Whole genome sequencing data and de novo draft assemblies for 66 teleost species

Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole K.; Jakobsen, Kjetill Sigurd; Jentoft, Sissel

doi:10.1038/sdata.2016.132

Cited by 75 publications

(87 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S2, Supplementary Material online). This genome size is consistent with those of three other genomes available (Malmstrøm, et al 2017) and estimations of the genome size of other Ophidiiformes (Gregory 2019). To assess the quality of the assembly, raw sequences were realigned to the assembly: 95% of the reads realigned correctly resulting in a mean coverage of 134x.…”

Section: Resultssupporting

confidence: 89%

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Policarpo

Fumey

Lafargeas

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

Section: Resultssupporting

confidence: 89%

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Policarpo

Fumey

Lafargeas

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…This reflects its two to three times larger genome size likely due to its higher content in repetitive sequences (44.92% vs. 24.02-28.82%). All four genomes were sequenced with coverage depth above 24 (between 24x and 85x), which is most likely sufficient to get the whole gene set [43]. Accordingly, a BUSCO[61] analysis revealed that the vast majority of the 1066 single copy genes expected to be found in most arthropods are indeed present in all four assemblies (from 96.6% in G. brasiliensis to 99.1% in L. boulardi ), making these assemblies suitable for HGT detection ( Table 1: Statistics for the assemblies of wasp genomes.…”

Section: Resultsmentioning

confidence: 99%

A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps

Lepetit

Boulesteix

et al. 2018

Preprint

View full text Add to dashboard Cite

11To circumvent host immune response, some hymenopteran endo-parasitoids produce 12 virus-like structures in their reproductive apparatus that are injected into the host 13 together with the eggs. These viral-like structures are absolutely necessary for 14 the reproduction of these wasps. The viral evolutionary origin of these viral-like 15 particles has been demonstrated in only a few cases of wasp species all belonging to 16 the Ichneumonoidea superfamily. In addition, the nature of the initial virus-wasp 17 association remains unknown for all. This is either because no closely related 18 descendant infects the wasps, because it has not been sampled yet, or because 19 the virus lineage went extinct. In this paper, we show that the virus-like particles 20 (VLPs) produced by endoparasitoids of Drosophila belonging to the Leptopilina 21 genus (superfamily Cynipoidea) do have a viral origin, solving the debate on their 22 origin. Furthermore, the ancestral donor virus still has close relatives infecting 23 one of the wasp species, thus giving us insights on the ecological interaction that 24 possibly allowed the domestication process. Intriguingly, this contemporary virus is 25 both vertically and horizontally transmitted and has the particularity to manipulate 26 the superparasitism behavior of the wasp. This raises the possibility that behavior 27 manipulation has been instrumental in the birth of such association between wasps 28 and viruses. 29 1 1 Introduction 30 Genetic information is typically passed on from generation to generation 31 through reproduction, ie vertical transmission. However, at some point during 32 the course of evolution, organisms may gain DNA from unrelated organisms, 33 through horizontal gene transfer (HGT). Most horizontally acquired DNA 34 is probably purged from the genomes of the population either because it 35 did not reach the germinal cells in case of metazoan species and/or because 36 no advantage is carried by the foreign sequence. However, natural selection 37 may retain the foreign DNA leading ultimately to genetic innovation in the 38 population/species [38]. 39 The high frequency and relevance of such phenomenon has been recognized 40 for decades for bacteria but was considered to have had a marginal impact 41 on the evolution of metazoans[40]. However, this view has been recently 42 challenged due to the discovery of numerous examples of HGT in metazoans 43 with some of them leading to genetic innovation[8]. The most notorious 44 example involves retroviral envelope genes that have been endogenized, 45 domesticated and multiply replaced in mammalian genomes[45]. In this 46 case, the fusogenic and immunosuppressive properties of these viral proteins 47 (syncitins) have been repeatedly recruited to permit the evolution of placental 48 structures during mammalian diversification. Interestingly, a similar case 49 of syncitin domestication was recently described in a clade of viviparous 50 Scincidae lizards that also rely on a placenta-like structure to feed their 51 o↵spring [...

show abstract

“…The steady decrease in sequencing cost promised by new technologies suggests that access to the genome sequence may in the near future no longer be an unsurmountable obstacle for nonmodel species (Goodwin et al., ). Proof of this are the multiple international initiatives that are collaboratively sequencing genomes of various taxa including fungi (Grigoriev et al, ), invertebrates (GIGA ), arthropods (Evans et al, ), birds (Zhang, ), fishes (Macqueen et al, (); Malmstrøm, Matschiner, Tørresen, Jakobsen, & Jentoft, ), mammals (Fontanesi et al, ), vertebrates (Koepfli, Paten, & O'Brien, ), among others.…”

Section: Genome Sequencing Techniquesmentioning

confidence: 99%

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

2017

View full text Add to dashboard Cite

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.

show abstract

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

Cited by 75 publications

References 51 publications

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

Contrasted gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals

A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Contact Info

Product

Resources

About