targets and Screening of Promising Lead Compounds for Drug Discovery. Antibiotics (Basel) 2020; 9:antibiotics9110819. [PMID: 33213029 PMCID: PMC7698547 DOI: 10.3390/antibiotics9110819] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (M. tuberculosis), is one of the leading causes of human deaths globally according to the WHO TB 2019 report. The continuous rise in multi- and extensive-drug resistance in M. tuberculosis broadens the challenges to control tuberculosis. The availability of a large number of completely sequenced genomes of M. tuberculosis has provided an opportunity to explore the pangenome of the species along with the pan-phylogeny and to identify potential novel drug targets leading to drug discovery. We attempt to calculate the pangenome of M. tuberculosis that comprises a total of 150 complete genomes and performed the phylo-genomic classification and analysis. Further, the conserved core genome (1251 proteins) is subjected to various sequential filters (non-human homology, essentiality, virulence, physicochemical parameters, and pathway analysis) resulted in identification of eight putative broad-spectrum drug targets. Upon molecular docking analyses of these targets with ligands available at the DrugBank database shortlisted a total of five promising ligands with projected inhibitory potential; namely, 2′deoxy-thymidine-5′-diphospho-alpha-d-glucose, uridine diphosphate glucose, 2′-deoxy-thymidine-beta-l-rhamnose, thymidine-5′-triphosphate, and citicoline. We are confident that with further lead optimization and experimental validation, these lead compounds may provide a sound basis to develop safe and effective drugs against tuberculosis disease in humans.
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154
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Abstract
A description of the genetic makeup of a species based on a single genome is often insufficient because it ignores the variability in gene repertoire among multiple strains. The estimation of the pangenome of a species is a solution to this issue as it provides an overview of genes that are shared by all strains and genes that are present in only some of the genomes. These different sets of genes can then be analyzed functionally to explore correlations with unique phenotypes and adaptations. This protocol presents the usage of Roary, a Linux-native pangenome application. Roary is a straightforward software that provides 1) an overview about core and accessory genes for those interested in general trends and, also, 2) detailed information on gene presence/absence in each genome for in-depth analyses. Results are provided both in text and graphic format.
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Affiliation(s)
- Farrah Sitto
- Department of Biological Sciences, Oakland University, Rochester, MI
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, MI
- Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI
- Corresponding author: E-mail:
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155
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Reid BN, Moran RL, Kopack CJ, Fitzpatrick SW. Rapture-ready darters: Choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference in Etheostoma. Mol Ecol Resour 2020; 21:404-420. [PMID: 33058399 DOI: 10.1111/1755-0998.13275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/17/2020] [Accepted: 10/01/2020] [Indexed: 11/26/2022]
Abstract
Researchers studying nonmodel organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, remain difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1,900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.
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Affiliation(s)
- Brendan N Reid
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Rachel L Moran
- Department of Evolution, Ecology, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | | | - Sarah W Fitzpatrick
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.,Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
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156
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Nagies FSP, Brueckner J, Tria FDK, Martin WF. A spectrum of verticality across genes. PLoS Genet 2020; 16:e1009200. [PMID: 33137105 PMCID: PMC7660906 DOI: 10.1371/journal.pgen.1009200] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/12/2020] [Accepted: 10/16/2020] [Indexed: 12/19/2022] Open
Abstract
Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, β-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners-an archaeal host, a mitochondrial symbiont, and a plastid ancestor-each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.
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Affiliation(s)
- Falk S. P. Nagies
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julia Brueckner
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fernando D. K. Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F. Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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157
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Tahir Ul Qamar M, Zhu X, Khan MS, Xing F, Chen LL. Pan-genome: A promising resource for noncoding RNA discovery in plants. THE PLANT GENOME 2020; 13:e20046. [PMID: 33217199 DOI: 10.1002/tpg2.20046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/08/2020] [Accepted: 06/22/2020] [Indexed: 05/05/2023]
Abstract
Plant genomes contain both protein-coding and noncoding sequences including transposable elements (TEs) and noncoding RNAs (ncRNAs). The ncRNAs are recognized as important elements that play fundamental roles in the structural organization and function of plant genomes. Despite various hypotheses, TEs are believed to be a major precursor of ncRNAs. Transposable elements are also prime factors that cause genomic variation among members of a species. Hence, TEs pose a major challenge in the discovery and analysis of ncRNAs. With the increase in the number of sequenced plant genomes, it is now accepted that a single reference genome is insufficient to represent the complete genomic diversity and contents of a species, and exploring the pan-genome of a species is critical. In this review, we summarize the recent progress in the field of plant pan-genomes. We also discuss TEs and their roles in ncRNA biogenesis and present our perspectives on the application of pan-genomes for the discovery of ncRNAs to fully explore and exploit their biological roles in plants.
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Affiliation(s)
- Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xitong Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Muhammad Sarwar Khan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Feng Xing
- College of Life Science, Xinyang Normal University, Xinyang, 464000, P. R. China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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158
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Zhou Z, Charlesworth J, Achtman M. Accurate reconstruction of bacterial pan- and core genomes with PEPPAN. Genome Res 2020; 30:1667-1679. [PMID: 33055096 PMCID: PMC7605250 DOI: 10.1101/gr.260828.120] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses, including the calculation of trees based on accessory gene content or allelic differences between core genes. To test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pangenomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pangenome pipelines using both empirical and simulated data sets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pangenome of approximately 40,000 genes from 3052 representative genomes spanning at least 80 species of Streptococcus The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of the entire Streptococcus genus.
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Affiliation(s)
- Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jane Charlesworth
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
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159
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Slizen MV, Galzitskaya OV. Comparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways. Int J Mol Sci 2020; 21:ijms21217839. [PMID: 33105850 PMCID: PMC7660090 DOI: 10.3390/ijms21217839] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 01/13/2023] Open
Abstract
Nosocomial (hospital-acquired) infections remain a serious challenge for health systems. The reason for this lies not only in the local imperfection of medical practices and protocols. The frequency of infection with antibiotic-resistant strains of bacteria is growing every year, both in developed and developing countries. In this work, a pangenome and comparative analysis of 201 genomes of Staphylococcus aureus, Enterobacter spp., Pseudomonas aeruginosa, and Mycoplasma spp. was performed on the basis of high-level functional annotations—KEGG pathways and KEGG modules. The first three organisms are serious nosocomial pathogens, often exhibiting multidrug resistance. Analysis of KEGG modules revealed methicillin resistance in 25% of S. aureus strains and resistance to carbapenems in 21% of Enterobacter spp. strains. P. aeruginosa has a wide range of unique efflux systems. One hundred percent of the analyzed strains have at least two drug resistance systems, and 75% of the strains have seven. Each of the organisms has a characteristic set of metabolic features, whose impact on drug resistance can be considered in future studies. Comparing the genomes of nosocomial pathogens with each other and with Mycoplasma genomes can expand our understanding of the versatility of certain metabolic features and mechanisms of drug resistance.
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Affiliation(s)
- Mikhail V. Slizen
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia;
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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160
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Chen J, Li JM, Tang YJ, Ma K, Li B, Zeng X, Liu XB, Li Y, Yang ZL, Xu WN, Xie BG, Liu HW, Guo SX. Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis. BMC Genomics 2020; 21:719. [PMID: 33069230 PMCID: PMC7568368 DOI: 10.1186/s12864-020-07108-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Background Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular level remains unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu355, predicted its biosynthetic gene clusters (BGCs) and profiled the expression of these genes in wild and cultivar strains and in different developmental stages of the wild F. filiformis strain by a comparative transcriptomic analysis. Results We found that the genome of the F. filiformis was 35.01 Mb in length and harbored 10,396 gene models. Thirteen putative terpenoid gene clusters were predicted and 12 sesquiterpene synthase genes belonging to four different groups and two type I polyketide synthase gene clusters were identified in the F. filiformis genome. The number of genes related to terpenoid biosynthesis was higher in the wild strain (119 genes) than in the cultivar strain (81 genes). Most terpenoid biosynthesis genes were upregulated in the primordium and fruiting body of the wild strain, while the polyketide synthase genes were generally upregulated in the mycelium of the wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase, which are involved in polysaccharide biosynthesis, had relatively high transcript levels both in the mycelium and fruiting body of the wild F. filiformis strain. Conclusions F. filiformis is enriched in a number of gene clusters involved in the biosynthesis of polysaccharides and terpenoid bioactive compounds and these genes usually display differential expression between wild and cultivar strains, even in different developmental stages. This study expands our knowledge of the biology of F. filiformis and provides valuable data for elucidating the regulation of secondary metabolites in this unique F. filiformis strain.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Jia-Mei Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yan-Jing Tang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ke Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Bing Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xu Zeng
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xiao-Bin Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, P. R. China
| | - Yang Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhu-Liang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, P. R. China
| | - Wei-Nan Xu
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Bao-Gui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Hong-Wei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Shun-Xing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
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161
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Li H, Feng X, Chu C. The design and construction of reference pangenome graphs with minigraph. Genome Biol 2020; 21:265. [PMID: 33066802 PMCID: PMC7568353 DOI: 10.1186/s13059-020-02168-z] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/23/2020] [Indexed: 12/21/2022] Open
Abstract
The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the integrated representation accessible to biologists remains an open challenge. Here, we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implement our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.
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Affiliation(s)
- Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02215, MA, USA.
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02215, MA, USA
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02215, MA, USA
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162
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Zhong C, Wang L, Ning K. Pan-genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption. Environ Microbiol 2020; 23:3599-3613. [PMID: 32939951 DOI: 10.1111/1462-2920.15234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/12/2020] [Indexed: 01/02/2023]
Abstract
Thermococcales has a strong adaptability to extreme environments, which is of profound interest in explaining how complex life forms emerge on earth. However, their gene composition, thermal stability and evolution in hyperthermal environments are still little known. Here, we characterized the pan-genome architecture of 30 Thermococcales species to gain insight into their genetic properties, evolutionary patterns and specific metabolisms adapted to niches. We revealed an open pan-genome of Thermococcales comprising 6070 gene families that tend to increase with the availability of additional genomes. The genome contents of Thermococcales were flexible, with a series of genes experienced gene duplication, progressive divergence, or gene gain and loss events exhibiting distinct functional features. These archaea had concise types of heat shock proteins, such as HSP20, HSP60 and prefoldin, which were constrained by strong purifying selection that governed their conservative evolution. Furthermore, purifying selection forced genes involved in enzyme, motility, secretion system, defence system and chaperones to differ in functional constraints and their disparity in the rate of evolution may be related to adaptation to specific niche. These results deepened our understanding of genetic diversity and adaptation patterns of Thermococcales, and provided valuable research models for studying the metabolic traits of early life forms.
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Affiliation(s)
- Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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163
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Hu Y, Xia H, Li M, Xu C, Ye X, Su R, Zhang M, Nash O, Sonstegard TS, Yang L, Liu GE, Zhou Y. Comparative analyses of copy number variations between Bos taurus and Bos indicus. BMC Genomics 2020; 21:682. [PMID: 33004001 PMCID: PMC7528262 DOI: 10.1186/s12864-020-07097-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. RESULTS Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. CONCLUSIONS This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.
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Affiliation(s)
- Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxun Li
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Chang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaowei Ye
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruixue Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
| | | | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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164
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Correia K, Mahadevan R. Pan‐Genome‐Scale Network Reconstruction: Harnessing Phylogenomics Increases the Quantity and Quality of Metabolic Models. Biotechnol J 2020; 15:e1900519. [DOI: 10.1002/biot.201900519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 07/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Kevin Correia
- Department of Chemical Engineering and Applied Chemistry University of Toronto 200 College Street Toronto Ontario M5S 3E5 Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry University of Toronto 200 College Street Toronto Ontario M5S 3E5 Canada
- Institute of Biomedical Engineering University of Toronto 164 College Street Toronto Ontario M5S 3G9 Canada
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165
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Bonnici V, Maresi E, Giugno R. Challenges in gene-oriented approaches for pangenome content discovery. Brief Bioinform 2020; 22:5901976. [PMID: 32893299 DOI: 10.1093/bib/bbaa198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/14/2020] [Accepted: 08/04/2020] [Indexed: 01/17/2023] Open
Abstract
Given a group of genomes, represented as the sets of genes that belong to them, the discovery of the pangenomic content is based on the search of genetic homology among the genes for clustering them into families. Thus, pangenomic analyses investigate the membership of the families to the given genomes. This approach is referred to as the gene-oriented approach in contrast to other definitions of the problem that takes into account different genomic features. In the past years, several tools have been developed to discover and analyse pangenomic contents. Because of the hardness of the problem, each tool applies a different strategy for discovering the pangenomic content. This results in a differentiation of the performance of each tool that depends on the composition of the input genomes. This review reports the main analysis instruments provided by the current state of the art tools for the discovery of pangenomic contents. Moreover, unlike previous works, the presented study compares pangenomic tools from a methodological perspective, analysing the causes that lead a given methodology to outperform other tools. The analysis is performed by taking into account different bacterial populations, which are synthetically generated by changing evolutionary parameters. The benchmarks used to compare the pangenomic tools, in addition to the computational pipeline developed for this purpose, are available at https://github.com/InfOmics/pangenes-review. Contact: V. Bonnici, R. Giugno Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
| | - Emiliano Maresi
- The Microsoft Research, University of Trento Centre for Computational and Systems Biology
| | - Rosalba Giugno
- Computer Science and Bioinformatics, referent of the Master Degree in Medical Bioinformatics
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166
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King J, Harder T, Beer M, Pohlmann A. Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses. BMC Infect Dis 2020; 20:648. [PMID: 32883215 PMCID: PMC7468549 DOI: 10.1186/s12879-020-05367-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Due to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, the MinION sequencing device (Oxford Nanopore Technologies) has become a serious competitor for routine whole-genome sequencing. Here, we established a novel, rapid and high-throughput MinION multiplexing workflow based on a universal RT-PCR. METHODS Twelve representative influenza A virus samples of multiple subtypes were universally amplified in a one-step RT-PCR and subsequently sequenced on the MinION instrument in conjunction with a barcoding library preparation kit from the rapid family and the MinIT performing live base-calling. The identical PCR products were sequenced on an IonTorrent platform and, after final consensus assembly, all data was compared for validation. To prove the practicability of the MinION-MinIT method in human and veterinary diagnostics, we sequenced recent and historical influenza strains for further benchmarking. RESULTS The MinION-MinIT combination generated over two million reads for twelve samples in a six-hour sequencing run, from which a total of 72% classified as quality screened, trimmed and mapped influenza reads to produce full genome sequences. Identities between the datasets of > 99.9% were achieved, with 100% coverage of all segments alongside a sufficient confidence and 4492fold mean depth. From RNA extraction to finished sequences, only 14 h were required. CONCLUSIONS Overall, we developed and validated a novel and rapid multiplex workflow for influenza A virus sequencing. This protocol suits both clinical and academic settings, aiding in real time diagnostics and passive surveillance.
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Affiliation(s)
- Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany.
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167
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Verma DK, Vasudeva G, Sidhu C, Pinnaka AK, Prasad SE, Thakur KG. Biochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate. Front Microbiol 2020; 11:2082. [PMID: 32983058 PMCID: PMC7490331 DOI: 10.3389/fmicb.2020.02082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Abstract
Haloarchaea are salt-loving archaea and potential source of industrially relevant halotolerant enzymes. In the present study, three reddish-pink, extremely halophilic archaeal strains, namely wsp1 (wsp-water sample Pondicherry), wsp3, and wsp4, were isolated from the Indian Solar saltern. The phylogenetic analysis based on 16S rRNA gene sequences suggests that both wsp3 and wsp4 strains belong to Halogeometricum borinquense while wsp1 is closely related to Haloferax volcanii species. The comparative genomics revealed an open pangenome for both genera investigated here. Whole-genome sequence analysis revealed that these isolates have multiple copies of industrially/biotechnologically important unique genes and enzymes. Among these unique enzymes, for recombinant expression and purification, we selected four putative α-amylases identified in these three isolates. We successfully purified functional halotolerant recombinant Amy2, from wsp1 using pelB signal sequence-based secretion strategy using Escherichia coli as an expression host. This method may prove useful to produce functional haloarchaeal secretory recombinant proteins suitable for commercial or research applications. Biochemical analysis of Amy2 suggests the halotolerant nature of the enzyme having maximum enzymatic activity observed at 1 M NaCl. We also report the isolation and characterization of carotenoids purified from these isolates. This study highlights the presence of several industrially important enzymes in the haloarchaeal strains which may potentially have improved features like stability and salt tolerance suitable for industrial applications.
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Affiliation(s)
- Dipesh Kumar Verma
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Gunjan Vasudeva
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Chandni Sidhu
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anil K Pinnaka
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Senthil E Prasad
- Biochemical Engineering Research and Process Development Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- G. N. Ramachandran Protein Centre, Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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168
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Li Z, Simianer H. Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction. PLoS Genet 2020; 16:e1008995. [PMID: 32833967 PMCID: PMC7470747 DOI: 10.1371/journal.pgen.1008995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 09/03/2020] [Accepted: 07/15/2020] [Indexed: 11/19/2022] Open
Abstract
Pan-genomic open reading frames (ORFs) potentially carry protein-coding gene or coding variant information in a population. In this study, we suggest that pan-genomic ORFs are promising to be utilized in estimation of heritability and genomic prediction. A Saccharomyces cerevisiae dataset with whole-genome SNPs, pan-genomic ORFs, and the copy numbers of those ORFs is used to test the effectiveness of ORF data as a predictor in three prediction models for 35 traits. Our results show that the ORF-based heritability can capture more genetic effects than SNP-based heritability for all traits. Compared to SNP-based genomic prediction (GBLUP), pan-genomic ORF-based genomic prediction (OBLUP) is distinctly more accurate for all traits, and the predictive abilities on average are more than doubled across all traits. For four traits, the copy number of ORF-based prediction(CBLUP) is more accurate than OBLUP. When using different numbers of isolates in training sets in ORF-based prediction, the predictive abilities for all traits increased as more isolates are added in the training sets, suggesting that with very large training sets the prediction accuracy will be in the range of the square root of the heritability. We conclude that pan-genomic ORFs have the potential to be a supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction.
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Affiliation(s)
- Zhengcao Li
- Animal Breeding and Genetics Group, Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- * E-mail:
| | - Henner Simianer
- Animal Breeding and Genetics Group, Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
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169
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Zhou L, Zhang T, Tang S, Fu X, Yu S. Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol. Antonie van Leeuwenhoek 2020; 113:1539-1558. [PMID: 32816227 DOI: 10.1007/s10482-020-01461-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
Abstract
Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.
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Affiliation(s)
- Liangliang Zhou
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Ting Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural university, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Shan Tang
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Xueqin Fu
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, Jiangxi, People's Republic of China
| | - Shuijing Yu
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China.
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170
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Kumar R, Bröms JE, Sjöstedt A. Exploring the Diversity Within the Genus Francisella - An Integrated Pan-Genome and Genome-Mining Approach. Front Microbiol 2020; 11:1928. [PMID: 32849479 PMCID: PMC7431613 DOI: 10.3389/fmicb.2020.01928] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/22/2020] [Indexed: 01/13/2023] Open
Abstract
Pan-genome analysis is a powerful method to explore genomic heterogeneity and diversity of bacterial species. Here we present a pan-genome analysis of the genus Francisella, comprising a dataset of 63 genomes and encompassing clinical as well as environmental isolates from distinct geographic locations. To determine the evolutionary relationship within the genus, we performed phylogenetic whole-genome studies utilizing the average nucleotide identity, average amino acid identity, core genes and non-recombinant loci markers. Based on the analyses, the phylogenetic trees obtained identified two distinct clades, A and B and a diverse cluster designated C. The sizes of the pan-, core-, cloud-, and shell-genomes of Francisella were estimated and compared to those of two other facultative intracellular pathogens, Legionella and Piscirickettsia. Francisella had the smallest core-genome, 692 genes, compared to 886 and 1,732 genes for Legionella and Piscirickettsia respectively, while the pan-genome of Legionella was more than twice the size of that of the other two genera. Also, the composition of the Francisella Type VI secretion system (T6SS) was analyzed. Distinct differences in the gene content of the T6SS were identified. In silico approaches performed to identify putative substrates of these systems revealed potential effectors targeting the cell wall, inner membrane, cellular nucleic acids as well as proteins, thus constituting attractive targets for site-directed mutagenesis. The comparative analysis performed here provides a comprehensive basis for the assessment of the phylogenomic relationship of members of the genus Francisella and for the identification of putative T6SS virulence traits.
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Affiliation(s)
- Rajender Kumar
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jeanette E Bröms
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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Abstract
Many biological contaminants are disseminated through water, and their occurrence has potential detrimental impacts on public and environmental health. Conventional monitoring tools rely on cultivation and are not robust in addressing modern water quality concerns. This review proposes metagenomics as a means to provide a rapid, nontargeted assessment of biological contaminants in water. When further coupled with appropriate methods (e.g., quantitative PCR and flow cytometry) and bioinformatic tools, metagenomics can provide information concerning both the abundance and diversity of biological contaminants in reclaimed waters. Further correlation between the metagenomic-derived data of selected contaminants and the measurable parameters of water quality can also aid in devising strategies to alleviate undesirable water quality. Here, we review metagenomic approaches (i.e., both sequencing platforms and bioinformatic tools) and studies that demonstrated their use for reclaimed-water quality monitoring. We also provide recommendations on areas of improvement that will allow metagenomics to significantly impact how the water industry performs reclaimed-water quality monitoring in the future.
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Affiliation(s)
- Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David Mantilla-Calderon
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Changzhi Wang
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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172
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Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis. DIVERSITY 2020. [DOI: 10.3390/d12080289] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.
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173
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Abstract
The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.
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174
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Fei X, Li Q, Olsen JE, Jiao X. A bioinformatic approach to identify core genome difference between Salmonella Pullorum and Salmonella Enteritidis. INFECTION GENETICS AND EVOLUTION 2020; 85:104446. [PMID: 32622081 DOI: 10.1016/j.meegid.2020.104446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/15/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
S. Pullorum and S. Enteritidis are closely related in genetic terms, but they show very different pathogenicity and host range. S. Enteritidis infects many different hosts, usually causing acute gastroenteritis, while S. Pullorum is restricted to avian, where it causes systemic disease in young animals. The reason why they differ in host range and pathogenicity is unknown. The core-genome denotes those genes that are present in all strains within a clade, and in the present work, an automated bioinformatics workflow was developed and applied to identify core-genome differences between these two serovars with the aim to identify genome features associated with host specificity of S. Pullorum. Results showed that S. Pullorum unique coding sequences (CDS) were mainly concentrated in three regions not present in S. Enteritidis, suggesting that such CDS were taken up probably during the separation of the two types from their common ancestor. One of the unique regions encoded Pathogenicity Islands 19 (SPI-19), which encodes a type VI secretion system (T6SS). Single-nucleotide polymorphism (SNP) analysis identified 1791 conserved SNPs in coding sequences between the two serovars, including several SNPs located in a type IV secretion system (T4SS). Analyzing of 100 bp regions upstream of coding sequences identified 443 conserved SNPs between the two serovars, including SNP variations in type III secretion system effector (T3SE). In conclusion, this analysis has identified genetic features encoding putative factors controlling host-specificity in S. Pullorum. The novel bioinformatic workflow and associated scripts can directly be applied to other bacteria to uncover the genome difference between clades.
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Affiliation(s)
- Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China; Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
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175
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Guillier L, Gourmelon M, Lozach S, Cadel-Six S, Vignaud ML, Munck N, Hald T, Palma F. AB_SA: Accessory genes-Based Source Attribution - tracing the source of Salmonella enterica Typhimurium environmental strains. Microb Genom 2020; 6:mgen000366. [PMID: 32320376 PMCID: PMC7478624 DOI: 10.1099/mgen.0.000366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/20/2020] [Indexed: 12/31/2022] Open
Abstract
The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on 'source-enriched' loci extracted from the accessory-genome profiles of a pangenomic dataset. Depending on the accuracy of the model's self-attribution step, the modeller selects the number of candidate accessory genes that best fit the model for calculating the likelihood of (source) category membership. The Accessory genes-Based Source Attribution (AB_SA) method was applied to a dataset of strains of Salmonella enterica Typhimurium and its monophasic variant (S. enterica 1,4,[5],12:i:-). The model was trained on 69 strains with known animal-source categories (i.e. poultry, ruminant and pig). The AB_SA method helped to identify 8 genes as predictors among the 2802 accessory genes. The self-attribution accuracy was 80 %. The AB_SA model was then able to classify 25 of the 29 S. enterica Typhimurium and S. enterica 1,4,[5],12:i:- isolates collected from the environment (considered to be of unknown source) into a specific category (i.e. animal source), with more than 85 % of probability. The AB_SA method herein described provides a user-friendly and valuable tool for performing source-attribution studies in only a few steps. AB_SA is written in R and freely available at https://github.com/lguillier/AB_SA.
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Affiliation(s)
- Laurent Guillier
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
- Risk Assessment Department, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Michèle Gourmelon
- RBE–SGMM, Health, Environment and Microbiology Laboratory, IFREMER, Plouzané, France
| | - Solen Lozach
- RBE–SGMM, Health, Environment and Microbiology Laboratory, IFREMER, Plouzané, France
| | - Sabrina Cadel-Six
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Marie-Léone Vignaud
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
| | - Nanna Munck
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Tine Hald
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Federica Palma
- Laboratory for Food Safety, ANSES, University of Paris-EST, Maisons-Alfort, France
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176
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Abstract
Motivation Bacterial metagenomics profiling for metagenomic whole sequencing (mWGS) usually starts by aligning sequencing reads to a collection of reference genomes. Current profiling tools are designed to work against a small representative collection of genomes, and do not scale very well to larger reference genome collections. However, large reference genome collections are capable of providing a more complete and accurate profile of the bacterial population in a metagenomics dataset. In this paper, we discuss a scalable, efficient and affordable approach to this problem, bringing big data solutions within the reach of laboratories with modest resources. Results We developed Flint, a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark’s built-in parallelism and streaming engine architecture to quickly map reads against a large (170 GB) reference collection of 43 552 bacterial genomes from Ensembl. Flint runs on Amazon’s Elastic MapReduce service, and is able to profile 1 million Illumina paired-end reads against over 40 K genomes on 64 machines in 67 s—an order of magnitude faster than the state of the art, while using a much larger reference collection. Streaming the sequencing reads allows this approach to sustain mapping rates of 55 million reads per hour, at an hourly cluster cost of $8.00 USD, while avoiding the necessity of storing large quantities of intermediate alignments. Availability and implementation Flint is open source software, available under the MIT License (MIT). Source code is available at https://github.com/camilo-v/flint. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Camilo Valdes
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Vitalii Stebliankin
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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177
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Yan F, Gao F. A systematic strategy for the investigation of vaccines and drugs targeting bacteria. Comput Struct Biotechnol J 2020; 18:1525-1538. [PMID: 32637049 PMCID: PMC7327267 DOI: 10.1016/j.csbj.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Infectious and epidemic diseases induced by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide. At present, many researchers are working on the discovery of viable drug and vaccine targets for bacteria through multiple methods, including the analyses of comparative subtractive genome, core genome, replication-related proteins, transcriptomics and riboswitches, which plays a significant part in the treatment of infectious and pandemic diseases. The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis. Meanwhile, molecular dynamics (MD) analysis of the constructed drug/epitope-protein complexes is an important standard for testing the suitability of these screened drugs and vaccines. Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria. We hope that this comprehensive strategy will help in the design of high-performance vaccines and drugs.
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Affiliation(s)
- Fangfang Yan
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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178
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König P, Beier S, Basterrechea M, Schüler D, Arend D, Mascher M, Stein N, Scholz U, Lange M. BRIDGE - A Visual Analytics Web Tool for Barley Genebank Genomics. FRONTIERS IN PLANT SCIENCE 2020; 11:701. [PMID: 32595658 PMCID: PMC7300248 DOI: 10.3389/fpls.2020.00701] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/04/2020] [Indexed: 05/05/2023]
Abstract
Genebanks harbor a large treasure trove of untapped plant genetic diversity. A growing world population and a changing climate require an increase in the production and development of stress resistant plant cultivars while decreasing the acreage. These requirements for improved plant cultivars can be supported by the broader exploitation of plant genetic resources (PGR) as inputs for genomics-assisted breeding. To support this process we have developed BRIDGE, a data warehouse and exploratory data analysis tool for genebank genomics of barley (Hordeum vulgare L.). Using efficient technologies for data storage, data transfer and web development, we facilitate access to digital genebank resources of barley by prioritizing the interactive and visual analysis of integrated genotypic and phenotypic data. The underlying data resulted from a barley genebank genomics study cataloging sequence and morphological data of 22,626 barley accessions, mainly from the German Federal ex situ genebank. BRIDGE consists of interactively coupled modules to visualize integrated, curated and quality checked data, such as variation data, results of dimensionality reduction and genome wide association studies (GWAS), phenotyping results, passport data as well as the geographic distribution of germplasm samples. The core component is a manager for custom collections of germplasm. A search module to find and select germplasm by passport and phenotypic attributes is included as well as modules to export genotypic data in gzip-compressed variant call format (VCF) files and phenotypic data in MIAPPE-compliant ISA-Tab files. BRIDGE is accessible at the following URL: https://bridge.ipk-gatersleben.de.
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Affiliation(s)
- Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Basterrechea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research, Georg-August University, Göttingen, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
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179
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Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E. Pangenome Graphs. Annu Rev Genomics Hum Genet 2020; 21:139-162. [PMID: 32453966 DOI: 10.1146/annurev-genom-120219-080406] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes. These approaches often use graphical models of the pangenome to support algorithms for sequence alignment, visualization, functional genomics, and association studies. The additional information provided to these methods by the pangenome allows them to achieve superior performance on a variety of bioinformatic tasks, including read alignment, variant calling, and genotyping. Pangenome graphs stand to become a ubiquitous tool in genomics. Although it is unclear whether they will replace linearreference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.
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Affiliation(s)
- Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Adam M Novak
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Jonas A Sibbesen
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Simon Heumos
- Quantitative Biology Center, University of Tübingen, 72076 Tübingen, Germany
| | - Ali Ghaffaari
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Saarbrücken Graduate School for Computer Science, Saarland University, 66123 Saarbrücken, Germany
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Xian Chang
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Josiah D Seaman
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom.,School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Robin Rounthwaite
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Jana Ebler
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Saarbrücken Graduate School for Computer Science, Saarland University, 66123 Saarbrücken, Germany
| | - Mikko Rautiainen
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Saarbrücken Graduate School for Computer Science, Saarland University, 66123 Saarbrücken, Germany
| | - Shilpa Garg
- Departments of Genetics and Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Jouni Sirén
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Erik Garrison
- Genomics Institute, University of California, Santa Cruz, California 95064, USA;
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180
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Gonzales-Siles L, Karlsson R, Schmidt P, Salvà-Serra F, Jaén-Luchoro D, Skovbjerg S, Moore ERB, Gomila M. A Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Front Cell Infect Microbiol 2020; 10:222. [PMID: 32509595 PMCID: PMC7248185 DOI: 10.3389/fcimb.2020.00222] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/22/2020] [Indexed: 01/28/2023] Open
Abstract
Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the “Xisco” gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the S. pneumoniae gene markers and for three of the S. pseudopneumoniae gene markers. Application of multiple species-level unique biomarkers of S. pneumoniae and S. pseudopneumoniae, is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.
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Affiliation(s)
- Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Patrik Schmidt
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Biology-Microbiology, Universitat de les Illes Balears, Palma, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Margarita Gomila
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma, Spain
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181
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Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. THE ISME JOURNAL 2020; 14:1247-1259. [PMID: 32047279 PMCID: PMC7174425 DOI: 10.1038/s41396-020-0600-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/04/2022]
Abstract
Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.
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Affiliation(s)
- Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Daniel R Mende
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Mechthild Luetge
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Institute of Immunobiology, Kantonsspital St. Gallen, 9007, St. Gallen, Switzerland
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Simone S Li
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - João F Matias Rodrigues
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, CH-8057, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, CH-8057, Zurich, Switzerland
| | - Luis Pedro Coelho
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Jaime Huerta-Cepas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Department of Biology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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182
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Li J, Gu T, Li L, Wu X, Shen L, Yu R, Liu Y, Qiu G, Zeng W. Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium. BMC Microbiol 2020; 20:106. [PMID: 32354325 PMCID: PMC7193398 DOI: 10.1186/s12866-020-01737-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. RESULTS Here, we identified a 5,436,472 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated. CONCLUSIONS The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.
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Affiliation(s)
- Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Tianyuan Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China.
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183
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Moulana A, Anderson RE, Fortunato CS, Huber JA. Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents. mSystems 2020; 5:e00673-19. [PMID: 32291353 PMCID: PMC7159903 DOI: 10.1128/msystems.00673-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.IMPORTANCE Microbes can alter their gene content through the gain and loss of genes. However, there is some debate as to whether natural selection or neutral processes play a stronger role in molding the gene content of microbial genomes. In this study, we examined variation in gene content for the Epsilonbacteraeota genus Sulfurovum from deep-sea hydrothermal vents, which are dynamic habitats known for extensive horizontal gene transfer within microbial populations. Our results show that natural selection is a strong driver of Sulfurovum gene content and that nutrient limitation in particular has shaped the Sulfurovum genome, leading to differences in gene content between ocean basins. Our results also suggest that recently acquired genes undergo stronger selection than genes that were acquired in the more distant past. Overall, our results highlight the importance of natural selection in driving the evolution of microbial populations in these dynamic habitats.
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Affiliation(s)
- Alief Moulana
- Biology Department, Carleton College, Northfield, Minnesota, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, Minnesota, USA
| | | | - Julie A Huber
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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184
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Van Poelvoorde LA, Saelens X, Thomas I, Roosens NH. Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza. Trends Biotechnol 2020; 38:360-367. [DOI: 10.1016/j.tibtech.2019.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022]
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185
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Ismail S, Ahmad S, Azam SS. Vaccinomics to design a novel single chimeric subunit vaccine for broad-spectrum immunological applications targeting nosocomial Enterobacteriaceae pathogens. Eur J Pharm Sci 2020; 146:105258. [DOI: 10.1016/j.ejps.2020.105258] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 12/21/2022]
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186
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Hurtado R, Maturrano L, Azevedo V, Aburjaile F. Pathogenomics insights for understanding Pasteurella multocida adaptation. Int J Med Microbiol 2020; 310:151417. [PMID: 32276876 DOI: 10.1016/j.ijmm.2020.151417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/01/2020] [Accepted: 03/19/2020] [Indexed: 12/16/2022] Open
Abstract
Pasteurella multocida is an important veterinary pathogen able to infect a wide range of animals in a broad spectrum of diseases. P. multocida is a complex microorganism in relation to its genomic flexibility, host adaptation and pathogenesis. Epidemiological analysis based on multilocus sequence typing, serotyping, genotyping, association with virulence genes and single nucleotide polymorphisms (SNPs), enables assessment of intraspecies diversity, phylogenetic and strain-specific relationships associated with host predilection or disease. A high number of sequenced genomes provides us a more accurate genomic and epidemiological interpretation to determine whether certain lineages can infect a host or produce disease. Comparative genomic analysis and pan-genomic approaches have revealed a flexible genome for hosting mobile genetic elements (MGEs) and therefore significant variation in gene content. Moreover, it was possible to find lineage-specific MGEs from the same niche, showing acquisition probably due to an evolutionary convergence event or to a genetic group with infective capacity. Furthermore, diversification selection analysis exhibits proteins exposed on the surface subject to selection pressures with an interstrain heterogeneity related to their ability to adapt. This article is the first review describing the genomic relationship to elucidate the diversity and evolution of P. multocida.
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Affiliation(s)
- Raquel Hurtado
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil; Laboratory of Molecular Biology and Genetics, Veterinary Medicine Faculty, San Marcos University, Lima, Peru
| | - Lenin Maturrano
- Laboratory of Molecular Biology and Genetics, Veterinary Medicine Faculty, San Marcos University, Lima, Peru
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil; Laboratory of Plant Genetics and Biotechnology, Federal University of Pernambuco, Recife, 50670-901, Pernambuco, Brazil.
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187
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Castro J, Jefferson KK, Cerca N. Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species. Trends Microbiol 2020; 28:202-211. [DOI: 10.1016/j.tim.2019.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/27/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022]
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188
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Choi JY, Kim SC, Lee PC. Comparative Genome Analysis of Psychrobacillus Strain PB01, Isolated from an Iceberg. J Microbiol Biotechnol 2020; 30:237-243. [PMID: 31838800 PMCID: PMC9728334 DOI: 10.4014/jmb.1909.09008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel psychrotolerant Psychrobacillus strain PB01, isolated from an Antarctic iceberg, was comparatively analyzed with five related strains. The complete genome of strain PB01 consists of a single circular chromosome (4.3 Mb) and a plasmid (19 Kb). As potential low-temperature adaptation strategies, strain PB01 has four genes encoding cold-shock proteins, two genes encoding DEAD-box RNA helicases, and eight genes encoding transporters for glycine betaine, which can serve as a cryoprotectant, on the genome. The pan-genome structure of the six Psychrobacillus strains suggests that strain PB01 might have evolved to adapt to extreme environments by changing its genome content to gain higher capacity for DNA repair, translation, and membrane transport. Notably, strain PB01 possesses a complete TCA cycle consisting of eight enzymes as well as three additional Helicobacter pylori-type enzymes: ferredoxin-dependent 2-oxoglutarate synthase, succinyl-CoA/acetoacetyl-CoA transferase, and malate/quinone oxidoreductase. The co-existence of the genes for TCA cycle enzymes has also been identified in the other five Psychrobacillus strains.
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Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea,Corresponding author Phone: +82-31-219-2461 Fax: +82-31-219-1610 E-mail:
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189
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Wu H, Wang D, Gao F. Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains. Brief Bioinform 2020; 22:1951-1971. [PMID: 32065216 DOI: 10.1093/bib/bbaa013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 02/05/2023] Open
Abstract
Pan-genome analysis is widely used to study the evolution and genetic diversity of species, particularly in bacteria. However, the impact of strain selection on the outcome of pan-genome analysis is poorly understood. Furthermore, a standard protocol to ensure high-quality pan-genome results is lacking. In this study, we carried out a series of pan-genome analyses of different strain sets of Bacillus subtilis to understand the impact of various strains on the performance and output quality of pan-genome analyses. Consequently, we found that the results obtained by pan-genome analyses of B. subtilis can be influenced by the inclusion of incorrectly classified Bacillus subspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains. Since the presence of these confounding strains can seriously affect the quality and true landscape of the pan-genome, we should remove these deviations in the process of pan-genome analyses. Our study provides new insights into the removal of biases from confounding strains in pan-genome analyses at the beginning of data processing, which enables the achievement of a closer representation of a high-quality pan-genome landscape of B. subtilis that better reflects the performance and credibility of the B. subtilis pan-genome. This procedure could be added as an important quality control step in pan-genome analyses for improving the efficiency of analyses, and ultimately contributing to a better understanding of genome function, evolution and genome-reduction strategies for B. subtilis in the future.
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Affiliation(s)
- Hao Wu
- Department of Physics, School of Science, Tianjin University
| | - Dan Wang
- Department of Physics, School of Science, Tianjin University
| | - Feng Gao
- Department of Physics, School of Science, and the Frontier Science Center of Synthetic Biology (MOE), Key Laboratory of Systems Bioengineering (MOE), Tianjin University
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190
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Ferrés I, Fresia P, Iraola G. simurg: simulate bacterial pangenomes in R. Bioinformatics 2020; 36:1273-1274. [PMID: 31584605 DOI: 10.1093/bioinformatics/btz735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/06/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models. RESULTS We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses. AVAILABILITY AND IMPLEMENTATION The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https://github.com/iferres/simurg). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ignacio Ferrés
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Uruguay
| | - Pablo Fresia
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Uruguay.,Unidad Mixta UMPI, Institut Pasteur Montevideo + INIA, Montevideo 11400, Uruguay
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Uruguay.,Center for Integrative Biology, Universidad Mayor, Santiago de Chile 7510041, Chile.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK
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191
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Wyatt NA, Richards JK, Brueggeman RS, Friesen TL. A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:173-188. [PMID: 31502507 DOI: 10.1094/mpmi-05-19-0128-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison, resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes, examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions, consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in subtelomeric regions of chromosomes, with 10 of the 14 accessory region QTL localizing to subtelomeric regions. Comparative analysis of the subtelomeric regions of P. teres f. teres chromosomes revealed translocation events in which homology was detected between nonhomologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the subtelomeric accessory genomic compartments not only harbor most of the known virulence loci but, also, that these regions have the capacity to rapidly evolve.
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Affiliation(s)
- Nathan A Wyatt
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, U.S.A
| | - Robert S Brueggeman
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University
| | - Timothy L Friesen
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, Fargo, ND, U.S.A
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192
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Abstract
AcCNET (Accessory genome Constellation Network) is a Perl application to determine the variation of content in any genomic unit (e.g., bacterial genomes, plasmids, and transposons) within large datasets. It provides functional information that can be handled and visualized interactively as a bipartite network. In this chapter, we explain how to perform a statistical analysis of AcCNET data.
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Affiliation(s)
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Research Institute (IRYCIS), Madrid, Spain
- CIBER in Epidemiology and Public Health, (CIBERESP), Madrid, Spain
| | - Val F Lanza
- Bioinformatics Unit, Ramón y Cajal Universitary Hospital (IRYCIS), Madrid, Spain.
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193
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Golicz AA, Bayer PE, Bhalla PL, Batley J, Edwards D. Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications. Trends Genet 2019; 36:132-145. [PMID: 31882191 DOI: 10.1016/j.tig.2019.11.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 02/01/2023]
Abstract
The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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194
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Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence. Sci Rep 2019; 9:19167. [PMID: 31844108 PMCID: PMC6915712 DOI: 10.1038/s41598-019-55795-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022] Open
Abstract
Bacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA–DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA–DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.
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195
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Pan-Genomic Analysis of African Swine Fever Virus. Virol Sin 2019; 35:662-665. [PMID: 31828586 PMCID: PMC7736430 DOI: 10.1007/s12250-019-00173-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
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196
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Akarsu H, Aguilar-Bultet L, Falquet L. deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes. BMC Bioinformatics 2019; 20:621. [PMID: 31791245 PMCID: PMC6889214 DOI: 10.1186/s12859-019-3234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 11/14/2019] [Indexed: 11/25/2022] Open
Abstract
Background Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content analysis of genomes at different phylogenetic levels (isolates, species). These tools rely on de novo assembly and/or multiple alignments that can be computationally intensive for large datasets. With a large number of similar genomes in particular, e.g., in surveillance and outbreak detection, assembling each genome can become a redundant and expensive step in the identification of genes potentially involved in a given clinical feature. Results We have developed deltaRpkm, an R package that performs a rapid differential gene presence evaluation between two large groups of closely related genomes. Starting from a standard gene count table, deltaRpkm computes the RPKM per gene per sample, then the inter-group δRPKM values, the corresponding median δRPKM (m) for each gene and the global standard deviation value of m (sm). Genes with m > = 2 ∗ sm (standard deviation s of all the m values) are considered as “differentially present” in the reference genome group. Our simple yet effective method of differential RPKM has been successfully applied in a recent study published by our group (N = 225 genomes of Listeria monocytogenes) (Aguilar-Bultet et al. Front Cell Infect Microbiol 8:20, 2018). Conclusions To our knowledge, deltaRpkm is the first tool to propose a straightforward inter-group differential gene presence analysis with large datasets of related genomes, including non-coding genes, and to output directly a list of genes potentially involved in a phenotype.
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Affiliation(s)
- Hatice Akarsu
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, BUGFri group, Fribourg, Switzerland
| | - Lisandra Aguilar-Bultet
- Swiss Institute of Bioinformatics, BUGFri group, Fribourg, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Currently at the Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland. .,Swiss Institute of Bioinformatics, BUGFri group, Fribourg, Switzerland.
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197
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Pot B, Salvetti E, Mattarelli P, Felis GE. The potential impact of the Lactobacillus name change: The results of an expert meeting organised by the Lactic Acid Bacteria Industrial Platform (LABIP). Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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198
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Mohapatra B, Kazy SK, Sar P. Comparative genome analysis of arsenic reducing, hydrocarbon metabolizing groundwater bacterium Achromobacter sp. KAs 3-5T explains its competitive edge for survival in aquifer environment. Genomics 2019; 111:1604-1619. [DOI: 10.1016/j.ygeno.2018.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/25/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022]
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199
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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200
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Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation. Food Microbiol 2019; 86:103341. [PMID: 31703875 DOI: 10.1016/j.fm.2019.103341] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/08/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022]
Abstract
The genomic and metabolic features of Lactobacillus sakei were investigated using its pan-genome and by analyzing the metatranscriptome of kimchi fermentation. In the genome-based relatedness analysis, the strains were divided into the Lb. sakei ssp. sakei and Lb. sakei ssp. carnosus lineage groups. Genomic and metabolic pathway analysis revealed that all Lb. sakei strains have the capability of producing d/l-lactate, ethanol, acetate, CO2, formate, l-malate, diacetyl, acetoin, and 2,3-butanediol from d-glucose, d-fructose, d-galactose, sucrose, d-lactose, l-arabinose, cellobiose, d-mannose, d-gluconate, and d-ribose through homolactic and heterolactic fermentation, whereas their capability of d-maltose, d-xylose, l-xylulose, d-galacturonate, and d-glucuronate metabolism is strain-specific. All strains carry genes for the biosynthesis of folate and thiamine, whereas genes for biogenic amine and toxin production, hemolysis, and antibiotic resistance were not identified. The metatranscriptomic analysis showed that the expression of Lb. sakei transcripts involved in carbohydrate metabolism increased as kimchi fermentation progressed, suggesting that Lb. sakei is more competitive during late fermentation stage. Homolactic fermentation pathway was highly expressed and generally constant during kimchi fermentation, whereas expression of heterolactic fermentation pathway increased gradually as fermentation progressed. l-Lactate dehydrogenase was more highly expressed than d-lactate dehydrogenase, suggesting that l-lactate is the major lactate metabolized by Lb. sakei.
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