The<i>de novo</i>genome of the “Spanish” slug<i>Arion vulgaris</i>Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

Chen, Zeyuan; Doğan, Özgül; Guiglielmoni, Nadège; Guichard, Anne; Schrödl, Michael

doi:10.1101/2020.11.30.403303

Cited by 6 publications

(11 citation statements)

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“…1 ). The topology of the species tree inferred is as described in Chen et al (2020) : Patellogastropoda is sister to all other gastropods with a low support (PP = 0.66), and the alternative topologies of Patellogastropoda being sister to Vetigastropoda + Neomphalina (PP = 0.27), Patellogastropoda sister to Heterobranchia + Caenogastropoda (PP = 0.07) even less likely ( Fig. 2 , Fig.…”

Section: Resultsmentioning

confidence: 91%

“…Our results support this hypothesis: excluding C. consors , we got a total of 847 SOGs (767,180 sites) among the rest of the 15 species, increasing SOG numbers 2.15 times. Then we used the 847 SOGs for phylogenetic reconstruction using a concatenation method and compared it with Chen et al (2020) who used 233 SOGs (158,094 sites) identified in all 16 species. In contrast to Chen et al (2020) , Patellogastropoda clustered as sister to Vetigastropoda plus Neomphalina with a highly increased support (bootstrap value 89 compared to 48) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Species were selected as in the A. vulgaris genome study ( Chen et al, 2020 ). These species include bivalve species, Argopecten purpuratus Lamarck, 1819 ( Li et al, 2018 ) and Saccostrea glomerata Gould, 1850 ( Powell et al, 2018 ) as the outgroup.…”

Section: Methodsmentioning

confidence: 99%

“…SOGs thus hold great information potential for phylogenetic reconstruction, especially where universal markers are not able to generate strong phylogenetic hypotheses ( Sang, 2002 ; Wu et al, 2006 ). Several newly published gastropod genome studies have tried to reconstruct gastropod phylogeny using hundreds of SOGs ( Table 1 ); Lan et al (2021) and Sun et al (2020) recovered Psilogastropoda, while Chen et al (2020) inferred Orthogastropoda ( Table S1 ). Therefore, the conflict still remains when using SOGs in different taxon and gene sets with different species coverage.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, the conflict still remains when using SOGs in different taxon and gene sets with different species coverage. To explain the foundations leading to inconsistent topologies, we re-analyzed and expanded Chen et al’s (2020) study. In our new analyses, establishing sets of SOGs we allowed species missing per SOG successively to a certain degree (0–20% of all species) and reconstructed the phylogenies.…”

Section: Introductionmentioning

confidence: 99%

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How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

Chen

Schrödl

2022

PeerJ

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The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.

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Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

Chen

Schrödl

2022

PeerJ

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A method of culturing and breeding slugs through several generations

McDonald-Howard

Williams

Jones

et al. 2022

Journal of Molluscan Studies

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There is very little published information about how to culture slugs. There are at least 36 species of slug in the UK (Anderson, 2008) and as many as 44 (Rowson et al., 2014), many of which are nonnative (Cameron, 2016). They are important in terms of causing economic damage to crops (South, 1992), as well as hosts for medically important parasites such as Angiostrongylus cantonensis (Barratt et al., 2016). The aim of our study was to discover whether three species of slug, Deroceras invadens Reise, Hutchinson, Schunack & Schlitt 2011, Arion hortensis Férussac 1819 and Ambigolimax valentianus (Férussac 1822), could be cultured and mated to produce offspring and whether these offspring would be viable enough to produce more progeny. Ultimately, by providing information on how to maintain and breed slugs through several generations, perhaps a 'model slug' could be developed, which could benefit an array of subjects including genetics, genomics and developmental biology.Preliminary observations in the laboratory showed that D. invadens and A. hortensis preferred to lay eggs in peat-free compost (SylvaGrow ® , Melcourt, UK) as compared to garden bed or turf soil. Observations also demonstrated differences in egg development for the three species at different temperatures. Specifically, D. invadens at 10 °C, and A. hortensis and A. valentianus at 15 °C produced the highest level of viable eggs, presumably due to differences in the ecological niches they inhabit. The slugs were collected from a garden in Maghull, Liverpool (UK OS grid reference SD373027). They were kept in nonairtight plastic boxes (35 x 23 x 22 cm) at 5 °C with moistened paper and fed lettuce ad libitum for 1 week before use to check for any signs of ill health. Compost (10-15% moisture content) was added to a

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A chromosome-level genome for the nudibranch gastropodBerghia stephanieaehelps parse clade-specific gene expression in novel and conserved phenotypes

Goodheart,

Rio,

Taraporevala

et al. 2023

Preprint

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How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropodBerghia stephanieae(Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filteredBerghiagenome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

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Thede novogenome of the “Spanish” slugArion vulgarisMoquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

Cited by 6 publications

References 84 publications

How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?

A method of culturing and breeding slugs through several generations

A chromosome-level genome for the nudibranch gastropodBerghia stephanieaehelps parse clade-specific gene expression in novel and conserved phenotypes

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