Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids

Boer, Johan G. de; Yazawa, Ryosuke; Davidson, William S.; Koop, Ben F.

doi:10.1186/1471-2164-8-422

Cited by 135 publications

(145 citation statements)

References 47 publications

Supporting

Mentioning

139

Contrasting

Unclassified

Order By: Relevance

“…This situation could be induced via hypomethylation associated with cancers [Daskalos et al, 2009] or due to chromosomal rearrangements interrupting normal patterns of methylation and subsequently removing TE silencing [O'Neill et al, 1998;Dobigny et al, 2004]. Here, a cascade of genomic changes could promote evolutionary diversification and is consistent with several studies identifying coincident bursts of diversification and high TE activity and accumulation [Pascale et al, 1990;de Boer et al, 2007;Ray et al, 2008]. While genomic changes induced by TEs may promote speciation, the overall accumulation of TEs in the genome may have the opposite effect; lineages with larger genome sizes appear to have slower speciation rates relative to lineages with smaller genome sizes [Kraaijeveld, 2010].…”

Section: The Impact Of Transposable Elements On the Genome Of Their Hostsupporting

confidence: 63%

The Mobilome of Reptiles: Evolution, Structure, and Function

Boissinot¹,

Bourgeois²,

Manthey

et al. 2019

Cytogenet Genome Res

View full text Add to dashboard Cite

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

show abstract

Section: The Impact Of Transposable Elements On the Genome Of Their Hostsupporting

confidence: 63%

The Mobilome of Reptiles: Evolution, Structure, and Function

Boissinot¹,

Bourgeois²,

Manthey

et al. 2019

Cytogenet Genome Res

View full text Add to dashboard Cite

show abstract

“…All four fad genes had identical coding exon structures, being comprised of 12 coding exons, with a high degree of sequence identity, and sequence identity extended to intron sequence ( Fig.1). Intron regions that could not be aligned across all four genes had high identity to multiple sequences in diverse salmon database entries and included degenerate salmon Class I transposons [33], or could be aligned with sequences of RepBase (http://www.girinst.org/repbase/index.html) entries for various transposons [32]. The first coding exons of Δ6fad_b and Δ6fad_c contain a nine base pair insertion compared to Δ6fad_a and Δ5fad, resulting in a three amino acid insertion in the predicted polypeptide sequences.…”

Section: Salmon Fatty Acyl Desaturase Gene Structurementioning

confidence: 99%

Multiple genes for functional ∆6 fatty acyl desaturases (Fad) in Atlantic salmon (Salmo salar L.): Gene and cDNA characterization, functional expression, tissue distribution and nutritional regulation

Monroig

Zheng

Morais

et al. 2010

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biolog

120

104

View full text Add to dashboard Cite

Fish are the primary source in the human food basket of the n-3 long-chain polyunsaturated fatty acids (LC-PUFA), eicosapentaenoate (EPA; 20:5n-3) and docosahexaenoate (DHA;, that are crucial to the health of higher vertebrates. Atlantic salmon are able to synthesis EPA and DHA from 18:3n-3 through reactions catalyzed by fatty acyl desaturases (Fad) and elongases of very long fatty acids (Elovl). Previously, two cDNAs encoding functionally distinct Δ5 and Δ6 Fads were isolated, but screening of a genomic DNA library revealed the existence of more putative fad genes in the Atlantic salmon genome. In the present study, we show that there are at least four genes encoding putative Fad proteins in Atlantic salmon. Two genes, Δ6fad_a and Δ5fad, corresponded to the previously cloned Δ6 and Δ5 Fad cDNAs. Functional characterization by heterologous expression in yeast showed that the cDNAs for both the two further putative fad genes, Δ6fad_b and Δ6fad_c, had only Δ6 activity, converting 47 and 12 % of 18:3n-3 to 18:4n-3, and 25 and 7 % of 18:2n-6 to 18:3n-6, for ∆6Fad_b and Δ6Fad_c, respectively. Both ∆6fad_a and ∆6fad_b genes were highly expressed in intestine (pyloric caeca), liver and brain, with ∆6fad_b also highly expressed in gill, whereas ∆6fad_c transcript was found predominantly in brain, with lower expression levels in all other tissues. The expression levels of the ∆6fad_a gene in liver and the ∆6fad_b gene in intestine were significantly higher in fish fed diets containing vegetable oil compared to fish fed fish oil suggesting up-regulation in response to reduced dietary EPA and DHA. In contrast, no significant differences were found between transcript levels for ∆6fad_a in intestine, ∆6fad_b in liver, or ∆6fad_c in liver or intestine of fish fed vegetable oil compared to fish fed fish oil. The observed differences in tissue expression and nutritional regulation of the fad genes were discussed in relation to gene structures and fish physiology.3

show abstract

“…The best documented instances of HT between the nuclear genomes of multicellular eukaryotes involve mobile genetic elements, and in particular class 2 or DNA mediated transposons (7,8). Thus far, conspicuous cases of HT of DNA transposons have been detected among insects (8)(9)(10)(11)(12), fish (13) and, in one example, between plants (14). Germline invasions by retroviruses have been documented for several mammals (15)(16)(17)(18), and there is mounting evidence supporting the horizontal introduction of a snake retroposon in ruminants (19,20).…”

mentioning

confidence: 99%

Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods

Pace

Gilbert

Clark

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

194

214

View full text Add to dashboard Cite

Horizontal transfer (HT) is central to the evolution of prokaryotic species. Selfish and mobile genetic elements, such as phages, plasmids, and transposons, are the primary vehicles for HT among prokaryotes. In multicellular eukaryotes, the prevalence and evolutionary significance of HT remain unclear. Here, we identified a set of DNA transposon families dubbed SPACE INVADERS (or SPIN) whose consensus sequences are Ϸ96% identical over their entire length (2.9 kb) in the genomes of murine rodents (rat/mouse), bushbaby (prosimian primate), little brown bat (laurasiatherian), tenrec (afrotherian), opossum (marsupial), and two non-mammalian tetrapods (anole lizard and African clawed frog). In contrast, SPIN elements were undetectable in other species represented in the sequence databases, including 19 other mammals with draft whole-genome assemblies. This patchy distribution, coupled with the extreme level of SPIN identity in widely divergent tetrapods and the overall lack of selective constraint acting on these elements, is incompatible with vertical inheritance, but strongly indicative of multiple horizontal introductions. We show that these germline infiltrations likely occurred around the same evolutionary time (15-46 mya) and spawned some of the largest bursts of DNA transposon activity ever recorded in any species lineage (nearly 100,000 SPIN copies per haploid genome in tenrec). The process also led to the emergence of a new gene in the murine lineage derived from a SPIN transposase. In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species. genome evolution ͉ lateral gene transfer ͉ transposable elements ͉ transposase L ateral or horizontal transfer (HT), the transfer of genetic material between reproductively isolated species, is a frequent occurrence in prokaryotes with selfish and mobile genetic elements such as phages, plasmids, and transposons, serving as the primary vehicles for HT of prokaryotic genes (1). In contrast, reports of HT are scarce in eukaryotes and most cases of nuclear acquisition implicate transfers from prokaryotes or endosymbionts (2-6). The best documented instances of HT between the nuclear genomes of multicellular eukaryotes involve mobile genetic elements, and in particular class 2 or DNA mediated transposons (7,8). Thus far, conspicuous cases of HT of DNA transposons have been detected among insects (8-12), fish (13) and, in one example, between plants (14). Germline invasions by retroviruses have been documented for several mammals (15-18), and there is mounting evidence supporting the horizontal introduction of a snake retroposon in ruminants (19,20). However, to our knowledge, there has been no substantiated report of HT of DNA transposons in mammals. Here, we present unequivocal evidence for the repeated HT of a DNA transposon family named SPACE INVADERS in 7 tetrapod lineages, including 5 mammalian orders. ResultsDiscovery of SPIN Transposons. While surveying DNA transposons in the draft...

show abstract

Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids

Cited by 135 publications

References 47 publications

The Mobilome of Reptiles: Evolution, Structure, and Function

The Mobilome of Reptiles: Evolution, Structure, and Function

Multiple genes for functional ∆6 fatty acyl desaturases (Fad) in Atlantic salmon (Salmo salar L.): Gene and cDNA characterization, functional expression, tissue distribution and nutritional regulation

Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods

Contact Info

Product

Resources

About