De novo Genome Assembly of the Raccoon Dog (Nyctereutes procyonoides)

Chueca, Luis J.; Kochmann, Judith; Schell, Tilman; Greve, Carola; Janke, Axel; Pfenninger, Markus; Klimpel, Sven

doi:10.3389/fgene.2021.658256

Cited by 12 publications

(7 citation statements)

References 54 publications

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“…However, several included empirical examples (e.g. Chueca et al, 2021) suggested that estimating the bases sequenced from the target genome with PacBio long reads worked equally well. In principle, as long as the assumption of random sequencing of bases from the genome is fulfilled, every sequencing platform should yield reliable estimates.…”

Section: Discussionmentioning

confidence: 99%

ModEst: Accurate estimation of genome size from next generation sequencing data

Pfenninger

Schönnenbeck

Schell

2021

Molecular Ecology Resources

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Petrov, 2001), yet the underlying processes for this variability are not yet fully understood (Elliott & Gregory, 2015). To understand and study the mechanisms of genome size variation, such as proliferation of repetitive elements (Blommaert et al., 2019), effective population size (Lefébure et al., 2017;Lynch & Conery, 2003) or correlation to other traits (Gardner et al., 2020;Prokopowich et al., 2003), reliable estimates for the taxon under scrutiny are therefore mandatory. This is all the more important as substantial changes in genome size may even occur among closely related sister species, that is over relatively short evolutionary timescales (Agudo et al., 2019;Keyl, 1965;Vitales et al., 2020). An accurate estimation of genome size is also important for genomic projects. For example, in the assembly of genomes, the proportion of the true genome size covered by a given assembly draft is a quality criterion and limits the maximum size of the draft. In addition, resequencing projects requiring a certain sequencing depth (e.g., for genotyping) profit from a reliable genome size estimate (Fountain et al., 2016).Flow cytometry is generally deemed to yield reliable estimates of genome size (Doležel & Greilhuber, 2010;Johnston et al., 2019). Yet, this method is not without caveats (Wang et al., 2015) and requires specialized laboratory skills and availability of the relatively expensive equipment. Moreover, the method depends on the availability of fresh or frozen tissue with largely intact cells, which narrows the range of taxa for which such analyses are practically feasible (Johnston et al., 2019). Bioinformatical analysis of next generation sequencing (NGS) dataprovides an alternative for estimating genome size (Vurture et al., 2017). Besides the widely used k-mer-based methods (Li & Waterman, 2003;Lipovský et al., 2017), Schell et al. (2017 introduced a very simple method for genome size estimation, relying on mapping statistics

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Section: Discussionmentioning

confidence: 99%

ModEst: Accurate estimation of genome size from next generation sequencing data

Pfenninger

Schönnenbeck

Schell

2021

Molecular Ecology Resources

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“…Next, we independently ran the module GeMoMa pipeline for each reference species using MMseqs2 72 as alignment tools, on the mapped RNA-seq data. Finally, the eleven individual annotation results were combined into a final annotation by using the GeMoMa modules GAF and AnnotationFinalizer 73 . Moreover, for immunoglobulin heavy chain genes ( ighvs ), the genome of the tiger tail seahorse has been fully predicted in Ensembl.…”

Section: Methodsmentioning

confidence: 99%

Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia

Liu

Jiang

et al. 2022

Nat Commun

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In the highly derived syngnathid fishes (pipefishes, seadragons & seahorses), the evolution of sex-role reversed brooding behavior culminated in the seahorse lineage’s male pregnancy, whose males feature a specialized brood pouch into which females deposit eggs during mating. Then, eggs are intimately engulfed by a placenta-like tissue that facilitates gas and nutrient exchange. As fathers immunologically tolerate allogenic embryos, it was suggested that male pregnancy co-evolved with specific immunological adaptations. Indeed, here we show that a specific amino-acid replacement in the tlx1 transcription factor is associated with seahorses’ asplenia (loss of spleen, an organ central in the immune system), as confirmed by a CRISPR-Cas9 experiment using zebrafish. Comparative genomics across the syngnathid phylogeny revealed that the complexity of the immune system gene repertoire decreases as parental care intensity increases. The synchronous evolution of immunogenetic alterations and male pregnancy supports the notion that male pregnancy co-evolved with the immunological tolerance of the embryo.

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“…Genome size was estimated following a ow cytometry protocol with propidium iodide-stained nuclei described in Chueca et al 2021 55 . Fresh mantle and gill tissues of S. plicata were separately chopped with a razor blade in independent Petri dishes containing 2 ml of ice-cold Galbraith and Otto buffer, respectively 56,57 .…”

Section: Genome Size Estimationsmentioning

confidence: 99%

Genomic richness enables worldwide invasive success

Galià-Camps,

Schell,

Pegueroles

et al. 2024

Preprint

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Biological invasions are a major threat to biodiversity. Therefore, monitoring genomic features of invasive species is crucial to understand their population structure and adaptive processes. However, genomic resources of invasive species are scarce, compromising the study of their invasive success. Here, we present the reference genome of Styela plicata, one of the most widespread marine invasive species, combined with genomic data of 24 individuals from 6 populations distributed worldwide. We characterized large inversions in four chromosomes, accounting for ~ 15% of the genome size. These inversions are polymorphic through the species’ distribution area, and are enriched with genes enhancing fitness in estuary and harbor environments. Nonetheless, inversions mask detection of S. plicata population structure. When these structural variants are removed, we successfully identify the main oceanographic barriers and accurately characterize population differentiation between and within ocean basins. Several genes located in chromosome 3 are showcased as the main adaptive drivers between biogeographic regions. Moreover, we recover three major mitogenomic clades, involving structural rearrangements leading to cyto-nuclear coevolution likely involved in mitochondrion distribution during cell division. Our results suggest that genomic and structural variants contribute to S. plicata population structuring and adaptation processes, potentially enhancing the species success when colonizing new habitats.

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De novo Genome Assembly of the Raccoon Dog (Nyctereutes procyonoides)

Cited by 12 publications

References 54 publications

ModEst: Accurate estimation of genome size from next generation sequencing data

ModEst: Accurate estimation of genome size from next generation sequencing data

Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia

Genomic richness enables worldwide invasive success

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