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Detecting Structural Variants and Associated Gene Presence–Absence Variation Phenomena in the Genomes of Marine Organisms

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Marine Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2498))

Abstract

As complete genomes become easier to attain, even from previously difficult-to-sequence species, and as genomic resequencing becomes more routine, it is becoming obvious that genomic structural variation is more widespread than originally thought and plays an important role in maintaining genetic variation in populations. Structural variants (SVs) and associated gene presence–absence variation (PAV) can be important players in local adaptation, allowing the maintenance of genetic variation and taking part in other evolutionarily relevant phenomena. While recent studies have highlighted the importance of structural variation in Mollusca, the prevalence of this phenomenon in the broader context of marine organisms remains to be fully investigated.

Here, we describe a straightforward and broadly applicable method for the identification of SVs in fully assembled diploid genomes, leveraging the same reads used for assembly. We also explain a gene PAV analysis protocol, which could be broadly applied to any species with a fully sequenced reference genome available. Although the strength of these approaches have been tested and proven in marine invertebrates, which tend to have high levels of heterozygosity, possibly due to their lifestyle traits, they are also applicable to other species across the tree of life, providing a ready means to begin investigations into this potentially widespread phenomena.

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Author information

Author notes

  1. Nathan J. Kenny

    Present address: Department of Biochemistry, University of Otago, Dunedin, New Zealand

Authors and Affiliations

  1. Department of Life Sciences, Università degli Studi di Trieste, Trieste, Italy

    Marco Sollitto, Samuele Greco, Carmen Federica Tucci & Marco Gerdol

  2. Faculty of Health and Life Sciences, Oxford Brookes, Oxford, UK

    Nathan J. Kenny

  3. Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Vienna, Austria

    Andrew D. Calcino

Authors
  1. Marco Sollitto
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  2. Nathan J. Kenny
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  3. Samuele Greco
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  4. Carmen Federica Tucci
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  5. Andrew D. Calcino
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  6. Marco Gerdol
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Corresponding author

Correspondence to Marco Gerdol .

Editor information

Editors and Affiliations

  1. Institute of Biosciences and BioResources (IBBR), National Research Council, Naples, Italy

    Cinzia Verde

  2. Institute of Biosciences and BioResources (IBBR), National Research Council, Naples, Italy

    Daniela Giordano

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Sollitto, M., Kenny, N.J., Greco, S., Tucci, C.F., Calcino, A.D., Gerdol, M. (2022). Detecting Structural Variants and Associated Gene Presence–Absence Variation Phenomena in the Genomes of Marine Organisms. In: Verde, C., Giordano, D. (eds) Marine Genomics. Methods in Molecular Biology, vol 2498. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2313-8_4

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  • DOI: https://doi.org/10.1007/978-1-0716-2313-8_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2312-1

  • Online ISBN: 978-1-0716-2313-8

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