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Wang Z, Garcia F, Ehlers RU, Molina C. Dauer juvenile recovery transcriptome of two contrasting EMS mutants of the entomopathogenic nematode Heterorhabditis bacteriophora. World J Microbiol Biotechnol 2024; 40:128. [PMID: 38451353 DOI: 10.1007/s11274-024-03902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024]
Abstract
The entomopathogenic nematode Heterorhabditis bacteriophora, symbiotically associated with enterobacteria of the genus Photorhabdus, is a biological control agent against many insect pests. Dauer Juveniles (DJ) of this nematode are produced in industrial-scale bioreactors up to 100 m3 in liquid culture processes lasting approximately 11 days. A high DJ yield (> 200,000 DJ·mL-1) determines the success of the process. To start the mass production, a DJ inoculum proceeding from a previous monoxenic culture is added to pre-cultured (24 h) Photorhabdus bacteria. Within minutes after contact with the bacteria, DJ are expected to perceive signals that trigger their further development (DJ recovery) to reproductive hermaphrodites. A rapid, synchronized, and high DJ recovery is a key factor for an efficient culture process. In case of low percentage of DJ recovery, the final DJ yield is drastically reduced, and the amount of non-desired stages (males and non-fertilized females) hinders the DJ harvest. In a preliminary work, a huge DJ recovery phenotypic variability in H. bacteriophora ethyl methanesulphonate (EMS) mutants was determined. In the present study, two EMS-mutant lines (M31 and M88) with high and low recovery phenotypes were analyzed concerning their differences in gene expression during the first hours of contact with Photorhabdus supernatant containing food signals triggering recovery. A snapshot (RNA-seq analysis) of their transcriptome was captured at 0.5, 1, 3 and 6 h after exposure. Transcripts (3060) with significant regulation changes were identified in the two lines. To analyze the RNA-seq data over time, we (1) divided the expression profiles into clusters of similar regulation, (2) identified over and under-represented gene ontology categories for each cluster, (3) identified Caenorhabditis elegans homologous genes with recovery-related function, and (4) combined the information with available single nucleotide polymorphism (SNP) data. We observed that the expression dynamics of the contrasting mutants (M31 and M88) differ the most within the first 3 h after Photorhabdus supernatant exposure, and during this time, genes related to changes in the DJ cuticle and molting are more active in the high-recovery line (M31). Comparing the gene expression of DJ exposed to the insect food signal in the haemolymph, genes related to host immunosuppressive factors were not found in DJ upon bacterial supernatant exposure. No link between the position of SNPs associated with high recovery and changes in gene expression was determined for genes with high differential expression. Concerning specific transcripts, nine H. bacteriophora gene models with differential expression are provided as candidate genes for further studies.
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Affiliation(s)
- Zhen Wang
- e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Francisco Garcia
- e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Ralf-Udo Ehlers
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Carlos Molina
- e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany.
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Ogaya C, Huong N, Touceda-González M, Barg M, Dörfler V, Ehlers RU, Molina C. Monitoring the Photorhabdus spp. bacterial load in Heterorhabditis bacteriophora dauer juveniles over different storage times and temperatures: A molecular approach. J Invertebr Pathol 2024; 203:108048. [PMID: 38159796 DOI: 10.1016/j.jip.2023.108048] [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: 10/06/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Biological control products based on the entomopathogenic nematode Heterorhabditis bacteriophora can vary in virulence (quality). The influence of their symbiotic bacteria Photorhabdus spp. inside the infective dauer juvenile (DJ) on DJ quality has not received much attention in the past. The presence of the bacteria in the DJ is crucial for its biocontrol potential. This investigation provides a method to quantify the bacterial load inside the DJ based on a qPCR technique. Information from the genome of Photorhabdus laumondii strain DE2 was used to identify single copy genes with no homology to any other bacterial accessions. One gene (hereby named CG2) was selected for primers design and for further qPCR experiments. Cross-amplification tests with P. thracensis and P. kayaii, also symbionts of H. bacteriophora, were positive, whereas no amplicons were produced for P. temperata or Xenorhabdus nematophila. We tested our qPCR system in DJ populations carrying defined proportions of bacteria-free (axenic) vs bacteria-carrying nematodes. With an increasing proportion of axenic DJ in a population, virulence declined, and the virulence was proportional to the amount of bacterial DNA detected in the population by qPCR. Along liquid storage over long time, virulence also decreased, and this factor correlated with the reduction of bacterial DNA on the respective DJ population. We observed that stored DJ kept virulent up to 90 days and thereafter the virulence as well as the amount of bacterial DNA drastically decreased. Storage temperature also influenced the bacterial survival. Inside formulated DJ, the loss of bacterial DNA on the DJ population was accelerated under storage temperatures below 7.5 °C, suggesting that reproduction of the bacterial cells takes place when growth temperature is favorable. The role of bacterial survival inside stored DJ can now be adequately addressed using this molecular quality-control technique.
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Affiliation(s)
- Christopher Ogaya
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany; e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Nontarak Huong
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | | | - Mike Barg
- e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Verena Dörfler
- e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany
| | - Ralf-Udo Ehlers
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118 Kiel, Germany; Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Carlos Molina
- e-nema GmbH, Klausdorfer Str. 28-36, 24223 Schwentinental, Germany.
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3
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Wang Z, Ogaya C, Dörfler V, Barg M, Ehlers RU, Molina C. Pheno- and genotyping in vitro dauer juvenile recovery in the nematode Heterorhabditis bacteriophora. Appl Microbiol Biotechnol 2023; 107:7181-7196. [PMID: 37733051 DOI: 10.1007/s00253-023-12775-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/25/2023] [Accepted: 09/03/2023] [Indexed: 09/22/2023]
Abstract
The entomopathogenic nematode (EPN) Heterorhabditis bacteriophora is an effective biological-control agent of insect pests. The dauer juveniles (DJs) seek for, infect insects, and release cells of the carried symbiotic bacterium of the genus Photorhabdus. Inside the host, the DJs perceive signals from the insect's haemolymph that trigger the exit from the arrested stage and the further development to mature adults. This developmental step is called DJ recovery. In commercial production, a high and synchronous DJ recovery determines the success of liquid-culture mass production. To enhance the understanding about genetic components regulating DJ recovery, more than 160 mutant- and 25 wild type inbred lines (WT ILs) were characterized for DJ recovery induced by cell-free bacterial supernatant. The mutant lines exhibited a broader DJ recovery range than WT ILs (4.6-67.2% vs 1.6-35.7%). A subset of mutant lines presented high variability of virulence against mealworm (Tenebrio molitor) (from 22 to 78% mortality) and mean time survival under oxidative stress (70 mM H2O2; from 10 to 151 h). Genotyping by sequencing of 96 mutant lines resulted in more than 150 single nucleotide polymorphisms (SNPs), of which four results are strongly associated with the DJ recovery trait. The present results are the basis for future approaches in improving DJ recovery by breeding under in vitro liquid-culture mass production in H. bacteriophora. This generated platform of EMS-mutants is as well a versatile tool for the investigation of many further traits of interest in EPNs. KEYPOINTS: • Exposure to bacterial supernatants of Photorhabdus laumondii induces the recovery of Heterorhabditis bacteriophora dauer juveniles (DJs). Both, the bacteria and the nematode partner, influence this response. However, the complete identity of its regulators is not known. • We dissected the genetic component of DJ recovery regulation in H. bacteriophora nematodes by generating a large array of EMS mutant lines and characterizing their recovery pheno- and genotypes. • We determined sets of mutants with contrasting DJ recovery and genotyped a subset of the EMS-mutant lines via genotyping by sequencing (GBS) and identified SNPs with significant correlation to the recovery trait.
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Affiliation(s)
- Zhen Wang
- , e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Christopher Ogaya
- , e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
| | - Verena Dörfler
- , e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
| | - Mike Barg
- , e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
| | - Ralf-Udo Ehlers
- , e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
- Faculty of Agricultural and Nutritional Sciences, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 4, 24118, Kiel, Germany
- Department of Biology, Ghent University-Campus Ledeganck, Karel Lodewijk Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Carlos Molina
- , e-nema GmbH, Klausdorfer Str. 28-36, 24223, Schwentinental, Germany.
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Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Res 2023; 51:8035-8047. [PMID: 37526286 PMCID: PMC10450198 DOI: 10.1093/nar/gkad647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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Affiliation(s)
- Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
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Maushe D, Ogi V, Divakaran K, Verdecia Mogena AM, Himmighofen PA, Machado RAR, Towbin BD, Ehlers RU, Molina C, Parisod C, Maud Robert CA. Stress tolerance in entomopathogenic nematodes: Engineering superior nematodes for precision agriculture. J Invertebr Pathol 2023:107953. [PMID: 37336478 DOI: 10.1016/j.jip.2023.107953] [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: 03/10/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
Entomopathogenic nematodes (EPNs) are soil-dwelling parasitic roundworms commonly used as biocontrol agents of insect pests in agriculture. EPN dauer juveniles locate and infect a host in which they will grow and multiply until resource depletion. During their free-living stage, EPNs face a series of internal and environmental stresses. Their ability to overcome these challenges is crucial to determine their infection success and survival. In this review, we provide a comprehensive overview of EPN response to stresses associated with starvation, low/elevated temperatures, desiccation, osmotic stress, hypoxia, and ultra-violet light. We further report EPN defense strategies to cope with biotic stressors such as viruses, bacteria, fungi, and predatory insects. By comparing the genetic and biochemical basis of these strategies to the nematode model Caenorhabditis elegans, we provide new avenues and targets to select and engineer precision nematodes adapted to specific field conditions.
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Affiliation(s)
- Dorothy Maushe
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Vera Ogi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Keerthi Divakaran
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | | | - Paul Anton Himmighofen
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Ricardo A R Machado
- Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Benjamin Daniel Towbin
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
| | - Ralf-Udo Ehlers
- e- nema GmbH, Klausdorfer Str. 28-36, DE-24223 Schwentinental, Germany
| | - Carlos Molina
- e- nema GmbH, Klausdorfer Str. 28-36, DE-24223 Schwentinental, Germany
| | - Christian Parisod
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Christelle Aurélie Maud Robert
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland; Oeschger Centre for Climate Change Research, University of Bern, Hochschulstrasse 4, CH-3012 Bern, Switzerland.
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Kundu A, Jaiswal N, Rao U, Somvanshi VS. Stringent in-silico identification of putative G-protein-coupled receptors (GPCRs) of the entomopathogenic nematode Heterorhabditis bacteriophora. J Nematol 2023; 55:20230038. [PMID: 38026552 PMCID: PMC10670001 DOI: 10.2478/jofnem-2023-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Indexed: 12/01/2023] Open
Abstract
The infective juveniles (IJs) of entomopathogenic nematode (EPN) Heterorhabditis bacteriophora find and infect their host insects in heterogeneous soil ecosystems by sensing a universal host cue (CO2) or insect/plant-derived odorants, which bind to various sensory receptors, including G protein-coupled receptors (GPCRs). Nematode chemosensory GPCRs (NemChRs) bind to a diverse set of ligands, including odor molecules. However, there is a lack of information on the NemChRs in EPNs. Here we identified 21 GPCRs in the H. bacteriophora genome sequence in a triphasic manner, combining various transmembrane detectors and GPCR predictors based on different algorithms, and considering inherent properties of GPCRs. The pipeline was validated by reciprocal BLAST, InterProscan, GPCR-CA, and NCBI CDD search. Functional classification of predicted GPCRs using Pfam revealed the presence of four NemChRs. Additionally, GPCRs were classified into various families based on the reciprocal BLAST approach into a frizzled type, a secretin type, and 19 rhodopsin types of GPCRs. Gi/o is the most abundant kind of G-protein, having a coupling specificity to all the fetched GPCRs. As the 21 GPCRs identified are expected to play a crucial role in the host-seeking behavior, these might be targeted to develop novel insect-pest management strategies by tweaking EPN IJ behavior, or to design novel anthelminthic drugs. Our new and stringent GPCR detection pipeline may also be used to identify GPCRs from the genome sequence of other organisms.
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Affiliation(s)
- Artha Kundu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
| | - Nisha Jaiswal
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
| | - Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
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Bhat CG, Budhwar R, Godwin J, Dillman AR, Rao U, Somvanshi VS. RNA-Sequencing of Heterorhabditis nematodes to identify factors involved in symbiosis with Photorhabdus bacteria. BMC Genomics 2022; 23:741. [PMCID: PMC9639317 DOI: 10.1186/s12864-022-08952-4] [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: 08/08/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
Background Nematodes are a major group of soil inhabiting organisms. Heterorhabditis nematodes are insect-pathogenic nematodes and live in a close symbiotic association with Photorhabdus bacteria. Heterorhabditis-Photorhabdus pair offers a powerful and genetically tractable model to study animal-microbe symbiosis. It is possible to generate symbiont bacteria free (axenic) stages in Heterorhabditis. Here, we compared the transcriptome of symbiotic early-adult stage Heterorhabditis nematodes with axenic early-adult nematodes to determine the nematode genes and pathways involved in symbiosis with Photorhabdus bacteria. Results A de-novo reference transcriptome assembly of 95.7 Mb was created for H. bacteriophora by using all the reads. The assembly contained 46,599 transcripts with N50 value of 2,681 bp and the average transcript length was 2,054 bp. The differentially expressed transcripts were identified by mapping reads from symbiotic and axenic nematodes to the reference assembly. A total of 754 differentially expressed transcripts were identified in symbiotic nematodes as compared to the axenic nematodes. The ribosomal pathway was identified as the most affected among the differentially expressed transcripts. Additionally, 12,151 transcripts were unique to symbiotic nematodes. Endocytosis, cAMP signalling and focal adhesion were the top three enriched pathways in symbiotic nematodes, while a large number of transcripts coding for various responses against bacteria, such as bacterial recognition, canonical immune signalling pathways, and antimicrobial effectors could also be identified. Conclusions The symbiotic Heterorhabditis nematodes respond to the presence of symbiotic bacteria by expressing various transcripts involved in a multi-layered immune response which might represent non-systemic and evolved localized responses to maintain mutualistic bacteria at non-threatening levels. Subject to further functional validation of the identified transcripts, our findings suggest that Heterorhabditis nematode immune system plays a critical role in maintenance of symbiosis with Photorhabdus bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08952-4.
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Affiliation(s)
- Chaitra G. Bhat
- grid.418196.30000 0001 2172 0814Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012 India
| | - Roli Budhwar
- Bionivid Technology Private Limited, 209, 4th Cross Rd., B. Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043 India
| | - Jeffrey Godwin
- Bionivid Technology Private Limited, 209, 4th Cross Rd., B. Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043 India
| | - Adler R. Dillman
- grid.266097.c0000 0001 2222 1582Department of Nematology, University of California, Riverside, 92521 USA
| | - Uma Rao
- grid.418196.30000 0001 2172 0814Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012 India
| | - Vishal S. Somvanshi
- grid.418196.30000 0001 2172 0814Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012 India
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Abstract
The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.
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Affiliation(s)
- Peter M Carlton
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO 80045, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Shawn Ahmed
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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Rödelsperger C. The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes. BMC Genomics 2021; 22:216. [PMID: 33765927 PMCID: PMC7992802 DOI: 10.1186/s12864-021-07529-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/12/2021] [Indexed: 01/30/2023] Open
Abstract
Background The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Over the past years, it developed into an independent animal model organism for elucidating the genetic basis of phenotypic plasticity. Community-based curations were employed recently to improve the quality of gene annotations of P. pacificus and to more easily facilitate reverse genetic studies using candidate genes from C. elegans. Results Here, I demonstrate that the reannotation of phylogenomic data from nine related nematode species using the community-curated P. pacificus gene set as homology data substantially improves the quality of gene annotations. Benchmarking of universal single copy orthologs (BUSCO) estimates a median completeness of 84% which corresponds to a 9% increase over previous annotations. Nevertheless, the ability to infer gene models based on homology already drops beyond the genus level reflecting the rapid evolution of nematode lineages. This also indicates that the highly curated C. elegans genome is not optimally suited for annotating non-Caenorhabditis genomes based on homology. Furthermore, comparative genomic analysis of apparently missing BUSCO genes indicates a failure of ortholog detection by the BUSCO pipeline due to the insufficient sample size and phylogenetic breadth of the underlying OrthoDB data set. As a consequence, the quality of multiple divergent nematode genomes might be underestimated. Conclusions This study highlights the need for optimizing gene annotation protocols and it demonstrates the benefit of a high quality genome for phylogenomic data of related species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07529-x.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
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Eurmsirilerd E, Maduro MF. Evolution of Developmental GATA Factors in Nematodes. J Dev Biol 2020; 8:jdb8040027. [PMID: 33207804 PMCID: PMC7712238 DOI: 10.3390/jdb8040027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.
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Affiliation(s)
- Ethan Eurmsirilerd
- Undergraduate Program in Biology, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA;
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Morris F. Maduro
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Correspondence:
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11
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Levy N, Faigenboim A, Salame L, Molina C, Ehlers RU, Glazer I, Ment D. Characterization of the phenotypic and genotypic tolerance to abiotic stresses of natural populations of Heterorhabditis bacteriophora. Sci Rep 2020; 10:10500. [PMID: 32601402 PMCID: PMC7324380 DOI: 10.1038/s41598-020-67097-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/28/2020] [Indexed: 12/30/2022] Open
Abstract
Entomopathogenic nematodes are effective biocontrol agents against arthropod pests. However, their efficacy is limited due to sensitivity to environmental extremes. The objective of the present study was to establish a foundation of genetic-based selection tools for beneficial traits of heat and desiccation tolerance in entomopathogenic nematodes. Screening of natural populations enabled us to create a diverse genetic and phenotypic pool. Gene expression patterns and genomic variation were studied in natural isolates. Heterorhabditis isolates were phenotyped by heat- and desiccation-stress bioassays to determine their survival rates compared to a commercial line. Transcriptomic study was carried out for the commercial line, a high heat-tolerant strain, and for the natural, low heat-tolerant isolate. The results revealed a higher number of upregulated vs. downregulated transcripts in both isolates vs. their respective controls. Functional annotation of the differentially expressed transcripts revealed several known stress-related genes and pathways uniquely expressed. Genome sequencing of isolates with varied degrees of stress tolerance indicated variation among the isolates regardless of their phenotypic characterization. The obtained data lays the groundwork for future studies aimed at identifying genes and molecular markers as genetic selection tools for enhancement of entomopathogenic nematodes ability to withstand environmental stress conditions.
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Affiliation(s)
- Noa Levy
- Department of Entomology and the Nematology and Chemistry units, Plant Protection Institute; Agricultural Research Organization (ARO), the Volcani Center, Rishon Le Zion, Israel
- The Robert H. Smith Faculty of Agriculture, Food & Environment the Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Faigenboim
- Institute of Plant Science; Agricultural Research Organization (ARO), the Volcani Center, Rishon Le Zion, Israel
| | - Liora Salame
- Department of Entomology and the Nematology and Chemistry units, Plant Protection Institute; Agricultural Research Organization (ARO), the Volcani Center, Rishon Le Zion, Israel
| | - Carlos Molina
- e-nema GmbH, Gesellschaft für Biotechnologie und biologischen Pflanzenschutz Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
| | - Ralf-Udo Ehlers
- e-nema GmbH, Gesellschaft für Biotechnologie und biologischen Pflanzenschutz Klausdorfer Str. 28-36, 24223, Schwentinental, Germany
| | - Itamar Glazer
- Department of Entomology and the Nematology and Chemistry units, Plant Protection Institute; Agricultural Research Organization (ARO), the Volcani Center, Rishon Le Zion, Israel
| | - Dana Ment
- Department of Entomology and the Nematology and Chemistry units, Plant Protection Institute; Agricultural Research Organization (ARO), the Volcani Center, Rishon Le Zion, Israel.
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12
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Abstract
Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus
Photorhabdus
comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore
Photorhabdus
has three distinct and obligate roles to play during this life-cycle: (1)
Photorhabdus
must kill the insect host; (2)
Photorhabdus
must be capable of supporting nematode growth and development; and (3)
Photorhabdus
must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between
Photorhabdus
and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.
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Affiliation(s)
- David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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13
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Mathers TC. Improved Genome Assembly and Annotation of the Soybean Aphid ( Aphis glycines Matsumura). G3 (BETHESDA, MD.) 2020; 10:899-906. [PMID: 31969427 PMCID: PMC7056979 DOI: 10.1534/g3.119.400954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aphids are an economically important insect group due to their role as plant disease vectors. Despite this economic impact, genomic resources have only been generated for a small number of aphid species. The soybean aphid (Aphis glycines Matsumura) was the third aphid species to have its genome sequenced and the first to use long-read sequence data. However, version 1 of the soybean aphid genome assembly has low contiguity (contig N50 = 57 Kb, scaffold N50 = 174 Kb), poor representation of conserved genes and the presence of genomic scaffolds likely derived from parasitoid wasp contamination. Here, I use recently developed methods to reassemble the soybean aphid genome. The version 2 genome assembly is highly contiguous, containing half of the genome in only 40 scaffolds (contig N50 = 2.00 Mb, scaffold N50 = 2.51 Mb) and contains 11% more conserved single-copy arthropod genes than version 1. To demonstrate the utility of this improved assembly, I identify a region of conserved synteny between aphids and Drosophila containing members of the Osiris gene family that was split over multiple scaffolds in the original assembly. The improved genome assembly and annotation of A. glycines demonstrates the benefit of applying new methods to old data sets and will provide a useful resource for future comparative genome analysis of aphids.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
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14
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Rödelsperger C, Athanasouli M, Lenuzzi M, Theska T, Sun S, Dardiry M, Wighard S, Hu W, Sharma DR, Han Z. Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus. Sci Rep 2019; 9:18789. [PMID: 31827189 PMCID: PMC6906410 DOI: 10.1038/s41598-019-55359-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/20/2019] [Indexed: 01/15/2023] Open
Abstract
Nematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C. elegans facilitate the evolutionary study of biological functions using reverse genetics. However, the ability to identify orthologs of candidate genes in other species can be hampered by erroneous gene annotations. To improve gene annotation in the nematode model organism Pristionchus pacificus, we performed a genome-wide screen for C. elegans genes with potentially incorrectly annotated P. pacificus orthologs. We initiated a community-based project to manually inspect more than two thousand candidate loci and to propose new gene models based on recently generated Iso-seq and RNA-seq data. In most cases, misannotation of C. elegans orthologs was due to artificially fused gene predictions and completely missing gene models. The community-based curation raised the gene count from 25,517 to 28,036 and increased the single copy ortholog completeness level from 86% to 97%. This pilot study demonstrates how even small-scale crowdsourcing can drastically improve gene annotations. In future, similar approaches can be used for other species, gene sets, and even larger communities thus making manual annotation of large parts of the genome feasible.
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Affiliation(s)
- Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
| | - Marina Athanasouli
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Maša Lenuzzi
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Tobias Theska
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Shuai Sun
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Mohannad Dardiry
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Sara Wighard
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Wen Hu
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Devansh Raj Sharma
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ziduan Han
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
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15
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McLean F, Berger D, Laetsch DR, Schwartz HT, Blaxter M. Improving the annotation of the Heterorhabditis bacteriophora genome. Gigascience 2018; 7:4958981. [PMID: 29617768 PMCID: PMC5906903 DOI: 10.1093/gigascience/giy034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/23/2018] [Indexed: 12/03/2022] Open
Abstract
Background Genome assembly and annotation remain exacting tasks. As the tools available for these tasks improve, it is useful to return to data produced with earlier techniques to assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes. Findings We revisited the H. bacteriophora genome assembly and gene predictions to determine whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant. Conclusions Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species’ genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published genome assemblies.
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Affiliation(s)
- Florence McLean
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Duncan Berger
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Hillel T Schwartz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
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