Chromosome-level genome assembly of the bethylid ectoparasitoid wasp Sclerodermus sp. ‘alternatusi’ (2024)

References

  1. Dashevsky, D. et al. Functional and Proteomic Insights into Aculeata Venoms. Toxins (Basel) 15, 224–249 (2023).

    Article CAS PubMed Google Scholar

  2. Parkinson, N. M. et al. Towards a comprehensive view of the primary structure of venom proteins from the parasitoid wasp Pimpla hypochondriaca. Insect Biochem. Mol. Biol. 34, 565–571 (2004).

    Article CAS PubMed Google Scholar

  3. Belle, E. et al. Visualization of Polydnavirus Sequences in a Parasitoid Wasp Chromosome. J. Virol. 76, 5793–5796 (2002).

    Article CAS PubMed PubMed Central Google Scholar

  4. Dahlman, D. L. et al. A teratocyte gene from a parasitic wasp that is associated with inhibition of insect growth and development inhibits host protein synthesis. Insect Mol. Biol. 12, 527–534 (2003).

    Article CAS PubMed Google Scholar

  5. Luckhart, S. & Webb, B. A. Interaction of a wasp ovarian protein and polydnavirus in host immune suppression. Dev. Comp. Immunol. 20, 1–21 (1996).

    Article CAS PubMed Google Scholar

  6. Pennacchio, F. & Strand, M. R. Evolution of developmental strategies in parasitic hymenoptera. Annu. Rev. Entomol. 51, 233–258 (2006).

    Article CAS PubMed Google Scholar

  7. Wang, Z., Liu, Y., Shi, M., Huang, J. & Chen, X. Parasitoid wasps as effective biological control agents. J. Integr. Agric. 18, 705–715 (2019).

    Article Google Scholar

  8. Polaszek, A. & Vilhemsen, L. Biodiversity of hymenopteran parasitoids. Curr. Opin. Insect Sci. 56, 1–7 (2023).

    Google Scholar

  9. Li, B. et al. Chromosome-level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi-C technology. Mol. Eco.l Resour. 21, 941–954 (2021).

    Article CAS Google Scholar

  10. Singh, K. S. et al. Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae. Commun. Biol. 4, 847 (2021).

    Article CAS PubMed PubMed Central Google Scholar

  11. Häussling, B. J. M., Lienenlüke, J. & Stökl, J. The preference of Trichopria drosophilae for pupae of Drosophila suzukii is independent of host size. Sci. Rep. 11, 1–10 (2021).

    Article Google Scholar

  12. Ye, X. et al. Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps. Nat. Commun. 13, 6417 (2022).

    Article ADS CAS PubMed PubMed Central Google Scholar

  13. Beckage, N. E. & Gelman, D. B. Wasp Parasitoid Disruption of Host Development: Implications for New Biologically Based Strategies for Insect Control. Annu. Rev. Entomol. 49, 299–330 (2004).

    Article CAS PubMed Google Scholar

  14. Brazidec, M. & Perrichot, V. Two new chrysidoid wasps (Hymenoptera: Bethylidae, Chrysididae) from mid-Miocene Zhangpu amber. Palaeoworld 32, 699–708 (2023).

    Article Google Scholar

  15. Tang, Y. et al. Parasitism Ability and Offspring Development of Sclerodermus alternatusi Yang (Hymenoptera: Bethylidae) in Different Female Oviposition Times. Chin. J. Biol. Control 39, 499–506 (2023).

    Google Scholar

  16. Wang, S. Y., Hackney, P. J. & Zhang, D. Hydrocarbons catalysed by TmCYP4G122 and TmCYP4G123 in Tenebrio molitor modulate the olfactory response of the parasitoid Scleroderma guani. Insect Mol. Biol. 28, 637–648 (2019).

    Article CAS PubMed Google Scholar

  17. Li, Z. et al. The ectoparasitoid Scleroderma guani (Hymenoptera: Bethylidae) uses innate and learned chemical cues to locate its host, larvae of the pine sawyer Monochamus alternatus (Coleoptera: Cerambycidae). Fla. Entomol. 98, 1182–1187 (2015).

    Article CAS Google Scholar

  18. Luo, C. W. & Chen, Y. Phototactic Behavior of Scleroderma guani (Hymenoptera: Bethylidae) - Parasitoid of Pissodes punctatus (Coleoptera: Curculionidae). J. Insect Behav. 29, 605–614 (2016).

    Article Google Scholar

  19. Li, L., Wei, W., Liu, Z. & Sun, J. Host adaptation of a gregarious parasitoid Sclerodermus harmandi in artificial rearing. BioControl 55, 465–472 (2010).

    Article Google Scholar

  20. Lauzière, I., Brodeur, J. & Pérez-Lachaud, G. Host stage selection and suitability in Cephalonomia stephanoderis betrem (hymenoptera: Bethylidae), a parasitoid of the coffee berry borer. Biol. Control 21, 128–133 (2001).

    Article Google Scholar

  21. Li, L. F. et al. Parasitism and venom of ectoparasitoid Scleroderma guani impairs host cellular immunity. Arch. Insect Biochem. Physiol. 98, 1–13 (2018).

    Article Google Scholar

  22. Yahav, T. & Privman, E. A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples. Sci. Rep. 9, 6480 (2019).

    Article ADS PubMed PubMed Central Google Scholar

  23. Mei, Y. et al. InsectBase 2.0: A comprehensive gene resource for insects. Nucleic Acids Res. 50, 1040–1045 (2022).

    Article ADS Google Scholar

  24. Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11, 1432 (2020).

    Article ADS CAS PubMed PubMed Central Google Scholar

  25. Marçais, G., Kingsford, C. & Bateman, A. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).

    Article PubMed PubMed Central Google Scholar

  26. Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).

    Article CAS PubMed Google Scholar

  27. Roach, M. J., Schmidt, S. A. & Borneman, A. R. Purge Haplotigs: Allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinform. 19, 460 (2018).

    Article CAS Google Scholar

  28. Huang, S., Kang, M. & Xu, A. HaploMerger2: Rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics 33, 2577–2579 (2017).

    Article CAS PubMed PubMed Central Google Scholar

  29. Nagano, T. et al. Comparison of Hi-C results using in-solution versus in-nucleus ligation. Genome Biol. 16, 175 (2015).

    Article PubMed PubMed Central Google Scholar

  30. Zhang, H. et al. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat. Commun. 12, 6566 (2021).

    Article ADS CAS PubMed PubMed Central Google Scholar

  31. Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39, btac808 (2022).

    Article PubMed Central Google Scholar

  32. Robinson, J. T. et al. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst 6, 256–258 (2018).

    Article CAS PubMed PubMed Central Google Scholar

  33. Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8, 1494–1512 (2013).

    Article CAS PubMed Google Scholar

  34. Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6, (2015).

  35. Stanke, M. et al. AUGUSTUS: A b initio prediction of alternative transcripts. Nucleic Acids Res 34, (2006).

  36. Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31, 5654–5666 (2003).

    Article CAS PubMed PubMed Central Google Scholar

  37. Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res 14, 988–995 (2004).

    Article CAS PubMed PubMed Central Google Scholar

  38. Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 9, (2008).

  39. Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28, 45–48 (2000).

    Article CAS PubMed PubMed Central Google Scholar

  40. Tatusov, R. L. et al. The COG database: An updated vesion includes eukaryotes. BMC Bioinformatics 4, 1–14 (2003).

    Article Google Scholar

  41. Finn, R. D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45, 190–199 (2017).

    Article Google Scholar

  42. Huerta-Cepas, J. et al. EggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47, 309–314 (2019).

    Article Google Scholar

  43. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP495066 (2024).

  44. Wan, Y. et al. Sclerodermus sp. ‘alternatusi’ isolate ZJU-2024a, whole genome shotgun sequencing project. GenBank https://identifiers.org/ncbi/insdc:JBBEEM000000000 (2024).

  45. NGDC/CNCB Genome Sequence Archive https://ngdc.cncb.ac.cn/gsa/browse/CRA012526 (2023).

  46. Chen, M. et al. Genome Warehouse: A Public Repository Housing Genome-scale Data. Genomics Proteomics Bioinformatics 19, 584–589 (2021).

    Article PubMed PubMed Central Google Scholar

  47. Xue, Y. et al. Database resources of the national genomics data center, china national center for bioinformation in 2021. Nucleic Acids Res. 49, 18–28 (2021).

    Article Google Scholar

  48. Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: Assessing Genomic Data Quality and Beyond. Curr. Protoc. 1, e323 (2021).

    Article PubMed Google Scholar

  49. Ye, X. et al. A chromosome-level genome assembly of the parasitoid wasp Pteromalus puparum. Mol. Ecol. Resour. 20, 1384–1402 (2020).

    Article CAS PubMed Google Scholar

  50. Wittmeyer, K. T., Oppenheim, S. J. & Hopper, K. R. Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage. G3 (Bethesda) 12, jkad386 (2022).

    Article Google Scholar

  51. Ye, X. et al. Genome of the parasitoid wasp Cotesia chilonis sheds light on amino acid resource exploitation. BMC Biol. 20, 1–17 (2022).

    Article CAS Google Scholar

  52. Gauthier, J. et al. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun. Biol. 4, 104 (2021).

    Article PubMed PubMed Central Google Scholar

  53. Pinto, B. J. et al. A Chromosome-Level Genome Assembly of the Parasitoid Wasp, Cotesia glomerata (Hymenoptera: Braconidae). J. Hered 112, 558–564 (2021).

    Article PubMed Google Scholar

  54. Mao, M. et al. A chromosome scale assembly of the parasitoid wasp Venturia canescens provides insight into the process of virus domestication. G3 (Bethesda) 13, jkad137 (2023).

    Article CAS PubMed Google Scholar

  55. Xiao, S. et al. Genome assembly of the ectoparasitoid wasp Theocolax elegans. Sci. Data 10, 159 (2023).

    Article CAS PubMed PubMed Central Google Scholar

  56. Kuang, J. G. et al. Chromosome-level de novo genome assembly of two conifer-parasitic wasps, Megastigmus duclouxiana and Megastigmus sabinae, reveals genomic imprints of adaptation to hosts. Mol. Ecol. Resour. 23, 1142–1154 (2023).

    Article CAS PubMed Google Scholar

  57. Shu, X. et al. Chromosome-level genome assembly of Microplitis manilae Ashmead, 1904 (Hymenoptera: Braconidae). Sci. Data 10, 226 (2023).

    Article Google Scholar

  58. Dalla Benetta, E. et al. Genome elimination mediated by gene expression from a selfish chromosome. Sci. Adv. 6, eaaz9808 (2020).

    Article ADS PubMed PubMed Central Google Scholar

  59. Inwood, S. N. et al. Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus. BMC Genom. 24, 440 (2023).

    Article CAS Google Scholar

Download references

Chromosome-level genome assembly of the bethylid ectoparasitoid wasp Sclerodermus sp. ‘alternatusi’ (2024)

References

Top Articles
Latest Posts
Article information

Author: Dr. Pierre Goyette

Last Updated:

Views: 5245

Rating: 5 / 5 (50 voted)

Reviews: 89% of readers found this page helpful

Author information

Name: Dr. Pierre Goyette

Birthday: 1998-01-29

Address: Apt. 611 3357 Yong Plain, West Audra, IL 70053

Phone: +5819954278378

Job: Construction Director

Hobby: Embroidery, Creative writing, Shopping, Driving, Stand-up comedy, Coffee roasting, Scrapbooking

Introduction: My name is Dr. Pierre Goyette, I am a enchanting, powerful, jolly, rich, graceful, colorful, zany person who loves writing and wants to share my knowledge and understanding with you.