Genome projects in invasion biology

McCartney, Michael A.; Mallez, Sophie; Gohl, Daryl M.

doi:10.1007/s10592-019-01224-x

“…In particular, scaffolding methods using Hi-C data will represent one of the most promising routes to this purpose. We believe that our improved D. suzukii assembly will provide a solid genomic basis to investigate basic biological questions about D. suzukii, using high-throughput sequencing technologies as well as manipulative genetic technologies 35 .…”

Section: Resultsmentioning

confidence: 99%

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Paris

¹

,

Boyer

²

,

Jaenichen

³

et al. 2020

Sci Rep

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Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio longread sequencing data and assembled a novel, high-quality D. suzukii genome assembly. it is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii. Drosophila suzukii (Matsumura, 1931), the spotted wing Drosophila (Diptera: Drosophilidae), is an invasive fruit fly species originating from eastern Asia that has spread since 2008 in major parts of America and Europe. This species is still expanding its distribution 1,2 and is classified as a major pest on a variety of berries and stone fruit crops 3. Its behavior and phenotypic traits are now the subject of intense scrutiny both in the lab and in the field (reviewed in 4). Understanding the biology and the population dynamics of D. suzukii benefits from the production and mining of genomic and transcriptomic data, as well as manipulative genetic technologies including functional transgenesis and genome editing 5-7. Yet, the efficacy of these approaches relies critically on high-quality genomic resources. Currently, two D. suzukii genome assemblies, obtained from two different strains, have been generated based on short-read sequencing technologies 8,9. The utility of these valuable genomic resources is limited by the

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“…suzukii, using high-throughput sequencing technologies as well as manipulative genetic technologies (McCartney, Mallez, & Gohl, 2019). Regions assembled as distinct haplotypes, regions of higher nucleotide diversity, regions with structural variants, regions with higher one-nucleotide assembly errors (in the form of indels) are highlighted.…”

Section: Resultsmentioning

confidence: 99%

Near-chromosome level genome assembly of the fruit pestDrosophila suzukiiusing long-read sequencing

Paris

¹

,

Boyer

²

,

Jaenichen

³

et al. 2020

Preprint

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Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies based on short-read sequencing were released in 2013 for this species. Although valuable, these resources contain pervasive assembly errors and are highly fragmented, two features limiting their values. Our purpose here was to improve the assembly of the D. suzukii genome. For this, we generated PacBio long-read sequencing data at 160X sequence coverage and assembled a novel, contiguous D. suzukii genome. We obtained a high-quality assembly of 270 Mb (with 546 contigs, a N50 of 2.6Mb, a L50 of 15, and a BUSCO score of 95%) that we called WT3-2.0. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome (ca. 19Mb). As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our WT3-2.0 assembly provides a higher quality genomic resource compared to the previous one in terms of general assembly statistics, sequence quality and gene annotation. This new D. suzukii genome assembly is therefore an improved resource for high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.

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“…More recently, the advent of massively parallel (MPS; also known as next-or second generation; Margulies et al, 2005;Metzker, 2010) and single-molecule, long-read (also known as third-generation; Branton et al, 2008;Eid et al, 2009) DNA sequencing has elevated our ability to generate orders of magnitude more data and to make use of more robust molecular markers in the form of single nucleotide polymorphisms (SNPs), extending the depth and breadth of questions that can be addressed (Rius et al, 2015), while providing unprecedented insight into the processes underpinning biological invasions (McCartney et al, 2019). In particular, these technologies have enabled low-cost SNP discovery and genotyping-by-sequencing (GBS) of thousands of genetic markers for any species using a range of approaches including restriction site-associated DNA (RAD) sequencing (Baird et al, 2008) and others (e.g., nextRAD; Russello et al, 2015).…”

Section: Genetic and Genomic Tools For Informing The Study And Management Of Invasive Speciesmentioning

confidence: 99%

The Promise of Genetics and Genomics for Improving Invasive Mammal Management on Islands

Burgess

¹

,

Irvine

²

,

Howald³

et al. 2021

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Invasive species are major contributors to global biodiversity decline. Invasive mammalian species (IMS), in particular, have profound negative effects in island systems that contain disproportionally high levels of species richness and endemism. The eradication and control of IMS have become important conservation tools for managing species invasions on islands, yet these management operations are often subject to failure due to knowledge gaps surrounding species- and system-specific characteristics, including invasion pathways and contemporary migration patterns. Here, we synthesize the literature on ways in which genetic and genomic tools have effectively informed IMS management on islands, specifically associated with the development and modification of biosecurity protocols, and the design and implementation of eradication and control programs. In spite of their demonstrated utility, we then explore the challenges that are preventing genetics and genomics from being implemented more frequently in IMS management operations from both academic and non-academic perspectives, and suggest possible solutions for breaking down these barriers. Finally, we discuss the potential application of genome editing to the future management of invasive species on islands, including the current state of the field and why islands may be effective targets for this emerging technology.

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Genome projects in invasion biology

Cited by 23 publications

References 130 publications

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Near-chromosome level genome assembly of the fruit pestDrosophila suzukiiusing long-read sequencing

The Promise of Genetics and Genomics for Improving Invasive Mammal Management on Islands

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