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Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism. Curr Biol 2015; 26:161-172. [PMID: 26725202 PMCID: PMC4728078 DOI: 10.1016/j.cub.2015.11.055] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 01/01/2023]
Abstract
The evolution of parasitism is a recurrent event in the history of life and a core problem in evolutionary biology. Trypanosomatids are important parasites and include the human pathogens Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp., which in humans cause African trypanosomiasis, Chagas disease, and leishmaniasis, respectively. Genome comparison between trypanosomatids reveals that these parasites have evolved specialized cell-surface protein families, overlaid on a well-conserved cell template. Understanding how these features evolved and which ones are specifically associated with parasitism requires comparison with related non-parasites. We have produced genome sequences for Bodo saltans, the closest known non-parasitic relative of trypanosomatids, and a second bodonid, Trypanoplasma borreli. Here we show how genomic reduction and innovation contributed to the character of trypanosomatid genomes. We show that gene loss has “streamlined” trypanosomatid genomes, particularly with respect to macromolecular degradation and ion transport, but consistent with a widespread loss of functional redundancy, while adaptive radiations of gene families involved in membrane function provide the principal innovations in trypanosomatid evolution. Gene gain and loss continued during trypanosomatid diversification, resulting in the asymmetric assortment of ancestral characters such as peptidases between Trypanosoma and Leishmania, genomic differences that were subsequently amplified by lineage-specific innovations after divergence. Finally, we show how species-specific, cell-surface gene families (DGF-1 and PSA) with no apparent structural similarity are independent derivations of a common ancestral form, which we call “bodonin.” This new evidence defines the parasitic innovations of trypanosomatid genomes, revealing how a free-living phagotroph became adapted to exploiting hostile host environments. The Bodo saltans genome reveals evolutionary changes at the origin of parasitism Parasite genomes are streamlined, consistent with a loss of functional redundancy Expanded parasite transporter genes reflect a reorientation of membrane function Non-homologous, parasite cell-surface proteins evolved from a common ancestor
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Zhang YC, Zhang Y, Zhu BR, Zhang BW, Ni C, Zhang DY, Huang Y, Pang E, Lin K. Genome sequences of two closely related strains of Escherichia coli K-12 GM4792. Stand Genomic Sci 2015; 10:125. [PMID: 26664654 PMCID: PMC4675052 DOI: 10.1186/s40793-015-0114-x] [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: 06/05/2015] [Accepted: 11/09/2015] [Indexed: 11/15/2022] Open
Abstract
Escherichia coli lab strains K-12 GM4792 Lac+ and GM4792 Lac- carry opposite lactose markers, which are useful for distinguishing evolved lines as they produce different colored colonies. The two closely related strains are chosen as ancestors for our ongoing studies of experimental evolution. Here, we describe the genome sequences, annotation, and features of GM4792 Lac+ and GM4792 Lac-. GM4792 Lac+ has a 4,622,342-bp long chromosome with 4,061 protein-coding genes and 83 RNA genes. Similarly, the genome of GM4792 Lac- consists of a 4,621,656-bp chromosome containing 4,043 protein-coding genes and 74 RNA genes. Genome comparison analysis reveals that the differences between GM4792 Lac+ and GM4792 Lac- are minimal and limited to only the targeted lac region. Moreover, a previous study on competitive experimentation indicates the two strains are identical or nearly identical in survivability except for lactose utilization in a nitrogen-limited environment. Therefore, at both a genetic and a phenotypic level, GM4792 Lac+ and GM4792 Lac-, with opposite neutral markers, are ideal systems for future experimental evolution studies.
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Affiliation(s)
- Yan-Cong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Yan Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China ; Present address: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bi-Ru Zhu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Chuan Ni
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China ; Present address: The second high school attached to Beijing Normal University, Beijing, 100192 China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Ying Huang
- State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
| | - Erli Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Street, Beijing, 100875 China
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Valdivia HO, Reis-Cunha JL, Rodrigues-Luiz GF, Baptista RP, Baldeviano GC, Gerbasi RV, Dobson DE, Pratlong F, Bastien P, Lescano AG, Beverley SM, Bartholomeu DC. Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis. BMC Genomics 2015; 16:715. [PMID: 26384787 PMCID: PMC4575464 DOI: 10.1186/s12864-015-1928-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/09/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Leishmania (Viannia) braziliensis complex is responsible for most cases of New World tegumentary leishmaniasis. This complex includes two closely related species but with different geographic distribution and disease phenotypes, L. (V.) peruviana and L. (V.) braziliensis. However, the genetic basis of these differences is not well understood and the status of L. (V.) peruviana as distinct species has been questioned by some. Here we sequenced the genomes of two L. (V.) peruviana isolates (LEM1537 and PAB-4377) using Illumina high throughput sequencing and performed comparative analyses against the L. (V.) braziliensis M2904 reference genome. Comparisons were focused on the detection of Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs), aneuploidy and gene copy number variations. RESULTS We found 94,070 variants shared by both L. (V.) peruviana isolates (144,079 in PAB-4377 and 136,946 in LEM1537) against the L. (V.) braziliensis M2904 reference genome while only 26,853 variants separated both L. (V.) peruviana genomes. Analysis in coding sequences detected 26,750 SNPs and 1,513 indels shared by both L. (V.) peruviana isolates against L. (V.) braziliensis M2904 and revealed two L. (V.) braziliensis pseudogenes that are likely to have coding potential in L. (V.) peruviana. Chromosomal read density and allele frequency profiling showed a heterogeneous pattern of aneuploidy with an overall disomic tendency in both L. (V.) peruviana isolates, in contrast with a trisomic pattern in the L. (V.) braziliensis M2904 reference. Read depth analysis allowed us to detect more than 368 gene expansions and 14 expanded gene arrays in L. (V.) peruviana, and the likely absence of expanded amastin gene arrays. CONCLUSIONS The greater numbers of interspecific SNP/indel differences between L. (V.) peruviana and L. (V.) braziliensis and the presence of different gene and chromosome copy number variations support the classification of both organisms as closely related but distinct species. The extensive nucleotide polymorphisms and differences in gene and chromosome copy numbers in L. (V.) peruviana suggests the possibility that these may contribute to some of the unique features of its biology, including a lower pathology and lack of mucosal development.
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Affiliation(s)
- Hugo O Valdivia
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. .,Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru.
| | - João L Reis-Cunha
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Gabriela F Rodrigues-Luiz
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Rodrigo P Baptista
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Robert V Gerbasi
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru.
| | - Deborah E Dobson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
| | - Francine Pratlong
- Centre Hospitalier Universitaire de Montpellier, Departement de Parasitologie-Mycologie, Centre National de Reference des Leishmanioses, Montpellier, France.
| | - Patrick Bastien
- Centre Hospitalier Universitaire de Montpellier, Departement de Parasitologie-Mycologie, Centre National de Reference des Leishmanioses, Montpellier, France.
| | - Andrés G Lescano
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru. .,Universidad Peruana Cayetano Heredia, School of Public Health and Management, Lima, Peru.
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
| | - Daniella C Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Farrant GK, Hoebeke M, Partensky F, Andres G, Corre E, Garczarek L. WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. BMC Bioinformatics 2015; 16:281. [PMID: 26335184 PMCID: PMC4559175 DOI: 10.1186/s12859-015-0705-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 08/17/2015] [Indexed: 01/12/2023] Open
Abstract
Background The sequencing depth provided by high-throughput sequencing technologies has allowed a rise in the number of de novo sequenced genomes that could potentially be closed without further sequencing. However, genome scaffolding and closure require costly human supervision that often results in genomes being published as drafts. A number of automatic scaffolders were recently released, which improved the global quality of genomes published in the last few years. Yet, none of them reach the efficiency of manual scaffolding. Results Here, we present an innovative semi-automatic scaffolder that additionally helps with chimerae resolution and generates valuable contig maps and outputs for manual improvement of the automatic scaffolding. This software was tested on the newly sequenced marine cyanobacterium Synechococcus sp. WH8103 as well as two reference datasets used in previous studies, Rhodobacter sphaeroides and Homo sapiens chromosome 14 (http://gage.cbcb.umd.edu/). The quality of resulting scaffolds was compared to that of three other stand-alone scaffolders: SSPACE, SOPRA and SCARPA. For all three model organisms, WiseScaffolder produced better results than other scaffolders in terms of contiguity statistics (number of genome fragments, N50, LG50, etc.) and, in the case of WH8103, the reliability of the scaffolds was confirmed by whole genome alignment against a closely related reference genome. We also propose an efficient computer-assisted strategy for manual improvement of the scaffolding, using outputs generated by WiseScaffolder, as well as for genome finishing that in our hands led to the circularization of the WH8103 genome. Conclusion Altogether, WiseScaffolder proved more efficient than three other scaffolders for both prokaryotic and eukaryotic genomes and is thus likely applicable to most genome projects. The scaffolding pipeline described here should be of particular interest to biologists wishing to take advantage of the high added value of complete genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0705-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory K Farrant
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7144, Station Biologique, CS 90074, 29688, Roscoff cedex, France.,CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Oceanic Plankton Group, Marine Phototrophic Prokaryotes team, Place Georges Teissier, CS 90074, 29688, Roscoff cedex, France
| | - Mark Hoebeke
- CNRS, FR 2424, ABiMS Platform, Station Biologique, Place Georges Teissier, CS 90074, 29688, Roscoff cedex, France
| | - Frédéric Partensky
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7144, Station Biologique, CS 90074, 29688, Roscoff cedex, France.,CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Oceanic Plankton Group, Marine Phototrophic Prokaryotes team, Place Georges Teissier, CS 90074, 29688, Roscoff cedex, France
| | - Gwendoline Andres
- CNRS, FR 2424, ABiMS Platform, Station Biologique, Place Georges Teissier, CS 90074, 29688, Roscoff cedex, France
| | - Erwan Corre
- CNRS, FR 2424, ABiMS Platform, Station Biologique, Place Georges Teissier, CS 90074, 29688, Roscoff cedex, France
| | - Laurence Garczarek
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7144, Station Biologique, CS 90074, 29688, Roscoff cedex, France. .,CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Oceanic Plankton Group, Marine Phototrophic Prokaryotes team, Place Georges Teissier, CS 90074, 29688, Roscoff cedex, France.
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105
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Hadfield SJ, Pachebat JA, Swain MT, Robinson G, Cameron SJ, Alexander J, Hegarty MJ, Elwin K, Chalmers RM. Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples. BMC Genomics 2015; 16:650. [PMID: 26318339 PMCID: PMC4552982 DOI: 10.1186/s12864-015-1805-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 07/31/2015] [Indexed: 12/20/2022] Open
Abstract
Background Whole genome sequencing (WGS) of Cryptosporidium spp. has previously relied on propagation of the parasite in animals to generate enough oocysts from which to extract DNA of sufficient quantity and purity for analysis. We have developed and validated a method for preparation of genomic Cryptosporidium DNA suitable for WGS directly from human stool samples and used it to generate 10 high-quality whole Cryptosporidium genome assemblies. Our method uses a combination of salt flotation, immunomagnetic separation (IMS), and surface sterilisation of oocysts prior to DNA extraction, with subsequent use of the transposome-based Nextera XT kit to generate libraries for sequencing on Illumina platforms. IMS was found to be superior to caesium chloride density centrifugation for purification of oocysts from small volume stool samples and for reducing levels of contaminant DNA. Results The IMS-based method was used initially to sequence whole genomes of Cryptosporidium hominis gp60 subtype IbA10G2 and Cryptosporidium parvum gp60 subtype IIaA19G1R2 from small amounts of stool left over from diagnostic testing of clinical cases of cryptosporidiosis. The C. parvum isolate was sequenced to a mean depth of 51.8X with reads covering 100 % of the bases of the C. parvum Iowa II reference genome (Bioproject PRJNA 15586), while the C. hominis isolate was sequenced to a mean depth of 34.7X with reads covering 98 % of the bases of the C. hominis TU502 v1 reference genome (Bioproject PRJNA 15585). The method was then applied to a further 17 stools, successfully generating another eight new whole genome sequences, of which two were C. hominis (gp60 subtypes IbA10G2 and IaA14R3) and six C. parvum (gp60 subtypes IIaA15G2R1 from three samples, and one each of IIaA17G1R1, IIaA18G2R1, and IIdA22G1), demonstrating the utility of this method to sequence Cryptosporidium genomes directly from clinical samples. This development is especially important as it reduces the requirement to propagate Cryptosporidium oocysts in animal models prior to genome sequencing. Conclusion This represents the first report of high-quality whole genome sequencing of Cryptosporidium isolates prepared directly from human stool samples.
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Affiliation(s)
- Stephen J Hadfield
- Cryptosporidium Reference Unit, Public Health Wales Microbiology ABM, Singleton Hospital, Sgeti, Swansea, SA2 8QA, United Kingdom.
| | - Justin A Pachebat
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, United Kingdom.
| | - Martin T Swain
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, United Kingdom.
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology ABM, Singleton Hospital, Sgeti, Swansea, SA2 8QA, United Kingdom.
| | - Simon Js Cameron
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, United Kingdom.
| | - Jenna Alexander
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, United Kingdom.
| | - Matthew J Hegarty
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, United Kingdom.
| | - Kristin Elwin
- Cryptosporidium Reference Unit, Public Health Wales Microbiology ABM, Singleton Hospital, Sgeti, Swansea, SA2 8QA, United Kingdom.
| | - Rachel M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology ABM, Singleton Hospital, Sgeti, Swansea, SA2 8QA, United Kingdom.
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Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I, Dias da Silveira W, Semmler T, Wieler LH, Jenkins C, Cravioto A, Faruque SM, Parkhill J, Wook Kim D, Keddy KH, Thomson NR. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 2015; 4:e07335. [PMID: 26238191 PMCID: PMC4522646 DOI: 10.7554/elife.07335] [Citation(s) in RCA: 79] [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: 03/10/2015] [Accepted: 07/04/2015] [Indexed: 12/15/2022] Open
Abstract
Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.
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Affiliation(s)
- Thomas R Connor
- Cardiff School of Biosciences, Cardiff, United Kingdom
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | | | - Kate S Baker
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | | | - Kaisar Ali Talukder
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Malika Gouali
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ishrat Jahan Azmi
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Wanderley Dias da Silveira
- Department of Genetics, Evolution, and Bioagents, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Torsten Semmler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Lothar H Wieler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom
| | | | - Shah M Faruque
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | - Dong Wook Kim
- Department of Pharmacy, School of Pharmacy, Hanyang University, Ansan, Republic of Korea
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicholas R Thomson
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
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107
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Chu CC, Zavala JA, Spencer JL, Curzi MJ, Fields CJ, Drnevich J, Siegfried BD, Seufferheld MJ. Patterns of differential gene expression in adult rotation-resistant and wild-type western corn rootworm digestive tracts. Evol Appl 2015; 8:692-704. [PMID: 26240606 PMCID: PMC4516421 DOI: 10.1111/eva.12278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/21/2015] [Indexed: 01/03/2023] Open
Abstract
The western corn rootworm (WCR,Diabrotica virgifera virgifera LeConte) is an important pest of corn. Annual crop rotation between corn and soybean disrupts the corn-dependent WCR life cycle and is widely adopted to manage this pest. This strategy selected for rotation-resistant (RR) WCR with reduced ovipositional fidelity to corn. Previous studies revealed that RR-WCR adults exhibit greater tolerance of soybean diets, different gut physiology, and host-microbe interactions compared to rotation-susceptible wild types (WT). To identify the genetic mechanisms underlying these phenotypic changes, a de novo assembly of the WCR adult gut transcriptome was constructed and used for RNA-sequencing analyses of RNA libraries from different WCR phenotypes fed with corn or soybean diets. Global gene expression profiles of WT- and RR-WCR were similar when feeding on corn diets, but different when feeding on soybean. Using network-based methods, we identified gene modules transcriptionally correlated with the RR phenotype. Gene ontology enrichment analyses indicated that the functions of these modules were related to metabolic processes, immune responses, biological adhesion, and other functions/processes that appear to correlate to documented traits in RR populations. These results suggest that gut transcriptomic divergence correlated with brief soybean feeding and other physiological traits may exist between RR- and WT-WCR adults.
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Affiliation(s)
- Chia-Ching Chu
- Department of Crop Sciences, University of Illinois Urbana, IL, USA
| | - Jorge A Zavala
- Facultad de Agronomía, Cátedra de Bioquímica INBA-CONICET, University of Buenos Aires-CONICET Buenos Aires, Argentina
| | - Joseph L Spencer
- Illinois Natural History Survey, University of Illinois Champaign, IL, USA
| | | | - Christopher J Fields
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center Urbana, IL, USA
| | - Jenny Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center Urbana, IL, USA
| | | | - Manfredo J Seufferheld
- Department of Entomology, University of Illinois Urbana, IL, USA ; Illinois Natural History Survey, University of Illinois Champaign, IL, USA
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108
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Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife 2015; 4:e06974. [PMID: 26175406 PMCID: PMC4501334 DOI: 10.7554/elife.06974] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/16/2015] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga. DOI:http://dx.doi.org/10.7554/eLife.06974.001 Single-celled parasites cause many severe diseases in humans and animals. The apicomplexans form probably the most successful group of these parasites and include the parasites that cause malaria. Apicomplexans infect a broad range of hosts, including humans, reptiles, birds, and insects, and often have complicated life cycles. For example, the malaria-causing parasites spread by moving from humans to female mosquitoes and then back to humans. Despite significant differences amongst apicomplexans, these single-celled parasites also share a number of features that are not seen in other living species. How and when these features arose remains unclear. It is known from previous work that apicomplexans are closely related to single-celled algae. But unlike apicomplexans, which depend on a host animal to survive, these algae live freely in their environment, often in close association with corals. Woo et al. have now sequenced the genomes of two photosynthetic algae that are thought to be close living relatives of the apicomplexans. These genomes were then compared to each other and to the genomes of other algae and apicomplexans. These comparisons reconfirmed that the two algae that were studied were close relatives of the apicomplexans. Further analyses suggested that thousands of genes were lost as an ancient free-living algae evolved into the apicomplexan ancestor, and further losses occurred as these early parasites evolved into modern species. The lost genes were typically those that are important for free-living organisms, but are either a hindrance to, or not needed in, a parasitic lifestyle. Some of the ancestor's genes, especially those that coded for the building blocks of flagella (structures which free-living algae use to move around), were repurposed in ways that helped the apicomplexans to invade their hosts. Understanding this repurposing process in greater detail will help to identify key molecules in these deadly parasites that could be targeted by drug treatments. It will also offer answers to one of the most fascinating questions in evolutionary biology: how parasites have evolved from free-living organisms. DOI:http://dx.doi.org/10.7554/eLife.06974.002
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Affiliation(s)
- Yong H Woo
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hifzur Ansari
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas D Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | | | - Martin Kolisko
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jan Michálek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alka Saxena
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Annageldi Tayyrov
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alaguraj Veluchamy
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Paris, France
| | - Shahjahan Ali
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Axel Bernal
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Javier del Campo
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jaromír Cihlář
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Eva Hajdušková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jan Janouškovec
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Fred D Mast
- Seattle Biomedical Research Institute, Seattle, United States
| | - Diego Miranda-Saavedra
- Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, Madrid, Spain
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raeece Naeem
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mridul Nair
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aswini K Panigrahi
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neil D Rawlings
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eriko Padron-Regalado
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nadira Samad
- School of Botany, University of Melbourne, Parkville, Australia
| | - Aleš Tomčala
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jon Wilkes
- Wellcome Trust Centre For Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel E Neafsey
- Broad Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton, Australia
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Paris, France
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Thomas J Templeton
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ross F Waller
- School of Botany, University of Melbourne, Parkville, Australia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease. Genome Biol 2015; 15:505. [PMID: 25370836 DOI: 10.1186/preaccept-1086350395137407] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. RESULTS We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. CONCLUSIONS Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains.
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Gomez-Escribano JP, Castro JF, Razmilic V, Chandra G, Andrews B, Asenjo JA, Bibb MJ. The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genomics 2015; 16:485. [PMID: 26122045 PMCID: PMC4487206 DOI: 10.1186/s12864-015-1652-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Background Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potentially revealing novel chemistry and enzymology involved in their biosynthesis. This approach also allows rapid insights into the biosynthetic potential of microorganisms isolated from unexploited habitats and ecosystems, which in many cases may prove difficult to culture and manipulate in the laboratory. Streptomyces leeuwenhoekii (formerly Streptomyces sp. strain C34) was isolated from the hyper-arid high-altitude Atacama Desert in Chile and shown to produce novel polyketide antibiotics. Results Here we present the de novo sequencing of the S. leeuwenhoekii linear chromosome (8 Mb) and two extrachromosomal replicons, the circular pSLE1 (86 kb) and the linear pSLE2 (132 kb), all in single contigs, obtained by combining Pacific Biosciences SMRT (PacBio) and Illumina MiSeq technologies. We identified the biosynthetic gene clusters for chaxamycin, chaxalactin, hygromycin A and desferrioxamine E, metabolites all previously shown to be produced by this strain (J Nat Prod, 2011, 74:1965) and an additional 31 putative gene clusters for specialised metabolites. As well as gene clusters for polyketides and non-ribosomal peptides, we also identified three gene clusters encoding novel lasso-peptides. Conclusions The S. leeuwenhoekii genome contains 35 gene clusters apparently encoding the biosynthesis of specialised metabolites, most of them completely novel and uncharacterised. This project has served to evaluate the current state of NGS for efficient and effective genome mining of high GC actinomycetes. The PacBio technology now permits the assembly of actinomycete replicons into single contigs with >99 % accuracy. The assembled Illumina sequence permitted not only the correction of omissions found in GC homopolymers in the PacBio assembly (exacerbated by the high GC content of actinomycete DNA) but it also allowed us to obtain the sequences of the termini of the chromosome and of a linear plasmid that were not assembled by PacBio. We propose an experimental pipeline that uses the Illumina assembled contigs, in addition to just the reads, to complement the current limitations of the PacBio sequencing technology and assembly software. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1652-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo Gomez-Escribano
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Jean Franco Castro
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom. .,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Valeria Razmilic
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom. .,Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Barbara Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, Universidad de Chile, Beauchef 850, Santiago, Chile.
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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111
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Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00486-15. [PMID: 25999575 PMCID: PMC4440955 DOI: 10.1128/genomea.00486-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genomes from four Clostridium sp. strains considered to be mesophilic anaerobic bacteria, isolated from crop soil in Colombia, with a strong potential to produce alcohols like 1,3-propanediol, were analyzed. We present the draft genome of these strains, which will be useful for developing genetic engineering strategies.
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112
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Steinig EJ, Andersson P, Harris SR, Sarovich DS, Manoharan A, Coupland P, Holden MTG, Parkhill J, Bentley SD, Robinson DA, Tong SYC. Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus. BMC Genomics 2015; 16:388. [PMID: 25981586 PMCID: PMC4432960 DOI: 10.1186/s12864-015-1599-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/28/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated globally and is increasingly prevalent in India. Here, we present the complete genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors. RESULTS Sequencing using single-molecule real-time technology resulted in the assembly of a single continuous chromosomal sequence, which was error-corrected, annotated and compared to nine draft genome assemblies of ST772-MRSA-V from Australia, Malaysia and India. We discovered numerous and redundant resistance genes associated with mobile genetic elements (MGEs) and known core genome mutations that explain the highly antibiotic resistant phenotype of DAR4145. Staphylococcal toxins and superantigens, including the leukotoxin Panton-Valentinin Leukocidin, were predominantly associated with genomic islands and the phage φ-IND772PVL. Some of these mobile resistance and virulence factors were variably present in other strains of the ST772-MRSA-V lineage. CONCLUSIONS The genomic characteristics presented here emphasize the contribution of MGEs to the emergence of multidrug-resistant and highly virulent strains of community-associated MRSA. Antibiotic resistance was further augmented by chromosomal mutations and redundancy of resistance genes. The complete genome of DAR4145 provides a valuable resource for future investigations into the global dissemination and phylogeography of ST772-MRSA-V.
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Affiliation(s)
- Eike J Steinig
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Patiyan Andersson
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Simon R Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Derek S Sarovich
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
| | - Anand Manoharan
- Pushpagiri Research Center, Pushpagiri Institute of Medical Sciences and Research Center, Thiruvalla, India.
| | - Paul Coupland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | | | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - D Ashley Robinson
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS, USA.
| | - Steven Y C Tong
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
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113
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Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, Panigrahi A, Vermont SJ, Otto TD, Wastling J, Pain A. Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PLoS One 2015; 10:e0124473. [PMID: 25875305 PMCID: PMC4395442 DOI: 10.1371/journal.pone.0124473] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/02/2015] [Indexed: 11/25/2022] Open
Abstract
Toxoplasma gondii is an important protozoan parasite that infects all warm-blooded animals and causes opportunistic infections in immuno-compromised humans. Its closest relative, Neospora caninum, is an important veterinary pathogen that causes spontaneous abortion in livestock. Comparative genomics of these two closely related coccidians has been of particular interest to identify genes that contribute to varied host cell specificity and disease. Here, we describe a manual evaluation of these genomes based on strand-specific RNA sequencing and shotgun proteomics from the invasive tachyzoite stages of these two parasites. We have corrected predicted structures of over one third of the previously annotated gene models and have annotated untranslated regions (UTRs) in over half of the predicted protein-coding genes. We observe distinctly long UTRs in both the organisms, almost four times longer than other model eukaryotes. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). We have significantly improved the annotation quality in these genomes that would serve as a manually curated dataset for Toxoplasma and Neospora research communities.
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Affiliation(s)
- Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raeece Naeem
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Tareq B. Malas
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Ehab Moussa
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Aswini Panigrahi
- Bioscience Core Laboratory (BCL), King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
| | - Sarah J. Vermont
- Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Thomas D. Otto
- Parasite Genomics Group, Wellcome Trust Sanger Institute (WTSI), Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jonathan Wastling
- Institute of Infection and Global Health and School of Veterinary Science, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia
- * E-mail:
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114
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Sahl JW, Allender CJ, Colman RE, Califf KJ, Schupp JM, Currie BJ, Van Zandt KE, Gelhaus HC, Keim P, Tuanyok A. Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence. PLoS One 2015; 10:e0121052. [PMID: 25803742 PMCID: PMC4372212 DOI: 10.1371/journal.pone.0121052] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/27/2015] [Indexed: 01/06/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against B. pseudomallei infection, the US Food and Drug Administration (FDA) animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 B. pseudomallei isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP) phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR) analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in B. pseudomallei were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of B. pseudomallei. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving B. pseudomallei pathogenesis, differential virulence, and efficacy to therapeutics.
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Affiliation(s)
- Jason W. Sahl
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Christopher J. Allender
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Rebecca E. Colman
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Katy J. Califf
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Schupp
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Bart J. Currie
- Department of Tropical and Emerging Infectious Diseases, Menzies School of Health Research, Casuarina NT, Australia
| | | | - H. Carl Gelhaus
- Battelle Biomedical Research Center (BBRC), Columbus, Ohio, United States of America
| | - Paul Keim
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, and Pacific Center for Emerging Infections Diseases Research, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
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115
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Spence JM, Spence JP, Abumoussa A, Burack WR. Ultradeep analysis of tumor heterogeneity in regions of somatic hypermutation. Genome Med 2015; 7:24. [PMID: 25874000 PMCID: PMC4395979 DOI: 10.1186/s13073-015-0147-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/26/2015] [Indexed: 01/06/2023] Open
Abstract
Tumor heterogeneity is of growing importance in the treatment of cancers. Mutational hot spots are prime locations for determining number and proportions of low variant allele frequency (VAF) tumor subclones by next generation sequencing. Low VAF detection is complicated by poor mapping efficiency in regions with high mutation density. Our Deep-Drilling with iterative Mapping (DDiMAP) method retains variant allele patterns to aid in single nucleotide variation detection and generation of additional reference alleles, with remapping increasing coverage of highly mutated regions to capture data critical to heterogeneity analysis and enhancing sensitivity. DDiMAP outputs variant patterns with frequencies, enabling rapid phylogenetic analysis of ongoing mutation.
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Affiliation(s)
- Janice M Spence
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - John P Spence
- NGS Tech, 936 Little Pond Way, Webster, NY 14580 USA
| | - Andrew Abumoussa
- Department of Computer Science, University of Rochester, Rochester, NY 14642 USA
| | - W Richard Burack
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642 USA
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Abstract
We resequenced the genome of equid herpesvirus 2 (EHV2) strain 86/67 and sequenced the genomes of EHV2 strain G9/92 and equid herpesvirus 5 (EHV5) strain 2-141/67. The most prominent genetic differences are the dissimilar locations of the interleukin-10 (IL-10)-like genes and the presence of an OX-2-like gene in EHV5 only.
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117
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Llanes A, Restrepo CM, Del Vecchio G, Anguizola FJ, Lleonart R. The genome of Leishmania panamensis: insights into genomics of the L. (Viannia) subgenus. Sci Rep 2015; 5:8550. [PMID: 25707621 PMCID: PMC4338418 DOI: 10.1038/srep08550] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
Kinetoplastid parasites of the Leishmania genus cause several forms of leishmaniasis. Leishmania species pathogenic to human are separated into two subgenera, Leishmania (Leishmania) and L. (Viannia). Species from the Viannia subgenus cause predominantly cutaneous leishmaniasis in Central and South America, occasionally leading to more severe clinical presentations. Although the genomes of several species of Leishmania have been sequenced to date, only one belongs to this rather different subgenus. Here we explore the unique features of the Viannia subgenus by sequencing and analyzing the genome of L. (Viannia) panamensis. Against a background of conservation in gene content and synteny, we found key differences at the genomic level that may explain the occurrence of molecular processes involving nucleic acid manipulation and differential modification of surface glycoconjugates. These differences may in part explain some phenotypic characteristics of the Viannia parasites, including their increased adaptive capacity and enhanced metastatic ability.
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Affiliation(s)
- Alejandro Llanes
- 1] Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá [2] Facultad de Ciencias de la Salud Dr. William C. Gorgas, Universidad Latina de Panamá, Panamá, Panamá [3] Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Carlos Mario Restrepo
- 1] Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá [2] Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Gina Del Vecchio
- Facultad de Ciencias de la Salud Dr. William C. Gorgas, Universidad Latina de Panamá, Panamá, Panamá
| | - Franklin José Anguizola
- Facultad de Ciencias de la Salud Dr. William C. Gorgas, Universidad Latina de Panamá, Panamá, Panamá
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá
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Wang Q, Jia P, Zhao Z. VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome Med 2015; 7:2. [PMID: 25699093 PMCID: PMC4333248 DOI: 10.1186/s13073-015-0126-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/05/2015] [Indexed: 12/28/2022] Open
Abstract
Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
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Affiliation(s)
- Qingguo Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
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119
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Peña-Montenegro TD, Lozano L, Dussán J. Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5. Stand Genomic Sci 2015; 10:2. [PMID: 25685257 PMCID: PMC4317669 DOI: 10.1186/1944-3277-10-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/21/2014] [Indexed: 12/18/2022] Open
Abstract
Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in the Easter Planes of Colombia. This strain has potential in bioremediation of heavy-metal polluted environments and biological control of Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus taxonomic group 1 that comprises mosquito pathogenic strains. After a combination assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60 contigs and 5,209 predicted-coding sequences) revealed strong functional and syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx), binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik, ars, czc, mnt, ter, cop, cad, and znu operons were identified.
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Affiliation(s)
| | - Lucía Lozano
- Centro de Investigaciones Microbiológicas - CIMIC, Universidad de los Andes, Bogotá, Colombia
| | - Jenny Dussán
- Centro de Investigaciones Microbiológicas - CIMIC, Universidad de los Andes, Bogotá, Colombia
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120
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Marinier E, Brown DG, McConkey BJ. Pollux: platform independent error correction of single and mixed genomes. BMC Bioinformatics 2015; 16:10. [PMID: 25592313 PMCID: PMC4307147 DOI: 10.1186/s12859-014-0435-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/17/2014] [Indexed: 12/13/2022] Open
Abstract
Background Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads. Results We have developed a general-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software. Conclusions Pollux is highly effective at correcting errors across platforms, and is consistently able to perform as well or better than currently available error correction software. Pollux provides general-purpose error correction and may be used in applications with or without assembly.
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Affiliation(s)
- Eric Marinier
- David R. Cheriton School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
| | - Daniel G Brown
- David R. Cheriton School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
| | - Brendan J McConkey
- Department of Biology, University of Waterloo, 200 University Ave W, N2L3G1 Waterloo, Canada.
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Abstract
Shigellae cause significant diarrheal disease and mortality in humans, as there are approximately 163 million episodes of shigellosis and 1.1 million deaths annually. While significant strides have been made in the understanding of the pathogenesis, few studies on the genomic content of the Shigella species have been completed. The goal of this study was to characterize the genomic diversity of Shigella species through sequencing of 55 isolates representing members of each of the four Shigella species: S. flexneri, S. sonnei, S. boydii, and S. dysenteriae. Phylogeny inferred from 336 available Shigella and Escherichia coli genomes defined exclusive clades of Shigella; conserved genomic markers that can identify each clade were then identified. PCR assays were developed for each clade-specific marker, which was combined with an amplicon for the conserved Shigella invasion antigen, IpaH3, into a multiplex PCR assay. This assay demonstrated high specificity, correctly identifying 218 of 221 presumptive Shigella isolates, and sensitivity, by not identifying any of 151 diverse E. coli isolates incorrectly as Shigella. This new phylogenomics-based PCR assay represents a valuable tool for rapid typing of uncharacterized Shigella isolates and provides a framework that can be utilized for the identification of novel genomic markers from genomic data.
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122
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Koren S, Harhay GP, Smith TPL, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2015; 14:R101. [PMID: 24034426 PMCID: PMC4053942 DOI: 10.1186/gb-2013-14-9-r101] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. RESULTS To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. CONCLUSIONS Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.
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123
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Next-Generation Sequencing of 5' Untranslated Region of Hepatitis C Virus in Search of Minor Viral Variant in a Patient Who Revealed New Genotype While on Antiviral Treatment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 885:11-23. [PMID: 26747069 DOI: 10.1007/5584_2015_186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The role of mixed infections with different hepatitis C virus (HCV) genotypes in viral persistence, treatment effects, and tissue tropism is unclear. Next-generation sequencing (NGS), which is suitable for analysis of large, genetically diverse populations offers unparalleled advantages for the study of mixed infections. The aim of the study was to determine, using two different deep sequencing strategies (pyrosequencing - 454 Life Sciences/Roche and reversible terminator sequencing-by-synthesis by Illumina), the origin of a novel HCV genotype transiently detectable during antiviral therapy (pre-existing minor population vs. de novo superinfection). Secondly, we compared 5' untranslated region (5'-UTR) variants obtained by the two NGS approaches. 5' UTR amplification products from 9 samples collected from genotype 1b infected patient before, during, and after treatment (4 serum and 5 peripheral blood mononuclear cell - PBMC - samples) were subjected to the next-generation sequencing. The sequencing revealed the presence of two (454/Roche) and one (Illumina) genotype 4 variants in PBMC at Week 16. None of these variants were present either in the preceding or following samples as revealed by both platforms. 454/Roche sequencing detected 24 different 5'-UTR variants: 8 were present in serum and PBMC, 4 only in serum and 12 only in PBMC. Illumina sequencing detected 11 different 5'-UTR variants: 5 in serum and PBMC, 4 only in serum and 2 only in PBMC. Six variants were identical for both sequencing platforms. The difference in variants number was primarily due to variability in two 5'-UTR homopolymeric regions. In conclusion, longitudinal analysis of HCV variants, employing two independent deep sequencing methods, suggests that the transient presence of a different genotype strain in PBMC was a result of superinfection and not a selection of pre-existing minor variant.
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124
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Abstract
The development of "next-generation" high-throughput sequencing technologies has made it possible for many labs to undertake sequencing-based research projects that were unthinkable just a few years ago. Although the scientific applications are diverse, e.g., new genome projects, gene expression analysis, genome-wide functional screens, or epigenetics-the sequence data are usually processed in one of two ways: sequence reads are either mapped to an existing reference sequence, or they are built into a new sequence ("de novo assembly"). In this chapter, we first discuss some limitations of the mapping process and how these may be overcome through local sequence assembly. We then introduce the concept of de novo assembly and describe essential assembly improvement procedures such as scaffolding, contig ordering, gap closure, error evaluation, gene annotation transfer and ab initio gene annotation. The results are high-quality draft assemblies that will facilitate informative downstream analyses.
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Affiliation(s)
- Thomas D Otto
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK,
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125
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Complete genome sequence of a common midwife toad virus-like ranavirus associated with mass mortalities in wild amphibians in the Netherlands. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01293-14. [PMID: 25540340 PMCID: PMC4276818 DOI: 10.1128/genomea.01293-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A ranavirus associated with mass mortalities in wild water frogs (Pelophylax spp.) and other amphibians in the Netherlands since 2010 was isolated, and its complete genome sequence was determined. The virus has a genome of 107,772 bp and shows 96.5% sequence identity with the common midwife toad virus from Spain.
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126
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Weisenfeld NI, Yin S, Sharpe T, Lau B, Hegarty R, Holmes L, Sogoloff B, Tabbaa D, Williams L, Russ C, Nusbaum C, Lander ES, MacCallum I, Jaffe DB. Comprehensive variation discovery in single human genomes. Nat Genet 2014; 46:1350-5. [PMID: 25326702 PMCID: PMC4244235 DOI: 10.1038/ng.3121] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 09/29/2014] [Indexed: 12/27/2022]
Abstract
Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome; however, calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from the finished sequence of 103 randomly chosen fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity by several fold, with the greatest impact in challenging regions of the human genome.
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Affiliation(s)
- Neil I. Weisenfeld
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Shuangye Yin
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Ted Sharpe
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Bayo Lau
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Ryan Hegarty
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Laurie Holmes
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Brian Sogoloff
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Diana Tabbaa
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Louise Williams
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Carsten Russ
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Chad Nusbaum
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Eric S. Lander
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Iain MacCallum
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - David B. Jaffe
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
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127
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Vaidya AB, Morrisey JM, Zhang Z, Das S, Daly TM, Otto TD, Spillman NJ, Wyvratt M, Siegl P, Marfurt J, Wirjanata G, Sebayang BF, Price RN, Chatterjee A, Nagle A, Stasiak M, Charman SA, Angulo-Barturen I, Ferrer S, Belén Jiménez-Díaz M, Martínez MS, Gamo FJ, Avery VM, Ruecker A, Delves M, Kirk K, Berriman M, Kortagere S, Burrows J, Fan E, Bergman LW. Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum. Nat Commun 2014; 5:5521. [PMID: 25422853 PMCID: PMC4263321 DOI: 10.1038/ncomms6521] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 10/09/2014] [Indexed: 01/01/2023] Open
Abstract
The quest for new antimalarial drugs, especially those with novel modes of action, is essential in the face of emerging drug-resistant parasites. Here we describe a new chemical class of molecules, pyrazoleamides, with potent activity against human malaria parasites and showing remarkably rapid parasite clearance in an in vivo model. Investigations involving pyrazoleamide-resistant parasites, whole-genome sequencing and gene transfers reveal that mutations in two proteins, a calcium-dependent protein kinase (PfCDPK5) and a P-type cation-ATPase (PfATP4), are necessary to impart full resistance to these compounds. A pyrazoleamide compound causes a rapid disruption of Na+ regulation in blood-stage Plasmodium falciparum parasites. Similar effect on Na+ homeostasis was recently reported for spiroindolones, which are antimalarials of a chemical class quite distinct from pyrazoleamides. Our results reveal that disruption of Na+ homeostasis in malaria parasites is a promising mode of antimalarial action mediated by at least two distinct chemical classes. Novel antimalarial drugs are urgently needed to combat parasite drug resistance. Here, Vaidya et al. describe a new chemical class of potent antimalarial compounds that act by disrupting the parasite's sodium homeostasis.
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Affiliation(s)
- Akhil B Vaidya
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 190129, USA
| | - Joanne M Morrisey
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 190129, USA
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195, USA
| | - Sudipta Das
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 190129, USA
| | - Thomas M Daly
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 190129, USA
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB101SA, UK
| | - Natalie J Spillman
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Matthew Wyvratt
- Medicines for Malaria Venture, PO Box 1826, 20Rt de Pr-Bois, Geneva 15 1215, Switzerland
| | - Peter Siegl
- Medicines for Malaria Venture, PO Box 1826, 20Rt de Pr-Bois, Geneva 15 1215, Switzerland
| | - Jutta Marfurt
- Division of Global and Tropical Health, Menzies School of Health Research and Charles Darwin University, PO Box 41096, Casuarina, Northern Territory 0811, Australia
| | - Grennady Wirjanata
- Division of Global and Tropical Health, Menzies School of Health Research and Charles Darwin University, PO Box 41096, Casuarina, Northern Territory 0811, Australia
| | - Boni F Sebayang
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia
| | - Ric N Price
- 1] Division of Global and Tropical Health, Menzies School of Health Research and Charles Darwin University, PO Box 41096, Casuarina, Northern Territory 0811, Australia [2] Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Arnab Chatterjee
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
| | - Advait Nagle
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
| | - Marcin Stasiak
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195, USA
| | - Susan A Charman
- Center for Drug Candidate Optimisation, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Iñigo Angulo-Barturen
- GlaxoSmithKline, Malaria Support Group, Calle Severo Ochoa 2, Tres Cantos 28760, Spain
| | - Santiago Ferrer
- GlaxoSmithKline, Malaria Support Group, Calle Severo Ochoa 2, Tres Cantos 28760, Spain
| | | | - María Santos Martínez
- GlaxoSmithKline, Malaria Support Group, Calle Severo Ochoa 2, Tres Cantos 28760, Spain
| | - Francisco Javier Gamo
- GlaxoSmithKline, Malaria Support Group, Calle Severo Ochoa 2, Tres Cantos 28760, Spain
| | - Vicky M Avery
- Eskitis Institute, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Andrea Ruecker
- Department of Life Sciences, South Kensington Campus, Imperial College, London SW7 2AZ, UK
| | - Michael Delves
- Department of Life Sciences, South Kensington Campus, Imperial College, London SW7 2AZ, UK
| | - Kiaran Kirk
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | | | - Sandhya Kortagere
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 190129, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, PO Box 1826, 20Rt de Pr-Bois, Geneva 15 1215, Switzerland
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195, USA
| | - Lawrence W Bergman
- Department of Microbiology and Immunology, Center for Molecular Parasitology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 190129, USA
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128
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Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963. [PMID: 25409509 PMCID: PMC4237348 DOI: 10.1371/journal.pone.0112963] [Citation(s) in RCA: 5368] [Impact Index Per Article: 536.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/16/2014] [Indexed: 02/06/2023] Open
Abstract
Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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Affiliation(s)
- Bruce J. Walker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (BJW); (AME)
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Margaret Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Amr Abouelliel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sharadha Sakthikumar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jennifer Wortman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah K. Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ashlee M. Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (BJW); (AME)
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129
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High-Quality Draft Genome Sequence of Babesia divergens, the Etiological Agent of Cattle and Human Babesiosis. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01194-14. [PMID: 25395649 PMCID: PMC4241675 DOI: 10.1128/genomea.01194-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Babesia divergens causes significant morbidity and mortality in cattle and splenectomized or immunocompromised individuals. Here, we present a 10.7-Mb high-quality draft genome of this parasite close to chromosome resolution that will enable comparative genome analyses and synteny studies among related parasites.
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130
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Gomez-Valero L, Rusniok C, Rolando M, Neou M, Dervins-Ravault D, Demirtas J, Rouy Z, Moore RJ, Chen H, Petty NK, Jarraud S, Etienne J, Steinert M, Heuner K, Gribaldo S, Médigue C, Glöckner G, Hartland EL, Buchrieser C. Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires’ disease. Genome Biol 2014. [PMID: 25370836 PMCID: PMC4256840 DOI: 10.1186/s13059-014-0505-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. Results We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. Conclusions Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0505-0) contains supplementary material, which is available to authorized users.
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Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WAM, Religa AA, Robertson L, Sanders M, Ogun SA, Cunningham D, Erhart A, Billker O, Khan SM, Stunnenberg HG, Langhorne J, Holder AA, Waters AP, Newbold CI, Pain A, Berriman M, Janse CJ. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol 2014; 12:86. [PMID: 25359557 PMCID: PMC4242472 DOI: 10.1186/s12915-014-0086-0] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/10/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function. RESULTS We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family. CONCLUSIONS Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
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Affiliation(s)
- Thomas D Otto
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Ulrike Böhme
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Andrew P Jackson
- />Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Martin Hunt
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Blandine Franke-Fayard
- />Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wieteke A M Hoeijmakers
- />Department of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Agnieszka A Religa
- />Institute of Infection, Immunity & Inflammation, School of Medical, Veterinary & Life Sciences, & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland UK
| | | | - Mandy Sanders
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Solabomi A Ogun
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Deirdre Cunningham
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Annette Erhart
- />Unit of Malariology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Oliver Billker
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Shahid M Khan
- />Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hendrik G Stunnenberg
- />Department of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Jean Langhorne
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Anthony A Holder
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Andrew P Waters
- />Institute of Infection, Immunity & Inflammation, School of Medical, Veterinary & Life Sciences, & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland UK
| | - Chris I Newbold
- />Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- />Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford UK
| | - Arnab Pain
- />Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | | | - Chris J Janse
- />Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
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132
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Sutton ER, Harris SR, Parkhill J, Sinkins SP. Comparative genome analysis of Wolbachia strain wAu. BMC Genomics 2014; 15:928. [PMID: 25341639 PMCID: PMC4223829 DOI: 10.1186/1471-2164-15-928] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/15/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Wolbachia intracellular bacteria can manipulate the reproduction of their arthropod hosts, including inducing sterility between populations known as cytoplasmic incompatibility (CI). Certain strains have been identified that are unable to induce or rescue CI, including wAu from Drosophila. Genome sequencing and comparison with CI-inducing related strain wMel was undertaken in order to better understand the molecular basis of the phenotype. RESULTS Although the genomes were broadly similar, several rearrangements were identified, particularly in the prophage regions. Many orthologous genes contained single nucleotide polymorphisms (SNPs) between the two strains, but a subset containing major differences that would likely cause inactivation in wAu were identified, including the absence of the wMel ortholog of a gene recently identified as a CI candidate in a proteomic study. The comparative analyses also focused on a family of transcriptional regulator genes implicated in CI in previous work, and revealed numerous differences between the strains, including those that would have major effects on predicted function. CONCLUSIONS The study provides support for existing candidates and novel genes that may be involved in CI, and provides a basis for further functional studies to examine the molecular basis of the phenotype.
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Affiliation(s)
- Elizabeth R Sutton
- />Department of Zoology and Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon R Harris
- />Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK
| | - Julian Parkhill
- />Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge UK
| | - Steven P Sinkins
- />Department of Zoology and Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- />Biomedical and Life Sciences, Lancaster University, Lancaster, UK
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133
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Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type. J Clin Microbiol 2014; 53:282-6. [PMID: 25339397 DOI: 10.1128/jcm.02560-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Twelve Burkholderia pseudomallei isolates collected over a 32-month period from a patient with chronic melioidosis demonstrated identical multilocus sequence types (STs). However, whole-genome sequencing suggests a polyclonal infection. This study is the first to report a mixed infection with the same ST.
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134
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Otto TD, Rayner JC, Böhme U, Pain A, Spottiswoode N, Sanders M, Quail M, Ollomo B, Renaud F, Thomas AW, Prugnolle F, Conway DJ, Newbold C, Berriman M. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun 2014; 5:4754. [PMID: 25203297 PMCID: PMC4166903 DOI: 10.1038/ncomms5754] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 07/18/2014] [Indexed: 01/19/2023] Open
Abstract
Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis of P. falciparum adaptation to human hosts by fully sequencing the genome of the closely related chimpanzee parasite species P. reichenowi, and obtaining partial sequence data from a more distantly related chimpanzee parasite (P. gaboni). The close relationship between P. reichenowi and P. falciparum is emphasized by almost complete conservation of genomic synteny, but against this strikingly conserved background we observe major differences at loci involved in erythrocyte invasion. The organization of most virulence-associated multigene families, including the hypervariable var genes, is broadly conserved, but P. falciparum has a smaller subset of rif and stevor genes whose products are expressed on the infected erythrocyte surface. Genome-wide analysis identifies other loci under recent positive selection, but a limited number of changes at the host-parasite interface may have mediated host switching.
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Affiliation(s)
- Thomas D. Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Julian C. Rayner
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Ulrike Böhme
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Arnab Pain
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Biological and Environmental Sciences and Engineering (BESE) Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Natasha Spottiswoode
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mandy Sanders
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Michael Quail
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Benjamin Ollomo
- Centre International de Recherches Médicales de Franceville, CIRMF, BP 769 Franceville, Gabon
| | - François Renaud
- Laboratoire MIVEGEC, UMR 5290 CNRS-IRD-UMI-UMII, IRD, BP 64501, 34394 Montpellier, France
| | - Alan W. Thomas
- Biomedical Primate Research Centre, Department of Parasitology, 2280 GH Rijswijk, The Netherlands
| | - Franck Prugnolle
- Centre International de Recherches Médicales de Franceville, CIRMF, BP 769 Franceville, Gabon
- Laboratoire MIVEGEC, UMR 5290 CNRS-IRD-UMI-UMII, IRD, BP 64501, 34394 Montpellier, France
| | - David J. Conway
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Chris Newbold
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- These authors contributed equally to this work
| | - Matthew Berriman
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- These authors contributed equally to this work
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135
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Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Res 2014; 24:1676-85. [PMID: 25015382 PMCID: PMC4199364 DOI: 10.1101/gr.168955.113] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.
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Affiliation(s)
- Adam J Reid
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Damer P Blake
- Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Hifzur R Ansari
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Karen Billington
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Hilary P Browne
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Josephine Bryant
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Matt Dunn
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Stacy S Hung
- Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Fumiya Kawahara
- Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan
| | - Diego Miranda-Saavedra
- Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Tareq B Malas
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Hardeep Naghra
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Mridul Nair
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Neil D Rawlings
- European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Pierre Rivailler
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Apoyo Bioinformático, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Chandra Subramaniam
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom
| | - Yea-Ling Tay
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Yong Woo
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia
| | - Xikun Wu
- The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom; Amgen Limited, Uxbridge UB8 1DH, United Kingdom
| | - Bart Barrell
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton VIC 3800, Australia
| | - Arthur Gruber
- Departament of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Alasdair C Ivens
- Centre for Immunity, Infection and Evolution, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Marie-Adèle Rajandream
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Martin W Shirley
- The Pirbright Institute, Pirbright Laboratory, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia; Malaysia Genome Institute, Jalan Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Fiona M Tomley
- Royal Veterinary College, North Mymms, Hertfordshire AL9 7TA, United Kingdom; The Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, United Kingdom;
| | - Arnab Pain
- Computational Bioscience Research Center, Biological Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah 23955-6900, Kingdom of Saudi Arabia;
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136
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Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D, Echaide IE, Farber M, Gahlot S, Gamble J, Gupta D, Gupta Y, Jackson L, Malandrin L, Malas TB, Moussa E, Nair M, Reid AJ, Sanders M, Sharma J, Tracey A, Quail MA, Weir W, Wastling JM, Hall N, Willadsen P, Lingelbach K, Shiels B, Tait A, Berriman M, Allred DR, Pain A. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Res 2014; 42:7113-31. [PMID: 24799432 PMCID: PMC4066756 DOI: 10.1093/nar/gku322] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct.
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Affiliation(s)
- Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Ic2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Thomas D Otto
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alistair Darby
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Abhinay Ramaprasad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Dong Xia
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Ic2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | | | - Marisa Farber
- Centro Nacional de Investigaciones Agropecuarias, Instituto de Biotecnología INTA, Buenos Aires, Argentina
| | - Sunayna Gahlot
- Bioinformatics Laboratory, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - John Gamble
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Dinesh Gupta
- Bioinformatics Laboratory, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Yask Gupta
- Bioinformatics Laboratory, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Louise Jackson
- Department of Agriculture, Fisheries and Forestry, Biosecurity Sciences Laboratory, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Laurence Malandrin
- UMR1300 INRA/Oniris Biology, Epidemiology and Risk Analysis in Animal Health, BP 40706, F-44307 Nantes, France
| | - Tareq B Malas
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ehab Moussa
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mridul Nair
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Adam J Reid
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mandy Sanders
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jyotsna Sharma
- FG Parasitologie, Philipps Universität Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Alan Tracey
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mike A Quail
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - William Weir
- FG Parasitologie, Philipps Universität Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Jonathan M Wastling
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Ic2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Neil Hall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Peter Willadsen
- Department of Agriculture, Fisheries and Forestry, Biosecurity Sciences Laboratory, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Klaus Lingelbach
- FG Parasitologie, Philipps Universität Marburg, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Brian Shiels
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Andy Tait
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Matt Berriman
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David R Allred
- Department of Infectious Diseases and Pathology, and Genetics Institute, University of Florida, PO Box 110880, 2015 SW 16th Avenue, Gainesville FL 33611-0880, USA
| | - Arnab Pain
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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137
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Abstract
The genus Yersinia has been used as a model system to study pathogen evolution. Using whole-genome sequencing of all Yersinia species, we delineate the gene complement of the whole genus and define patterns of virulence evolution. Multiple distinct ecological specializations appear to have split pathogenic strains from environmental, nonpathogenic lineages. This split demonstrates that contrary to hypotheses that all pathogenic Yersinia species share a recent common pathogenic ancestor, they have evolved independently but followed parallel evolutionary paths in acquiring the same virulence determinants as well as becoming progressively more limited metabolically. Shared virulence determinants are limited to the virulence plasmid pYV and the attachment invasion locus ail. These acquisitions, together with genomic variations in metabolic pathways, have resulted in the parallel emergence of related pathogens displaying an increasingly specialized lifestyle with a spectrum of virulence potential, an emerging theme in the evolution of other important human pathogens.
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138
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Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C, Dickens NJ, Religa AA, Bushell E, Graham AL, Cameron R, Kafsack BF, Williams AE, Llinas M, Berriman M, Billker O, Waters AP. A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature 2014; 507:253-257. [PMID: 24572359 PMCID: PMC4105895 DOI: 10.1038/nature12970] [Citation(s) in RCA: 299] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 12/19/2013] [Indexed: 12/04/2022]
Abstract
Commitment to and completion of sexual development are essential for malaria parasites (protists of the genus Plasmodium) to be transmitted through mosquitoes. The molecular mechanism(s) responsible for commitment have been hitherto unknown. Here we show that PbAP2-G, a conserved member of the apicomplexan AP2 (ApiAP2) family of DNA-binding proteins, is essential for the commitment of asexually replicating forms to sexual development in Plasmodium berghei, a malaria parasite of rodents. PbAP2-G was identified from mutations in its encoding gene, PBANKA_143750, which account for the loss of sexual development frequently observed in parasites transmitted artificially by blood passage. Systematic gene deletion of conserved ApiAP2 genes in Plasmodium confirmed the role of PbAP2-G and revealed a second ApiAP2 member (PBANKA_103430, here termed PbAP2-G2) that significantly modulates but does not abolish gametocytogenesis, indicating that a cascade of ApiAP2 proteins are involved in commitment to the production and maturation of gametocytes. The data suggest a mechanism of commitment to gametocytogenesis in Plasmodium consistent with a positive feedback loop involving PbAP2-G that could be exploited to prevent the transmission of this pernicious parasite.
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Affiliation(s)
- Abhinav Sinha
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow
| | - Katie R. Hughes
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow
| | | | | | | | | | | | - Ellen Bushell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anne L. Graham
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow
| | - Rachael Cameron
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow
| | - Bjorn F.C. Kafsack
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - April E. Williams
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Manuel Llinas
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | | | | | - Andrew P. Waters
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow
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139
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Hunt M, Newbold C, Berriman M, Otto TD. A comprehensive evaluation of assembly scaffolding tools. Genome Biol 2014; 15:R42. [PMID: 24581555 PMCID: PMC4053845 DOI: 10.1186/gb-2014-15-3-r42] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 03/03/2014] [Indexed: 11/12/2022] Open
Abstract
Background Genome assembly is typically a two-stage process: contig assembly followed by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the focus of reported assembly statistics; longer scaffolds greatly facilitate the use of genome sequences in downstream analyses, and it is appealing to present larger numbers as metrics of assembly performance. However, scaffolds are highly prone to errors, especially when generated using short reads, which can directly result in inflated assembly statistics. Results Here we provide the first independent evaluation of scaffolding tools for second-generation sequencing data. We find large variations in the quality of results depending on the tool and dataset used. Even extremely simple test cases of perfect input, constructed to elucidate the behaviour of each algorithm, produced some surprising results. We further dissect the performance of the scaffolders using real and simulated sequencing data derived from the genomes of Staphylococcus aureus, Rhodobacter sphaeroides, Plasmodium falciparum and Homo sapiens. The results from simulated data are of high quality, with several of the tools producing perfect output. However, at least 10% of joins remains unidentified when using real data. Conclusions The scaffolders vary in their usability, speed and number of correct and missed joins made between contigs. Results from real data highlight opportunities for further improvements of the tools. Overall, SGA, SOPRA and SSPACE generally outperform the other tools on our datasets. However, the quality of the results is highly dependent on the read mapper and genome complexity.
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140
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Draft Genome Sequence of Highly Nematicidal Bacillus thuringiensis DB27. GENOME ANNOUNCEMENTS 2014; 2:2/1/e00101-14. [PMID: 24558243 PMCID: PMC3931364 DOI: 10.1128/genomea.00101-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we report the genome sequence of nematicidal Bacillus thuringiensis DB27, which provides first insights into the genetic determinants of its pathogenicity to nematodes. The genome consists of a 5.7-Mb chromosome and seven plasmids, three of which contain genes encoding nematicidal proteins.
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141
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Aw PPK, de Sessions PF, Wilm A, Hoang LT, Nagarajan N, Sessions OM, Hibberd ML. Next-generation whole genome sequencing of dengue virus. Methods Mol Biol 2014; 1138:175-95. [PMID: 24696338 DOI: 10.1007/978-1-4939-0348-1_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA viruses are notorious for their ability to quickly adapt to selective pressure from the host immune system and/or antivirals. This adaptability is likely due to the error-prone characteristics of their RNA-dependent, RNA polymerase [1, 2]. Dengue virus, a member of the Flaviviridae family of positive-strand RNA viruses, is also known to share these error-prone characteristics [3]. Utilizing high-throughput, massively parallel sequencing methodologies, or next-generation sequencing (NGS), we can now accurately quantify these populations of viruses and track the changes to these populations over the course of a single infection. The aim of this chapter is twofold: to describe the methodologies required for sample preparation prior to sequencing and to describe the bioinformatics analyses required for the resulting data.
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142
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Kulohoma BW, Gray K, Kamng'ona A, Cornick J, Bentley SD, Heyderman RS, Everett DB. Piliation of invasive Streptococcus pneumoniae isolates in the era before pneumococcal conjugate vaccine introduction in Malawi. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:1729-35. [PMID: 24027261 PMCID: PMC3837777 DOI: 10.1128/cvi.00403-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/30/2013] [Indexed: 12/25/2022]
Abstract
The pneumococcal pilus has been shown to be an important determinant of adhesion and virulence in mouse models of colonization, pneumonia, and bacteremia. A pilus is capable of inducing protective immunity, supporting its inclusion in next-generation pneumococcal protein vaccine formulations. Whether this vaccine target is common among pneumococci in sub-Saharan Africa is uncertain. To define the prevalence and genetic diversity of type I and II pili among invasive pneumococci in Malawi prior to the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) into routine childhood immunization, we examined 188 Streptococcus pneumoniae isolates collected between 2002 and 2008 (17% serotype 1). In this region of high disease burden, we found a low frequency of invasive piliated pneumococci (14%) and pilus gene sequence diversity similar to that seen previously in multiple global pneumococcal lineages. All common serotypes with pilus were covered by PCV13 and so we predict that pilus prevalence will be reduced in the Malawian pneumococcal population after PCV13 introduction.
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Affiliation(s)
- Benard W. Kulohoma
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Liverpool, Institute of Infection and Global Health, Liverpool, United Kingdom
| | | | - Arox Kamng'ona
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Liverpool, Institute of Infection and Global Health, Liverpool, United Kingdom
- University of Malawi, Blantyre, Malawi
| | - Jennifer Cornick
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Liverpool, Institute of Infection and Global Health, Liverpool, United Kingdom
| | - Stephen D. Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Robert S. Heyderman
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Dean B. Everett
- The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Liverpool, Institute of Infection and Global Health, Liverpool, United Kingdom
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143
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Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, Browall S, Zemlickova H, Parkhill J, Normark S, Henriques-Normark B, Hinds J, Mitchell TJ, Bentley SD. Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet 2013; 9:e1003868. [PMID: 24130509 PMCID: PMC3794909 DOI: 10.1371/journal.pgen.1003868] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/24/2013] [Indexed: 01/12/2023] Open
Abstract
Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex's entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that up-regulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype.
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Affiliation(s)
- Nicholas J. Croucher
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (NJC); (TJM)
| | - Andrea M. Mitchell
- Institute of Microbiology and Infection and School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Katherine A. Gould
- Bacterial Microarray Group, Division of Clinical Sciences, St. George's Hospital, University of London, London, United Kingdom
| | - Donald Inverarity
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Lars Barquist
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Theresa Feltwell
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Maria C. Fookes
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Simon R. Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Janina Dordel
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Susannah J. Salter
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah Browall
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Dept. of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Staffan Normark
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Dept. of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Dept. of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Jason Hinds
- Bacterial Microarray Group, Division of Clinical Sciences, St. George's Hospital, University of London, London, United Kingdom
| | - Tim J. Mitchell
- Institute of Microbiology and Infection and School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (NJC); (TJM)
| | - Stephen D. Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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144
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Peña-Montenegro TD, Dussán J. Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31. Stand Genomic Sci 2013; 9:42-56. [PMID: 24501644 PMCID: PMC3910547 DOI: 10.4056/sigs.4227894] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lysinibacillus sphaericus strain OT4b.31 is a native Colombian strain having no larvicidal activity against Culex quinquefasciatus and is widely applied in the bioremediation of heavy-metal polluted environments. Strain OT4b.31 was placed between DNA homology groups III and IV. By gap-filling and alignment steps, we propose a 4,096,672 bp chromosomal scaffold. The whole genome (consisting of 4,856,302 bp long, 94 contigs and 4,846 predicted protein-coding sequences) revealed differences in comparison to the L. sphaericus C3-41 genome, such as syntenial relationships, prophages and putative mosquitocidal toxins. Sphaericolysin B354, the coleopteran toxin Sip1A and heavy metal resistance clusters from nik, ars, czc, cop, chr, czr and cad operons were identified. Lysinibacillus sphaericus OT4b.31 has applications not only in bioremediation efforts, but also in the biological control of agricultural pests.
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Affiliation(s)
| | - Jenny Dussán
- Centro de Investigaciones Microbiológicas - CIMIC, Universidad de los Andes, Bogotá, Colombia
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145
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Liu T, Tsai CH, Lee WB, Chiang JH. Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. PLoS One 2013; 8:e69503. [PMID: 23922726 PMCID: PMC3726674 DOI: 10.1371/journal.pone.0069503] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/11/2013] [Indexed: 12/01/2022] Open
Abstract
Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/.
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Affiliation(s)
- Tsunglin Liu
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Hung Tsai
- Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Bin Lee
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan, Taiwan
| | - Jung-Hsien Chiang
- Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan
- * E-mail:
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146
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Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum. EUKARYOTIC CELL 2013; 12:1171-8. [PMID: 23813392 DOI: 10.1128/ec.00028-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intraerythrocytic development of the human malaria parasite Plasmodium falciparum appears as a continuous flow through growth and proliferation. To develop a greater understanding of the critical regulatory events, we utilized piggyBac insertional mutagenesis to randomly disrupt genes. Screening a collection of piggyBac mutants for slow growth, we isolated the attenuated parasite C9, which carried a single insertion disrupting the open reading frame (ORF) of PF3D7_1305500. This gene encodes a protein structurally similar to a mitogen-activated protein kinase (MAPK) phosphatase, except for two notable characteristics that alter the signature motif of the dual-specificity phosphatase domain, suggesting that it may be a low-activity phosphatase or pseudophosphatase. C9 parasites demonstrated a significantly lower growth rate with delayed entry into the S/M phase of the cell cycle, which follows the stage of maximum PF3D7_1305500 expression in intact parasites. Genetic complementation with the full-length PF3D7_1305500 rescued the wild-type phenotype of C9, validating the importance of the putative protein phosphatase PF3D7_1305500 as a regulator of pre-S-phase cell cycle progression in P. falciparum.
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147
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Abstract
Here, we describe the draft genome sequence of Burkholderia pseudomallei NCTC 13392. This isolate has been distributed as K96243, but distinct genomic differences have been identified. The genomic sequence of this isolate will provide the genomic context for previously conducted functional studies.
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148
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Ning J, Otto TD, Pfander C, Schwach F, Brochet M, Bushell E, Goulding D, Sanders M, Lefebvre PA, Pei J, Grishin NV, Vanderlaan G, Billker O, Snell WJ. Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes Dev 2013; 27:1198-215. [DOI: 10.1101/gad.212746.112] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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149
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Sahl JW, Gillece JD, Schupp JM, Waddell VG, Driebe EM, Engelthaler DM, Keim P. Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in Acinetobacter. PLoS One 2013; 8:e54287. [PMID: 23365658 PMCID: PMC3554770 DOI: 10.1371/journal.pone.0054287] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 12/10/2012] [Indexed: 01/20/2023] Open
Abstract
Acinetobacter baumannii is an emergent and global nosocomial pathogen. In addition to A. baumannii, other Acinetobacter species, especially those in the Acinetobacter calcoaceticus-baumannii (Acb) complex, have also been associated with serious human infection. Although mechanisms of attachment, persistence on abiotic surfaces, and pathogenesis in A. baumannii have been identified, the genetic mechanisms that explain the emergence of A. baumannii as the most widespread and virulent Acinetobacter species are not fully understood. Recent whole genome sequencing has provided insight into the phylogenetic structure of the genus Acinetobacter. However, a global comparison of genomic features between Acinetobacter spp. has not been described in the literature. In this study, 136 Acinetobacter genomes, including 67 sequenced in this study, were compared to identify the acquisition and loss of genes in the expansion of the Acinetobacter genus. A whole genome phylogeny confirmed that A. baumannii is a monophyletic clade and that the larger Acb complex is also a well-supported monophyletic group. The whole genome phylogeny provided the framework for a global genomic comparison based on a blast score ratio (BSR) analysis. The BSR analysis demonstrated that specific genes have been both lost and acquired in the evolution of A. baumannii. In addition, several genes associated with A. baumannii pathogenesis were found to be more conserved in the Acb complex, and especially in A. baumannii, than in other Acinetobacter genomes; until recently, a global analysis of the distribution and conservation of virulence factors across the genus was not possible. The results demonstrate that the acquisition of specific virulence factors has likely contributed to the widespread persistence and virulence of A. baumannii. The identification of novel features associated with transcriptional regulation and acquired by clades in the Acb complex presents targets for better understanding the evolution of pathogenesis and virulence in the expansion of the genus.
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Affiliation(s)
- Jason W Sahl
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
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150
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Draft genome sequence of Brevibacillus brevis strain X23, a biocontrol agent against bacterial wilt. J Bacteriol 2013; 194:6634-5. [PMID: 23144389 DOI: 10.1128/jb.01312-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brevibacillus brevis X23 is an appropriate biocontrol agent against bacterial wilt caused by Ralstonia solanacearum. We report herein the draft genome sequence (6,566,879 bp) and a circular plasmid (6,600 bp) of B. brevis X23, data which may be helpful for mining the antagonistic activity against R. solanacearum.
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