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Using BUSCO to Assess Insect Genomic Resources

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Insect Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1858))

Abstract

The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build “omics” resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.

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References

  1. Richards S, Murali SC (2015) Best practices in insect genome sequencing: what works and what doesn’t. Curr Opin Insect Sci 7:1–7

    Article  Google Scholar 

  2. Gurevich A, Saveliev V, Vyahhi N et al (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075

    Article  CAS  Google Scholar 

  3. Hunt M, Kikuchi T, Sanders M et al (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biol 14:R47

    Article  Google Scholar 

  4. Allen SL, Delaney EK, Kopp A et al (2017) Single-Molecule Sequencing of the Drosophila serrata Genome. G3: Genes, Genomes, Genetics 7:781–788

    Article  CAS  Google Scholar 

  5. Davey JW, Chouteau M, Barker SL et al (2016) Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution. G3: Genes, Genomes, Genetics 6:695–708

    Article  CAS  Google Scholar 

  6. Kanost MR, Arrese EL, Cao X et al (2016) Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochem Mol Biol 76:118–147

    Article  CAS  Google Scholar 

  7. Nowell RW, Elsworth B, Oostra V et al (2017) A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana. GigaScience 6:1–7

    Article  Google Scholar 

  8. Papanicolaou A, Schetelig MF, Arensburger P et al (2016) The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol 17:192

    Article  Google Scholar 

  9. Benoit JB, Adelman ZN, Reinhardt K et al (2016) Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun 7:10165

    Article  CAS  Google Scholar 

  10. McKenna DD, Scully ED, Pauchet Y et al (2016) Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biol 17:227

    Article  Google Scholar 

  11. Ioannidis P, Simão FA, Waterhouse RM et al (2017) Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders. Genome Biol Evol 9:415–430

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Simão FA, Waterhouse RM, Ioannidis P et al (2015) BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  Google Scholar 

  13. Waterhouse RM, Seppey M, Simão FA et al (2017) BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543–548

    Google Scholar 

  14. Zdobnov EM, Tegenfeldt F, Kuznetsov D et al (2017) OrthoDB v9.1: Cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. Nucleic Acids Res 45:D744–D749

    Article  CAS  Google Scholar 

  15. Waterhouse RM, Zdobnov EM, Kriventseva EV (2011) Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. Genome Biol Evol 3:75–86

    Article  CAS  Google Scholar 

  16. Waterhouse RM (2015) A maturing understanding of the composition of the insect gene repertoire. Curr Opin Insect Sci 7:15–23

    Article  Google Scholar 

  17. Eddy SR (2011) Accelerated Profile HMM Searches. PLoS Comput Biol 7:e1002195

    Article  CAS  Google Scholar 

  18. Keller O, Kollmar M, Stanke M et al (2011) A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics 27:757–763

    Article  CAS  Google Scholar 

  19. Camacho C, Coulouris G, Avagyan V et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421

    Article  Google Scholar 

  20. Holt RA, Subramanian GM, Halpern A et al (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129–149

    Article  CAS  Google Scholar 

  21. Jiang X, Peery A, Hall AB et al (2014) Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi. Genome Biol 15:459

    Article  Google Scholar 

  22. Neafsey DE, Waterhouse RM, Abai MR et al (2015) Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 347:1258522–1258522

    Article  Google Scholar 

  23. Giraldo-Calderón GI, Emrich SJ, MacCallum RM et al (2015) VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res 43:D707–D713

    Article  Google Scholar 

  24. Peters RS, Krogmann L, Mayer C et al (2017) Evolutionary history of the hymenoptera. Curr Biol 27:1013–1018

    Article  CAS  Google Scholar 

  25. Petersen M, Meusemann K, Donath A et al (2017) Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinformatics 18:111

    Article  Google Scholar 

  26. Li W, Godzik A (2006) CD-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659

    Article  CAS  Google Scholar 

  27. Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59

    Article  Google Scholar 

  28. Waterhouse RM, Chen X, Bonizzoni M et al (2017) The third International Workshop on Aedes albopictus: building scientific alliances in the fight against the globally invasive Asian tiger mosquito. Pathog Global Health 111:161–165

    Article  Google Scholar 

  29. Campbell MS, Holt C, Moore B et al (2014) Genome annotation and curation using MAKER and MAKER-P. Curr Protoc Bioinformatics 48:4.11.1-39

    PubMed  Google Scholar 

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Acknowledgments

R.M.W. was supported by Swiss National Science Foundation award PP00P3_170664.

Author information

Authors and Affiliations

  1. Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Robert M. Waterhouse

  2. University of Geneva and Swiss Institute of Bioinformatics, Geneva, Switzerland

    Mathieu Seppey, Felipe A. Simão & Evgeny M. Zdobnov

Authors
  1. Robert M. Waterhouse
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  2. Mathieu Seppey
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  3. Felipe A. Simão
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  4. Evgeny M. Zdobnov
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Corresponding author

Correspondence to Robert M. Waterhouse .

Editor information

Editors and Affiliations

  1. Division of Biology, Kansas State University, Manhattan, NY, USA

    Susan J. Brown

  2. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA

    Michael E. Pfrender

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Waterhouse, R.M., Seppey, M., Simão, F.A., Zdobnov, E.M. (2019). Using BUSCO to Assess Insect Genomic Resources. In: Brown, S., Pfrender, M. (eds) Insect Genomics. Methods in Molecular Biology, vol 1858. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8775-7_6

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  • DOI: https://doi.org/10.1007/978-1-4939-8775-7_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8774-0

  • Online ISBN: 978-1-4939-8775-7

  • eBook Packages: Springer Protocols

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