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Coke MC, Bell CA, Urwin PE. The Use of Caenorhabditis elegans as a Model for Plant-Parasitic Nematodes: What Have We Learned? ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:157-172. [PMID: 38848590 DOI: 10.1146/annurev-phyto-021622-113539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Nematoda is a diverse phylum that is estimated to contain more than a million species. More than 4,100 of these species have the ability to parasitize plants and cause agricultural losses estimated at US $173 billion annually. This has led to considerable research into their biology to minimize crop losses via control methods. At the infancy of plant-parasitic nematode molecular biology, researchers compared nematode genomes, genes, and biological processes to the model nematode species Caenorhabditis elegans, which is a free-living bacterial feeder. This well-annotated and researched model nematode assisted the molecular biology research, e.g., with genome assemblies, of plant-parasitic nematodes. However, as research into these plant parasites progressed, the necessity of relying on the free-living relative as a reference has reduced. This is partly driven by revealing the considerable divergence between the two types of nematodes both genomically and anatomically, forcing comparisons to be redundant as well as the increased quality of molecular plant nematology proposing more suitable model organisms for this clade of nematode. The major irregularity between the two types of nematodes is the unique anatomical structure and effector repertoire that plant nematodes utilize to establish parasitism, which C. elegans lacks, therefore reducing its value as a heterologous system to investigate parasitic processes. Despite this, C. elegans remains useful for investigating conserved genes via its utility as an expression system because of the current inability to transform plant-parasitic nematodes. Unfortunately, owing to the expertise that this requires, it is not a common and/or accessible tool. Furthermore, we believe that the application of C. elegans as an expression system for plant nematodes will be redundant once tools are established for stable reverse-genetics in these plant parasites. This will remove the restraints on molecular plant nematology and allow it to excel on par with the capabilities of C. elegans research.
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Affiliation(s)
- Mirela C Coke
- School of Biology, University of Leeds, Leeds, United Kingdom;
| | | | - P E Urwin
- School of Biology, University of Leeds, Leeds, United Kingdom;
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2
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Aguirre-Carvajal K, Munteanu CR, Armijos-Jaramillo V. Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina. BIOLOGY 2024; 13:469. [PMID: 39056664 PMCID: PMC11273514 DOI: 10.3390/biology13070469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/28/2024]
Abstract
Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.
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Affiliation(s)
- Kevin Aguirre-Carvajal
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, Campus Elviña s/n, 15071 Coruña, Spain; (K.A.-C.); (C.R.M.)
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito 170513, Ecuador
| | - Cristian R. Munteanu
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, Campus Elviña s/n, 15071 Coruña, Spain; (K.A.-C.); (C.R.M.)
| | - Vinicio Armijos-Jaramillo
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito 170513, Ecuador
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170513, Ecuador
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3
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Zarlenga DS, Hoberg EP, Thompson P, Rosenthal B. Trichinella: Becoming a parasite. Vet Parasitol 2024:110220. [PMID: 38910035 DOI: 10.1016/j.vetpar.2024.110220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024]
Abstract
Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.
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Affiliation(s)
- Dante S Zarlenga
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA.
| | - Eric P Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI, USA
| | - Peter Thompson
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA
| | - Benjamin Rosenthal
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA
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4
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Lu Y, Yang S, Chen W, Xie H, Xu C. Advances in Migratory Plant Endoparasitic Nematode Effectors. Int J Mol Sci 2024; 25:6435. [PMID: 38928141 PMCID: PMC11203926 DOI: 10.3390/ijms25126435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/01/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Unlike sedentary plant-parasitic nematodes, migratory plant endoparasitic nematodes (MPENs) are unable to establish permanent feeding sites, and all developmental stages (except eggs) can invade and feed on plant tissues and can be easily overlooked because of the unspecific symptoms. They cause numerous economic losses in agriculture, forestry, and horticulture. In order to understand the pathogenetic mechanism of MPENs, here we describe research on functions and host targets focused on currently identified effectors from six MPENs, namely Radopholus similis, Pratylenchus spp., Ditylenchus destructor, Bursaphelenchus xylophilus, Aphelenchoides besseyi, and Hirschmanniella oryzae. This information will provide valuable insights into understanding MPEN effectors and for future fostering advancements in plant protection.
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Affiliation(s)
| | | | | | | | - Chunling Xu
- Research Center of Nematodes of Plant Quarantine, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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Zarlenga D, Thompson P, Mitreva M, Rosa BA, Hoberg E. Horizontal gene transfer provides insights into the deep evolutionary history and biology of Trichinella. Food Waterborne Parasitol 2022; 27:e00155. [PMID: 35542181 PMCID: PMC9079694 DOI: 10.1016/j.fawpar.2022.e00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
Evolution involves temporal changes in the characteristics of a species that are subsequently propagated or rejected through natural selection. In the case of parasites, host switching also plays a prominent role in the evolutionary process. These changes are rooted in genetic variation and gene flow where genes may be deleted, mutated (sequence), duplicated, rearranged and/or translocated and then transmitted through vertical gene transfer. However, the introduction of new genes is not driven only by Mendelian inheritance and mutation but also by the introduction of DNA from outside a lineage in the form of horizontal gene transfer between donor and recipient organisms. Once introduced and integrated into the biology of the recipient, vertical inheritance then perpetuates the newly acquired genetic factor, where further functionality may involve co-option of what has become a pre-existing physiological capacity. Upon sequencing the Trichinella spiralis (Clade I) genome, a cyanate hydratase (cyanase) gene was identified that is common among bacteria, fungi, and plants, but rarely observed among other eukaryotes. The sequence of the Trichinella cyanase gene clusters with those derived from the Kingdom Plantae in contrast to the genes found in some Clade III and IV nematodes that cluster with cyanases of bacterial origin. Phylogenetic analyses suggest that the Trichinella cyanase was acquired during the Devonian period and independently from those of other nematodes. These data may help inform us of the deep evolutionary history and ecological connectivity of early ancestors within the lineage of contemporary Trichinella. Further, in many extant organisms, cyanate detoxification has been largely superseded by energy requirements for metabolism. Thus, deciphering the function of Trichinella cyanase may provide new avenues for treatment and control.
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Affiliation(s)
- Dante Zarlenga
- U.S. Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, B1180 BARC-East Beltsville, MD 20705, USA
| | - Peter Thompson
- U.S. Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, B1180 BARC-East Beltsville, MD 20705, USA
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnel Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Bruce A. Rosa
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnel Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eric Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
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Khadka B, Chatterjee T, Gupta BP, Gupta RS. Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies. Genes (Basel) 2019; 10:E739. [PMID: 31554175 PMCID: PMC6826867 DOI: 10.3390/genes10100739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/06/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify novel molecular characteristics that are distinctive features of this phylum, or specific taxonomic groups/clades within it, thereby providing innovative means for diagnostics as well as genetic and biochemical studies. Using genome sequences for 52 available nematodes, a robust phylogenetic tree was constructed based on concatenated sequences of 17 conserved proteins. The branching of species in this tree provides important insights into the evolutionary relationships among the studied nematode species. In parallel, detailed comparative analyses on protein sequences from nematodes (Caenorhabditis) species reported here have identified 52 novel molecular signatures (or synapomorphies) consisting of conserved signature indels (CSIs) in different proteins, which are uniquely shared by the homologs from either all genome-sequenced Caenorhabditis species or a number of higher taxonomic clades of nematodes encompassing this genus. Of these molecular signatures, 39 CSIs in proteins involved in diverse functions are uniquely present in all Caenorhabditis species providing reliable means for distinguishing this group of nematodes in molecular terms. The remainder of the CSIs are specific for a number of higher clades of nematodes and offer important insights into the evolutionary relationships among these species. The structural locations of some of the nematodes-specific CSIs were also mapped in the structural models of the corresponding proteins. All of the studied CSIs are localized within the surface-exposed loops of the proteins suggesting that they may potentially be involved in mediating novel protein-protein or protein-ligand interactions, which are specific for these groups of nematodes. The identified CSIs, due to their exclusivity for the indicated groups, provide reliable means for the identification of species within these nematodes groups in molecular terms. Further, due to the predicted roles of these CSIs in cellular functions, they provide important tools for genetic and biochemical studies in Caenorhabditis and other nematodes.
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Affiliation(s)
- Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L9H 6K5, Canada.
| | - Tonuka Chatterjee
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L9H 6K5, Canada.
| | - Bhagwati P Gupta
- Department of Biology, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L9H 6K5, Canada.
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Masonbrink R, Maier TR, Muppirala U, Seetharam AS, Lord E, Juvale PS, Schmutz J, Johnson NT, Korkin D, Mitchum MG, Mimee B, den Akker SEV, Hudson M, Severin AJ, Baum TJ. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 2019; 20:119. [PMID: 30732586 PMCID: PMC6367775 DOI: 10.1186/s12864-019-5485-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. RESULTS Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123 Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7 Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons. CONCLUSIONS This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.
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Affiliation(s)
- Rick Masonbrink
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Tom R. Maier
- Department of Plant Pathology, Iowa State University, Ames, IA USA
| | - Usha Muppirala
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Arun S. Seetharam
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Etienne Lord
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Nathan T. Johnson
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA USA
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Matthew Hudson
- Department of Crop Sciences University of Illinois, Urbana, IL USA
| | | | - Thomas J. Baum
- Department of Plant Pathology, Iowa State University, Ames, IA USA
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Abstract
All natural animals and plants are holobionts, consisting of the host and microbiome, which is composed of abundant and diverse microorganisms. Health and disease of holobionts depend as much on interactions between host and microbiome and within the microbiome, as on interactions between organs and body parts of the host. Recent evidence indicates that a significant fraction of the microbiome is transferred by a variety of mechanisms from parent to offspring for many generations. Genetic variation in holobionts can occur in the microbiome as well as in the host genome, and it occurs more rapidly and by more mechanisms in genomes of microbiomes than in host genomes (e.g. via acquisition of novel microbes and horizontal gene transfer of microbial genes into host chromosomes). Evidence discussed in this review supports the concept that holobionts with their hologenomes can be considered levels of selection in evolution. Though changes in the microbiome can lead to evolution of the holobiont, it can also lead to dysbiosis and diseases (e.g. obesity, diarrhea, inflammatory bowel disease, and autism). In practice, the possibility of manipulating microbiomes offers the potential to prevent and cure diseases.
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A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria. Parasitology 2018; 146:445-452. [PMID: 30301483 DOI: 10.1017/s0031182018001701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Horizontal gene transfer (HGT) has played an important role in the evolution of nematodes. Among candidate genes, cyanase, which is typically found only in plants, bacteria and fungi, is present in more than 35 members of the Phylum Nematoda, but absent from free-living and clade V organisms. Phylogenetic analyses showed that the cyanases of clade I organisms Trichinella spp., Trichuris spp. and Soboliphyme baturini (Subclass: Dorylaimia) represent a well-supported monophyletic clade with plant cyanases. In contrast, all cyanases found within the Subclass Chromadoria which encompasses filarioids, ascaridoids and strongyloids are homologous to those of bacteria. Western blots exhibited typical multimeric forms of the native molecule in protein extracts of Trichinella spiralis muscle larvae, where immunohistochemical staining localized the protein to the worm hypodermis and underlying muscle. Recombinant Trichinella cyanase was bioactive where gene transcription profiles support functional activity in vivo. Results suggest that: (1) independent HGT in parasitic nematodes originated from different Kingdoms; (2) cyanase acquired an active role in the biology of extant Trichinella; (3) acquisition occurred more than 400 million years ago (MYA), prior to the divergence of the Trichinellida and Dioctophymatida, and (4) early, free-living ancestors of the genus Trichinella had an association with terrestrial plants.
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Rosenberg E, Zilber-Rosenberg I. The hologenome concept of evolution after 10 years. MICROBIOME 2018; 6:78. [PMID: 29695294 PMCID: PMC5922317 DOI: 10.1186/s40168-018-0457-9] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/05/2018] [Indexed: 05/11/2023]
Abstract
The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution. The hologenome is comprised of two complimentary parts: host and microbiome genomes. Changes in either genome can result in variations that can be selected for or against. The host genome is highly conserved, and genetic changes within it occur slowly, whereas the microbiome genome is dynamic and can change rapidly in response to the environment by increasing or reducing particular microbes, by acquisition of novel microbes, by horizontal gene transfer, and by mutation. Recent experiments showing that microbiota can play an initial role in speciation have been suggested as an additional mode of enhancing evolution. Some of the genetic variations can be transferred to offspring by a variety of mechanisms. Strain-specific DNA analysis has shown that at least some of the microbiota can be maintained across hundreds of thousands of host generations, implying the existence of a microbial core. We argue that rapid changes in the microbiome genome could allow holobionts to adapt and survive under changing environmental conditions thus providing the time necessary for the host genome to adapt and evolve. As Darwin wrote, "It is not the strongest of the species that survives but the most adaptable".
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Affiliation(s)
- Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Ilana Zilber-Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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12
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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13
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Dunning Hotopp JC, Slatko BE, Foster JM. Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers. Sci Rep 2017; 7:857. [PMID: 28405008 PMCID: PMC5429809 DOI: 10.1038/s41598-017-00814-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/20/2017] [Indexed: 11/11/2022] Open
Abstract
Lateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16). Using a sequencing depth threshold of two or three standard deviations above the mean, 96.9% or 96.7% of positions, respectively, are predicted in the same manner between the two datasets, with 24.7% or 42.5% of the known 49.0 kbp of LGT sequence predicted correctly, respectively. Prior qPCR results for nuwts showed similar correlations for both datasets supporting our conclusion that oligonucleotide-based capture methods can be used to obtain sequences from Wolbachia-host LGT. However, at least 121 positions had a minority of the reads supporting the endosymbiont reference base call using the capture data, illustrating that sequence reads from endosymbiont-host LGTs can confound endosymbiont genome projects, erroneously altering the called consensus genome, a problem that is irrespective to the sequencing technology or platform.
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Affiliation(s)
- Julie C Dunning Hotopp
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, United States.
| | - Barton E Slatko
- Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States
| | - Jeremy M Foster
- Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States
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14
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Thomas L, Ram H, Singh VP. Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya. J Comput Biol 2017; 24:1029-1042. [PMID: 28177649 DOI: 10.1089/cmb.2016.0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities. Evolutionary relatedness was also observed in phylogenetic trees among a number of cellulase sequences of diverse taxa. In cellulases, propensity for alanine, glycine, leucine, serine, and threonine was high, but low for cysteine, histidine, and methionine. Catalytic aspartic acid had a higher propensity than glutamic acid, and both were involved in regular expression patterns. Characteristic group and multigroup-specific conserved signature indels located in the catalytic domains of cellulases were observed that further clarified evolutionary relationships. These indels can be distinctive molecular tools for understanding phylogeny and identification of unknown cellulolytic species of common evolutionary descent in different environments.
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Affiliation(s)
- Lebin Thomas
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
| | - Hari Ram
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
| | - Ved Pal Singh
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
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Sun B, Li T, Xiao J, Liu L, Zhang P, Murphy RW, He S, Huang D. Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis. Front Microbiol 2016; 7:1360. [PMID: 27630622 PMCID: PMC5005798 DOI: 10.3389/fmicb.2016.01360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/17/2016] [Indexed: 01/30/2023] Open
Abstract
Amphibian populations are experiencing catastrophic declines driven by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although horizontal gene transfer (HGT) facilitates the evolution and adaptation in many fungi by conferring novel function genes to the recipient fungi, inter-kingdom HGT in Bd remains largely unexplored. In this study, our investigation detects 19 bacterial genes transferred to Bd, including metallo-beta-lactamase and arsenate reductase that play important roles in the resistance to antibiotics and arsenates. Moreover, three probable HGT gene families in Bd are from plants and one gene family coding the ankyrin repeat-containing protein appears to come from oomycetes. The observed multi-copy gene families associated with HGT are probably due to the independent transfer events or gene duplications. Five HGT genes with extracellular locations may relate to infection, and some other genes may participate in a variety of metabolic pathways, and in doing so add important metabolic traits to the recipient. The evolutionary analysis indicates that all the transferred genes evolved under purifying selection, suggesting that their functions in Bd are similar to those of the donors. Collectively, our results indicate that HGT from diverse donors may be an important evolutionary driver of Bd, and improve its adaptations for infecting and colonizing host amphibians.
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Affiliation(s)
- Baofa Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Tong Li
- Key Laboratory of Crop Pests Control of Henan Province, Institute of Plant Protection, Henan Academy of Agricultural Sciences Zhengzhou, China
| | - Jinhua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Li Liu
- Network & Information Center, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Peng Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum Toronto, ON, Canada
| | - Shunmin He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences Beijing, China
| | - Dawei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijing, China; Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
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Trichinella spiralis: Adaptation and parasitism. Vet Parasitol 2016; 231:8-21. [PMID: 27425574 DOI: 10.1016/j.vetpar.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 06/29/2016] [Accepted: 07/02/2016] [Indexed: 11/21/2022]
Abstract
Publication of the genome from the clade I organism, Trichinella spiralis, has provided us an avenue to address more holistic problems in parasitology; namely the processes of adaptation and the evolution of parasitism. Parasitism among nematodes has evolved in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and adaptation in nematodes; however, data is now coming available to investigate adaptation, host switching and parasitism at the genomic level. Herein we compare proteomic data from the clade I parasite, Trichinella spiralis with data from Brugia malayi (clade III), Meloidogyne hapla and Meloidogyne incognita (clade IV), and free-living nematodes belonging to the genera Caenorhabditis and Pristionchus (clade V). We explore changes in protein family birth/death and expansion/reduction over the course of metazoan evolution using Homo sapiens, Drosophila melanogaster and Saccharomyces cerevisiae as outgroups for the phylum Nematoda. We further examine relationships between these changes and the ability and/or result of nematodes adapting to their environments. Data are consistent with gene loss occurring in conjunction with nematode specialization resulting from parasitic worms acclimating to well-defined, environmental niches. We observed evidence for independent, lateral gene transfer events involving conserved genes that may have played a role in the evolution of nematode parasitism. In general, parasitic nematodes gained proteins through duplication and lateral gene transfer, and lost proteins through random mutation and deletions. Data suggest independent acquisition rather than ancestral inheritance among the Nematoda followed by selective gene loss over evolutionary time. Data also show that parasitism and adaptation affected a broad range of proteins, especially those involved in sensory perception, metabolism, and transcription/translation. New protein gains with functions related to regulating transcription and translation, and protein family expansions with functions related to morphology and body development have occurred in association with parasitism. Further gains occurred as a result of lateral gene transfer and in particular, with the cyanase protein family In contrast, reductions and/or losses have occurred in protein families with functions related to metabolic process and signal transduction. Taking advantage of the independent occurrences of parasitism in nematodes, which enabled us to distinguish changes associated with parasitism from species specific niche adaptation, our study provides valuable insights into nematode parasitism at a proteome level using T. spiralis as a benchmark for early adaptation to or acquisition of parasitism.
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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Abstract
The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.
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Basyoni MMA, Rizk EMA. Nematodes ultrastructure: complex systems and processes. J Parasit Dis 2016; 40:1130-1140. [PMID: 27876901 DOI: 10.1007/s12639-015-0707-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/01/2015] [Indexed: 10/22/2022] Open
Abstract
Nematode worms are among the most ubiquitous organisms on earth. They include free-living forms as well as parasites of plants, insects, humans and other animals. Recently, there has been an explosion of interest in nematode biology, including the area of nematode ultrastructure. Nematodes are round with a body cavity. They have one way guts with a mouth at one end and an anus at the other. They have a pseudocoelom that is lined on one side with mesoderm and on the other side with endoderm. It appears that the cuticle is a very complex and evolutionarily plastic feature with important functions involving protection, body movement and maintaining shape. They only have longitudinal muscles so; they seem to thrash back and forth. While nematodes have digestive, reproductive, nervous and excretory systems, they do not have discrete circulatory or respiratory systems. Nematodes use chemosensory and mechanosensory neurons embedded in the cuticle to orient and respond to a wide range of environmental stimuli. Adults are made up of roughly 1000 somatic cells and hundreds of those cells are typically associated with the reproductive systems. Nematodes ultrastructure seeks to provide studies which enable their use as models for diverse biological processes including; human diseases, immunity, host-parasitic interactions and the expression of phylogenomics. The latter has, however, not been brought into a single inclusive entity. Consequently, in the current review we tried to provide a comprehensive approach to the current knowledge available for nematodes ultrastructures.
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Affiliation(s)
- Maha M A Basyoni
- Department of Medical Parasitology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Enas M A Rizk
- Department of Medical Parasitology, Faculty of Medicine, Cairo University, Cairo, Egypt
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Abstract
Nematodes are abundant and diverse, and include many parasitic species. Molecular phylogenetic analyses have shown that parasitism of plants and animals has arisen at least 15 times independently. Extant nematode species also display lifestyles that are proposed to be on the evolutionary trajectory to parasitism. Recent advances have permitted the determination of the genomes and transcriptomes of many nematode species. These new data can be used to further resolve the phylogeny of Nematoda, and identify possible genetic patterns associated with parasitism. Plant-parasitic nematode genomes show evidence of horizontal gene transfer from other members of the rhizosphere, and these genes play important roles in the parasite-host interface. Similar horizontal transfer is not evident in animal parasitic groups. Many nematodes have bacterial symbionts that can be essential for survival. Horizontal transfer from symbionts to the nematode is also common, but its biological importance is unclear. Over 100 nematode species are currently targeted for sequencing, and these data will yield important insights into the biology and evolutionary history of parasitism. It is important that these new technologies are also applied to free-living taxa, so that the pre-parasitic ground state can be inferred, and the novelties associated with parasitism isolated.
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Bauters L, Haegeman A, Kyndt T, Gheysen G. Analysis of the transcriptome of Hirschmanniella oryzae to explore potential survival strategies and host-nematode interactions. MOLECULAR PLANT PATHOLOGY 2014; 15:352-63. [PMID: 24279397 PMCID: PMC6638887 DOI: 10.1111/mpp.12098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The rice root nematode Hirschmanniella oryzae is the most abundant plant-parasitic nematode in flooded rice fields and is distributed world-wide. Although it is economically less important than sedentary nematodes, it can cause severe yield reductions and economic losses in specific environmental conditions. No transcriptome data for this genus were available until now. We have performed 454 sequencing on a mixed life stages population to gain an insight into nematode-plant interactions and nematode survival strategies. The results of two assembly strategies were combined to reduce the redundancy of the data, generating a final dataset of 21 360 contigs. The data were screened for putative plant cell wall-modifying proteins, which facilitate nematode migration through host roots. A β-mannanase, previously not reported in nematodes, was detected in the dataset. The data were screened for putative effector proteins that may alter the host defence mechanism. Two enzymes, chorismate mutase and isochorismatase, thought to be involved in the salicyclic acid pathway, were identified. Experimental treatments of H. oryzae with artificial seawater showed that late embryogenesis abundant (LEA) proteins and SXP/RAL-2 are induced, suggesting that these proteins are involved in the process of anhydrobiosis. The newly generated data can highlight potential differences between sedentary and migratory nematodes, and will be useful in the further study of host-nematode interactions and the developmental biology of this nematode.
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Affiliation(s)
- Lander Bauters
- Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
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Abstract
The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology; University of Chicago; Chicago, IL USA
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Mitchum MG, Hussey RS, Baum TJ, Wang X, Elling AA, Wubben M, Davis EL. Nematode effector proteins: an emerging paradigm of parasitism. THE NEW PHYTOLOGIST 2013; 199:879-894. [PMID: 23691972 DOI: 10.1111/nph.12323] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/05/2013] [Indexed: 05/18/2023]
Abstract
Phytonematodes use a stylet and secreted effectors to modify host cells and ingest nutrients to support their growth and development. The molecular function of nematode effectors is currently the subject of intense investigation. In this review, we summarize our current understanding of nematode effectors, with a particular focus on proteinaceous stylet-secreted effectors of sedentary endoparasitic phytonematodes, for which a wealth of information has surfaced in the past 10 yr. We provide an update on the effector repertoires of several of the most economically important genera of phytonematodes and discuss current approaches to dissecting their function. Lastly, we highlight the latest breakthroughs in effector discovery that promise to shed new light on effector diversity and function across the phylum Nematoda.
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Affiliation(s)
- Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Richard S Hussey
- Department of Plant Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Xiaohong Wang
- USDA-ARS, Robert W. Holley Center for Agriculture and Health and Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Axel A Elling
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Martin Wubben
- USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture Research Unit and Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Eric L Davis
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
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Sun BF, Xiao JH, He S, Liu L, Murphy RW, Huang DW. Multiple interkingdom horizontal gene transfers in Pyrenophora and closely related species and their contributions to phytopathogenic lifestyles. PLoS One 2013; 8:e60029. [PMID: 23555871 PMCID: PMC3612039 DOI: 10.1371/journal.pone.0060029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/20/2013] [Indexed: 12/13/2022] Open
Abstract
Many studies have reported horizontal gene transfer (HGT) events from eukaryotes, especially fungi. However, only a few investigations summarized multiple interkingdom HGTs involving important phytopathogenic species of Pyrenophora and few have investigated the genetic contributions of HGTs to fungi. We investigated HGT events in P. teres and P. tritici-repentis and discovered that both species harbored 14 HGT genes derived from bacteria and plants, including 12 HGT genes that occurred in both species. One gene coding a leucine-rich repeat protein was present in both species of Pyrenophora and it may have been transferred from a host plant. The transfer of genes from a host plant to pathogenic fungi has been reported rarely and we discovered the first evidence for this transfer in phytopathogenic Pyrenophora. Two HGTs in Pyrenophora underwent subsequent duplications. Some HGT genes had homologs in a few other fungi, indicating relatively ancient transfer events. Functional analyses indicated that half of the HGT genes encoded extracellular proteins and these may have facilitated the infection of plants by Pyrenophora via interference with plant defense-response and the degradation of plant cell walls. Some other HGT genes appeared to participate in carbohydrate metabolism. Together, these functions implied that HGTs may have led to highly efficient mechanisms of infection as well as the utilization of host carbohydrates. Evolutionary analyses indicated that HGT genes experienced amelioration, purifying selection, and accelerated evolution. These appeared to constitute adaptations to the background genome of the recipient. The discovery of multiple interkingdom HGTs in Pyrenophora, their significance to infection, and their adaptive evolution, provided valuable insights into the evolutionary significance of interkingdom HGTs from multiple donors.
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Affiliation(s)
- Bao-Fa Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jin-Hua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Da-Wei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
- * E-mail:
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Sun BF, Xiao JH, He SM, Liu L, Murphy RW, Huang DW. Multiple ancient horizontal gene transfers and duplications in lepidopteran species. INSECT MOLECULAR BIOLOGY 2013; 22:72-87. [PMID: 23211014 DOI: 10.1111/imb.12004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Eukaryotic horizontal gene transfer (HGT) events are increasingly being discovered yet few reports have summarized multiple occurrences in a wide range of species. We systematically investigated HGT events in the order Lepidoptera by employing a series of filters. Bombyx mori, Danaus plexippus and Heliconius melpomene had 13, 12 and 12 HGTs, respectively, from bacteria and fungi. These HGTs contributed a total of 64 predicted genes: 22 to B. mori, 22 to D. plexippus and 20 to H. melpomene. Several new genes were generated by post-transfer duplications. Post-transfer duplication of a suite of functional HGTs has rarely been reported in higher organisms. The distributional patterns of paralogues for certain genes differed in the three species, indicating potential independent duplication or loss events. All of these HGTs had homologues expressed in some other lepidopterans, indicating ancient transfer events. Most HGTs were involved in the metabolism of sugar and amino acids. These HGTs appeared to have experienced amelioration, purifying selection and accelerated evolution to adapt to the background genome of the recipient. The discovery of ancient, massive HGTs and duplications in lepidopterans and their adaptive evolution provides further insights into the evolutionary significance of the events from donors to multicellular host recipients.
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Affiliation(s)
- B F Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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26
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Wang Z, Zarlenga D, Martin J, Abubucker S, Mitreva M. Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. BMC Evol Biol 2012; 12:138. [PMID: 22862991 PMCID: PMC3483195 DOI: 10.1186/1471-2148-12-138] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 07/19/2012] [Indexed: 11/18/2022] Open
Abstract
Background Proteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new proteins and protein families. Processes that affect proteome evolution drive species diversity and adaptation. Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species. Results In studying members of the three major metazoan groups, the vertebrates, arthropods, and nematodes, we found that the number of protein families increased at the majority of lineages over the course of metazoan evolution where the magnitude of these increases was greatest at the lineages leading to mammals. In contrast, the number of protein domains decreased at most lineages and at all terminal lineages. This resulted in a weak correlation between protein family birth and domain birth; however, the correlation between domain birth and domain member duplication was quite strong. These data suggest that domain birth and protein family birth occur via different mechanisms, and that domain shuffling plays a role in the formation of protein families. The ratio of protein family birth to protein domain birth (domain shuffling index) suggests that shuffling had a more demonstrable effect on protein families in nematodes and arthropods than in vertebrates. Through the contrast of high and low domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, we propose a link between protein redundancy and evolutionary changes controlled by domain shuffling; however, the speed of adaptation among the different lineages was relatively invariant. Evaluating the functions of protein families that appeared or disappeared at the last common ancestors (LCAs) of the three metazoan clades supports a correlation with organism adaptation. Furthermore, bursts of new protein families and domains in the LCAs of metazoans and vertebrates are consistent with whole genome duplications. Conclusion Metazoan speciation and adaptation were explored by birth/death and duplication/deletion events among protein families and domains. Our results provide insights into protein evolution and its bearing on metazoan evolution.
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Affiliation(s)
- Zhengyuan Wang
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
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Murfin KE, Dillman AR, Foster JM, Bulgheresi S, Slatko BE, Sternberg PW, Goodrich-Blair H. Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age. THE BIOLOGICAL BULLETIN 2012; 223:85-102. [PMID: 22983035 PMCID: PMC3508788 DOI: 10.1086/bblv223n1p85] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.
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Affiliation(s)
- Kristen E. Murfin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Adler R. Dillman
- HHMI and Division of Biology, California Institute of Technology, 156-29, Pasadena, CA 91125, USA
| | - Jeremy M. Foster
- Parasitology Division, New England Biolabs, Inc., 240 County Rd, Ipswich, MA 01938, USA
| | - Silvia Bulgheresi
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Barton E. Slatko
- Parasitology Division, New England Biolabs, Inc., 240 County Rd, Ipswich, MA 01938, USA
| | - Paul W. Sternberg
- HHMI and Division of Biology, California Institute of Technology, 156-29, Pasadena, CA 91125, USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Corresponding author Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, , phone: 608-265-4537, fax: 608-262-9865
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The role of reticulate evolution in creating innovation and complexity. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:418964. [PMID: 22844638 PMCID: PMC3403396 DOI: 10.1155/2012/418964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 12/31/2022]
Abstract
Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.
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Mitchum MG, Wang X, Wang J, Davis EL. Role of nematode peptides and other small molecules in plant parasitism. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:175-95. [PMID: 22578179 DOI: 10.1146/annurev-phyto-081211-173008] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Molecular, genetic, and biochemical studies are demonstrating an increasingly important role of peptide signaling in nematode parasitism of plants. To date, the majority of nematode-secreted peptides identified share similarity with plant CLAVATA3/ESR (CLE) peptides, but bioinformatics analyses of nematode genomes have revealed sequences homologous to other classes of plant peptide hormones that may be utilized by these pests. Extracellular host receptors for secreted nematode peptides are beginning to be identified and their roles in parasitism elucidated. Here, we outline recent advances from studies of biologically active nematode-secreted peptides that function as molecular mimics of endogenous plant peptides to promote parasitism. Several strategies are being used to exploit this information to provide new targets for engineering nematode resistance.
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Affiliation(s)
- Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
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Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP. A rooted net of life. Biol Direct 2011; 6:45. [PMID: 21936906 PMCID: PMC3189188 DOI: 10.1186/1745-6150-6-45] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 09/21/2011] [Indexed: 01/29/2023] Open
Abstract
Abstract Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan-genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where incongruities between topologies exist. Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages. Reviewers W. Ford Doolittle, Eric Bapteste and Robert Beiko.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA.
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Rödelsperger C, Sommer RJ. Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects. BMC Evol Biol 2011; 11:239. [PMID: 21843315 PMCID: PMC3175473 DOI: 10.1186/1471-2148-11-239] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 08/15/2011] [Indexed: 11/10/2022] Open
Abstract
Background The recent sequencing of nematode genomes has laid the basis for comparative genomics approaches to study the impact of horizontal gene transfer (HGT) on the adaptation to new environments and the evolution of parasitism. In the beetle associated nematode Pristionchus pacificus HGT events were found to involve cellulase genes of microbial origin and Diapausin genes that are known from beetles, but not from other nematodes. The insect-to-nematode horizontal transfer is of special interest given that P. pacificus shows a tight association with insects. Results In this study we utilized the observation that horizontally transferred genes often exhibit codon usage patterns more similar to that of the donor than that of the acceptor genome. We introduced GC-normalized relative codon frequencies as a measure to detect characteristic features of P. pacificus orphan genes that show no homology to other nematode genes. We found that atypical codon usage is particularly prevalent in P. pacificus orphans. By comparing codon usage profiles of 71 species, we detected the most significant enrichment in insect-like codon usage profiles. In cross-species comparisons, we identified 509 HGT candidates that show a significantly higher similarity to insect-like profiles than genes with nematode homologs. The most abundant gene family among these genes are non-LTR retrotransposons. Speculating that retrotransposons might have served as carriers of foreign genetic material, we found a significant local clustering tendency of orphan genes in the vicinity of retrotransposons. Conclusions Our study combined codon usage bias, phylogenetic analysis, and genomic colocalization into a general picture of the computational archaeology of the P. pacificus genome and suggests that a substantial fraction of the gene repertoire is of insect origin. We propose that the Pristionchus-beetle association has facilitated HGT and discuss potential vectors of these events.
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Affiliation(s)
- Christian Rödelsperger
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
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32
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Haegeman A, Jones JT, Danchin EGJ. Horizontal gene transfer in nematodes: a catalyst for plant parasitism? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:879-87. [PMID: 21539433 DOI: 10.1094/mpmi-03-11-0055] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The origin of plant parasitism within the phylum Nematoda is intriguing. The ability to parasitize plants has originated independently at least three times during nematode evolution and, as more molecular data has emerged, it has become clear that multiple instances of horizontal gene transfer (HGT) from bacteria and fungi have played a crucial role in the nematode's adaptation to this new lifestyle. The first reported HGT cases in plant-parasitic nematodes were genes encoding plant cell wall-degrading enzymes. Other putative examples of HGT were subsequently described, including genes that may be involved in the modulation of the plant's defense system, the establishment of a nematode feeding site, and the synthesis or processing of nutrients. Although, in many cases, it is difficult to pinpoint the donor organism, candidate donors are usually soil dwelling and are either plant-pathogenic or plant-associated microorganisms, hence occupying the same ecological niche as the nematodes. The exact mechanisms of transfer are unknown, although close contacts with donor microorganisms, such as symbiotic or trophic interactions, are a possibility. The widespread occurrence of horizontally transferred genes in evolutionarily independent plant-parasitic nematode lineages suggests that HGT may be a prerequisite for successful plant parasitism in nematodes.
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Affiliation(s)
- Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
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Sommer RJ, Streit A. Comparative genetics and genomics of nematodes: genome structure, development, and lifestyle. Annu Rev Genet 2011; 45:1-20. [PMID: 21721943 DOI: 10.1146/annurev-genet-110410-132417] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nematodes are found in virtually all habitats on earth. Many of them are parasites of plants and animals, including humans. The free-living nematode, Caenorhabditis elegans, is one of the genetically best-studied model organisms and was the first metazoan whose genome was fully sequenced. In recent years, the draft genome sequences of another six nematodes representing four of the five major clades of nematodes were published. Compared to mammalian genomes, all these genomes are very small. Nevertheless, they contain almost the same number of genes as the human genome. Nematodes are therefore a very attractive system for comparative genetic and genomic studies, with C. elegans as an excellent baseline. Here, we review the efforts that were made to extend genetic analysis to nematodes other than C. elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT).
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Affiliation(s)
- Ralf J Sommer
- Max Planck Institute for Developmental Biology, D-72076 T?bingen, Germany.
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Elsworth B, Wasmuth J, Blaxter M. NEMBASE4: the nematode transcriptome resource. Int J Parasitol 2011; 41:881-94. [PMID: 21550347 DOI: 10.1016/j.ijpara.2011.03.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 11/28/2022]
Abstract
Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. To demonstrate the utility of NEMBASE4, we have used the database to examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets.
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Affiliation(s)
- Benjamin Elsworth
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK
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Mayer WE, Schuster LN, Bartelmes G, Dieterich C, Sommer RJ. Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover. BMC Evol Biol 2011; 11:13. [PMID: 21232122 PMCID: PMC3032686 DOI: 10.1186/1471-2148-11-13] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 01/13/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as Brugia, Meloidogyne, Bursaphelenchus and Pristionchus indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes. RESULTS We examine the transfer of cellulase genes to the free-living and beetle-associated nematode Pristionchus pacificus, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven Pristionchus species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of Pristionchus pacificus suggests these high evolutionary dynamics to be associated with copy number variations and positive selection. CONCLUSION We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.
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Affiliation(s)
- Werner E Mayer
- Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, 72076 Tübingen, Germany
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36
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Gladyshev EA, Arkhipova IR. Genome structure of bdelloid rotifers: shaped by asexuality or desiccation? J Hered 2010; 101 Suppl 1:S85-93. [PMID: 20421328 DOI: 10.1093/jhered/esq008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bdelloid rotifers are microscopic invertebrate animals best known for their ancient asexuality and the ability to survive desiccation at any life stage. Both factors are expected to have a profound influence on their genome structure. Recent molecular studies demonstrated that, although the gene-rich regions of bdelloid genomes are organized as colinear pairs of closely related sequences and depleted in repetitive DNA, subtelomeric regions harbor diverse transposable elements and horizontally acquired genes of foreign origin. Although asexuality is expected to result in depletion of deleterious transposons, only desiccation appears to have the power to produce all the uncovered genomic peculiarities. Repair of desiccation-induced DNA damage would require the presence of a homologous template, maintaining colinear pairs in gene-rich regions and selecting against insertion of repetitive DNA that might cause chromosomal rearrangements. Desiccation may also induce a transient state of competence in recovering animals, allowing them to acquire environmental DNA. Even if bdelloids engage in rare or obscure forms of sexual reproduction, all these features could still be present. The relative contribution of asexuality and desiccation to genome organization may be clarified by analyzing whole-genome sequences and comparing foreign gene and transposon content in species which lost the ability to survive desiccation.
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Affiliation(s)
- Eugene A Gladyshev
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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37
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McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. PLoS One 2010; 5:e11029. [PMID: 20543958 PMCID: PMC2882956 DOI: 10.1371/journal.pone.0011029] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 05/19/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Wolbachia are among the most abundant symbiotic microbes on earth; they are present in about 66% of all insect species, some spiders, mites and crustaceans, and most filarial nematode species. Infected filarial nematodes, including many pathogens of medical and veterinary importance, depend on Wolbachia for proper development and survival. The mechanisms behind this interdependence are not understood. Interestingly, a minority of filarial species examined to date are naturally Wolbachia-free. METHODOLOGY/PRINCIPAL FINDINGS We used 454 pyrosequencing to survey the genomes of two distantly related Wolbachia-free filarial species, Acanthocheilonema viteae and Onchocerca flexuosa. This screen identified 49 Wolbachia-like DNA sequences in A. viteae and 114 in O. flexuosa. qRT-PCR reactions detected expression of 30 Wolbachia-like sequences in A. viteae and 56 in O. flexuosa. Approximately half of these appear to be transcribed from pseudogenes. In situ hybridization showed that two of these pseudogene transcripts were specifically expressed in developing embryos and testes of both species. CONCLUSIONS/SIGNIFICANCE These results strongly suggest that the last common ancestor of extant filarial nematodes was infected with Wolbachia and that this former endosymbiont contributed to their genome evolution. Horizontally transferred Wolbachia DNA may explain the ability of some filarial species to live and reproduce without the endosymbiont while other species cannot.
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Affiliation(s)
- Samantha N. McNulty
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeremy M. Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Makedonka Mitreva
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - John Martin
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bo Wu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Paul J. Davis
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Sanjay Kumar
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Barton E. Slatko
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Gary J. Weil
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Transcript analysis of parasitic females of the sedentary semi-endoparasitic nematode Rotylenchulus reniformis. Mol Biochem Parasitol 2010; 172:31-40. [PMID: 20346373 DOI: 10.1016/j.molbiopara.2010.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/12/2010] [Accepted: 03/15/2010] [Indexed: 10/19/2022]
Abstract
Rotylenchulus reniformis, the reniform nematode, is a sedentary semi-endoparasitic nematode capable of infecting >300 plant species, including a large number of crops such as cotton, soybean, and pineapple. In contrast to other economically important plant-parasitic nematodes, molecular genetic data regarding the R. reniformis transcriptome is virtually nonexistant. Herein, we present a survey of R. reniformis ESTs that were sequenced from a sedentary parasitic female cDNA library. Cluster analysis of 2004 high quality ESTs produced 123 contigs and 508 singletons for a total of 631 R. reniformis unigenes. BLASTX analyses revealed that 39% of all unigenes showed similarity to known proteins (E<or=1.0e-04). R. reniformis genes homologous to known parasitism genes were identified and included beta-1,4-endoglucanase, fatty acid- and retinol-binding proteins, and an esophageal gland cell-specific gene from Heterodera glycines. Furthermore, a putative ortholog of an enzyme involved in thiamin biosynthesis, thought to exist solely in prokaryotes, fungi, and plants, was identified. Lastly, 114 R. reniformis unigenes orthologous to RNAi-lethal Caenorhabditis elegans genes were discovered. The work described here offers a glimpse into the transcriptome of a sedentary semi-endoparasitic nematode which (i) provides the transcript sequence data necessary for investigating engineered resistance against R. reniformis and (ii) hints at the existance of a thiamin biosynthesis pathway in an animal.
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Shapiro JA. Mobile DNA and evolution in the 21st century. Mob DNA 2010; 1:4. [PMID: 20226073 PMCID: PMC2836002 DOI: 10.1186/1759-8753-1-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 01/25/2010] [Indexed: 01/05/2023] Open
Abstract
Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science W123B, 929 E 57th Street, Chicago, IL 60637, USA.
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Paz-Y-Miño C G, Espinosa A. Integrating horizontal gene transfer and common descent to depict evolution and contrast it with "common design". J Eukaryot Microbiol 2009; 57:11-8. [PMID: 20021546 DOI: 10.1111/j.1550-7408.2009.00458.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life's diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD(+) as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking "common design" (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded.
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Affiliation(s)
- Guillermo Paz-Y-Miño C
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, USA
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Abstract
More than two billion people (one-third of humanity) are infected with parasitic roundworms or flatworms, collectively known as helminth parasites. These infections cause diseases that are responsible for enormous levels of morbidity and mortality, delays in the physical development of children, loss of productivity among the workforce, and maintenance of poverty. Genomes of the major helminth species that affect humans, and many others of agricultural and veterinary significance, are now the subject of intensive genome sequencing and annotation. Draft genome sequences of the filarial worm Brugia malayi and two of the human schistosomes, Schistosoma japonicum and S. mansoni, are now available, among others. These genome data will provide the basis for a comprehensive understanding of the molecular mechanisms involved in helminth nutrition and metabolism, host-dependent development and maturation, immune evasion, and evolution. They are likely also to predict new potential vaccine candidates and drug targets. In this review, we present an overview of these efforts and emphasize the potential impact and importance of these new findings.
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Affiliation(s)
- Paul J Brindley
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University Medical Center, Washington, D. C., USA.
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Rosso MN, Jones JT, Abad P. RNAi and functional genomics in plant parasitic nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2009; 47:207-32. [PMID: 19400649 DOI: 10.1146/annurev.phyto.112408.132605] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant nematology is currently undergoing a revolution with the availability of the first genome sequences as well as comprehensive expressed sequence tag (EST) libraries from a range of nematode species. Several strategies are being used to exploit this wealth of information. Comparative genomics is being used to explore the acquisition of novel genes associated with parasitic lifestyles. Functional analyses of nematode genes are moving toward larger scale studies including global transcriptome profiling. RNA interference (RNAi) has been shown to reduce expression of a range of plant parasitic nematode genes and is a powerful tool for functional analysis of nematode genes. RNAi-mediated suppression of genes essential for nematode development, survival, or parasitism is revealing new targets for nematode control. Plant nematology in the genomics era is now facing the challenge to develop RNAi screens adequate for high-throughput functional analyses.
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Affiliation(s)
- M N Rosso
- INRA, UNSA, UMR 1301, CNRS, UMR 6243, Interactions Biotiques et Santé Végétale, F-06903 Sophia Antipolis, France.
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