scholarly journals Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits (Laticauda)

2021 ◽  
Author(s):  
James D Galbraith ◽  
Alastair J Ludington ◽  
Kate L Sanders ◽  
Alexander SJ Suh ◽  
David L Adelson
Keyword(s):  
Horizontal Transfer ◽  
Driving Force ◽  
Regulatory Elements ◽  
Rapid Expansion ◽  
Marine Habitat ◽  
Dna Transposon ◽  
Genomic Changes ◽  
Genetic Sequences ◽  
New Hosts ◽  
Explosive Expansion

Transposable elements (TEs) are self replicating genetic sequences and are often described as important drivers of evolution. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions will be neutral or harmful, therefore host genomes have evolved machinery to supress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonise new genomes, and since new hosts may not be able to shut them down, these TEs may proliferate rapidly. Here we describe HTT of the Harbinger-Snek DNA transposon into sea kraits (Laticauda), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids ~15-25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8-12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.

scholarly journals Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits ( Laticauda )

2021 ◽  
Vol 17 (9) ◽  
pp. 20210342
Author(s):  
James D. Galbraith ◽  
Alastair J. Ludington ◽  
Kate L. Sanders ◽  
Alexander Suh ◽  
David L. Adelson
Keyword(s):  
Horizontal Transfer ◽  
Driving Force ◽  
Regulatory Elements ◽  
Rapid Expansion ◽  
Marine Habitat ◽  
Dna Transposon ◽  
Genomic Changes ◽  
Genetic Sequences ◽  
New Hosts ◽  
Explosive Expansion

Transposable elements (TEs) are self-replicating genetic sequences and are often described as important ‘drivers of evolution’. This driving force is because TEs promote genomic novelty by enabling rearrangement, and through exaptation as coding and regulatory elements. However, most TE insertions potentially lead to neutral or harmful outcomes, therefore host genomes have evolved machinery to suppress TE expansion. Through horizontal transposon transfer (HTT) TEs can colonize new genomes, and since new hosts may not be able to regulate subsequent replication, these TEs may proliferate rapidly. Here, we describe HTT of the Harbinger-Snek DNA transposon into sea kraits ( Laticauda ), and its subsequent explosive expansion within Laticauda genomes. This HTT occurred following the divergence of Laticauda from terrestrial Australian elapids approximately 15–25 Mya. This has resulted in numerous insertions into introns and regulatory regions, with some insertions into exons which appear to have altered UTRs or added sequence to coding exons. Harbinger-Snek has rapidly expanded to make up 8–12% of Laticauda spp. genomes; this is the fastest known expansion of TEs in amniotes following HTT. Genomic changes caused by this rapid expansion may have contributed to adaptation to the amphibious-marine habitat.

Uniform cell-autonomous tumorigenesis of the choroid plexus by papovavirus large T antigens

1991 ◽  
Vol 11 (12) ◽  
pp. 5968-5976
Author(s):  
J D Chen ◽  
T Van Dyke
Keyword(s):  
Transgenic Mice ◽  
Choroid Plexus ◽  
Simian Virus 40 ◽  
Regulatory Elements ◽  
Simian Virus ◽  
T Antigen ◽  
Rapid Expansion ◽  
Morphological Transformation ◽  
Large Tumor ◽  
Lymphotropic Papovavirus

The simian virus 40 (SV40) large tumor antigen (T antigen) under its natural regulatory elements induces choroid plexus papillomas in transgenic mice. Because these tumors develop focally after several months, it has been suggested that secondary cellular alterations are required to induce a tumor in this tissue. In contrast to SV40, the related lymphotropic papovavirus early region induces rapid nonfocal choroid plexus neoplasia in transgenic mice. Here, using hybrid gene constructs, we showed that T antigen from either virus in in fact sufficient to induce these tumors. Their abilities to induce proliferative abnormalities in other tissues, such as kidney and thymus, were also indistinguishable. Differences in the rate of choroid plexus tumorigenesis reflected differences in the control regions of the two viruses, rather than differences in T antigen per se. Under SV40 regulation, expression was limited to a fraction of the choroid plexus cells prior to the formation of focal tumors. When SV40 T antigen was placed under lymphotropic papovavirus control, in contrast, expression was generally uniform in the choroid plexus and rapid expansion of the tissue ensued. We found a direct relationship between T-antigen expression, morphological transformation, and proliferation of the choroid plexus epithelial cells. Analysis of mosaic transgenic mice indicated further that T antigen exerts its mitogenic effect cell autonomously. These studies form the foundation for elucidating the role of various T-antigen subactivities in tumorigenesis.

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

2008 ◽  
Vol 105 (44) ◽  
pp. 17023-17028 ◽  
Author(s):  
J. K. Pace ◽  
C. Gilbert ◽  
M. S. Clark ◽  
C. Feschotte
Keyword(s):  
Horizontal Transfer ◽  
Dna Transposon

scholarly journals New Environment, New Invaders—Repeated Horizontal Transfer of LINEs to Sea Snakes

2020 ◽  
Vol 12 (12) ◽  
pp. 2370-2383 ◽  
Author(s):  
James D. Galbraith ◽  
Alastair J. Ludington ◽  
Alexander Suh ◽  
Kate L. Sanders ◽  
David L. Adelson
Keyword(s):  
Marine Environment ◽  
Horizontal Transfer ◽  
Marine Invertebrates ◽  
Genomic Sequence ◽  
Marine Species ◽  
Ecological Interactions ◽  
Marine Habitat ◽  
Sea Snakes ◽  
The One ◽  
Genomic Material

Abstract Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway “Circadian Entrainment.” This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.

scholarly journals Next-Generation Sequencing Reveals Recent Horizontal Transfer of a DNA Transposon between Divergent Mosquitoes

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16743 ◽  
Author(s):  
Yupu Diao ◽  
Yumin Qi ◽  
Yajun Ma ◽  
Ai Xia ◽  
Igor Sharakhov ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Horizontal Transfer ◽  
Next Generation ◽  
Dna Transposon ◽  
Generation Sequencing

scholarly journals Parallel Genomic Changes Drive Repeated Evolution of Placentas in Live-Bearing Fish

2021 ◽  
Author(s):  
Henri van Kruistum ◽  
Reindert Nijland ◽  
David N Reznick ◽  
Martien A M Groenen ◽  
Hendrik-Jan Megens ◽  
...  
Keyword(s):  
Complex Traits ◽  
Evolutionary Rate ◽  
Complex Trait ◽  
Regulatory Elements ◽  
Evolutionary Origin ◽  
Regulatory Change ◽  
Protein Coding ◽  
Genomic Changes ◽  
Rate Analysis ◽  
Repeated Evolution

Abstract The evolutionary origin of complex organs challenges empirical study because most organs evolved hundreds of millions of years ago. The placenta of live-bearing fish in the family Poeciliidae represents a unique opportunity to study the evolutionary origin of complex organs, because in this family a placenta evolved at least nine times independently. It is currently unknown whether this repeated evolution is accompanied by similar, repeated, genomic changes in placental species. Here, we compare whole genomes of 26 poeciliid species representing six out of nine independent origins of placentation. Evolutionary rate analysis revealed that the evolution of the placenta coincides with convergent shifts in the evolutionary rate of 78 protein-coding genes, mainly observed in transporter- and vesicle-located genes. Furthermore, differences in sequence conservation showed that placental evolution coincided with similar changes in 76 noncoding regulatory elements, occurring primarily around genes that regulate development. The unexpected high occurrence of GATA simple repeats in the regulatory elements suggests an important function for GATA repeats in developmental gene regulation. The distinction in molecular evolution observed, with protein-coding parallel changes more often found in metabolic and structural pathways, compared with regulatory change more frequently found in developmental pathways, offers a compelling model for complex trait evolution in general: changing the regulation of otherwise highly conserved developmental genes may allow for the evolution of complex traits.

scholarly journals Transposon mediated horizontal transfer of the host-specific virulence protein ToxA between three fungal wheat pathogens

2019 ◽  
Author(s):  
Megan C. McDonald ◽  
Adam P. Taranto ◽  
Erin Hill ◽  
Benjamin Schwessinger ◽  
Zhaohui Liu ◽  
...  
Keyword(s):  
Horizontal Transfer ◽  
Genomic Island ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Type Ii ◽  
Dna Transposon ◽  
Coding Regions ◽  
Link Type ◽  
Pyrenophora Tritici Repentis ◽  
Virulence Protein

ABSTRACTMost known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where non-coding DNA is also reported. The gene encoding the wheat virulence protein ToxA and surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis and Bipolaris sorokiniana) as part of a conserved ∼14kb element, which contains coding and non-coding regions. Here we use long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal level assemblies enabled identification of terminal inverted repeats on either end of the 14kb region, typical of a Type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-250 kb) transposon-rich genomic island which is absent in toxA- isolates. We demonstrate that the horizontal transfer of ToxhAT between Pyrenophora tritici-repentis and P. nodorum occurred as part of a large ∼80kb HGT which is now undergoing extensive decay. In contrast, in B. sorokiniana ToxhAT and its resident genomic island are mobile within the genome. Together these data provide insight into the non-coding regions that facilitate HGT between eukaryotes and the genomic processes which mask the extent of HGT between these species.IMPORTANCEThis work dissects the tripartite horizontal transfer of ToxA; a gene that has a direct negative impact on global wheat yields. Defining the extent of horizontally transferred DNA is important because it can provide clues as to the mechanisms that facilitate HGT. Our analysis of ToxA and its surrounding 14kb suggests that this gene was horizontally transferred in two independent events, with one event likely facilitated by a Type II DNA transposon. These horizontal transfer events are now in various processes of decay in each species due to the repeated insertion of new transposons and subsequent rounds of targeted mutation by a fungal genome defense mechanism known as repeat induced point-mutation. This work highlights the role that HGT plays in the evolution of host adaptation in eukaryotic pathogens. It also increases the growing body of evidence that transposons facilitate adaptive HGT events between fungi present in similar environments and hosts.DATA AVAILABILITYAll raw sequencing data is available under NCBI BioProject PRJNA505097.The P. nodorum SN15 Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession SSHU00000000. The version SSHU01000000 is described in this paper. The P. nodorum SN79-1087 Whole Genome Shotgun project has been deposited under the accessions CP039668-CP039689. The Whole Genome shotgun project and accession numbers for B. sorokiniana isolates are as follows: CS10; SRZH00000000, CS27; SRZG00000000, WAI2406; SRZF00000000, WAI2411; SRZE00000000. Transposon annotations, CS10 and CS27 gene annotations are available at https://github.com/megancamilla/Transposon-Mediated-transfer-of-ToxA

scholarly journals Horizontal transfer and southern migration: the tale of Hydrophiinae′s marine journey.

2021 ◽  
Author(s):  
James Douglas Galbraith ◽  
Alastair J Ludington ◽  
Richard J Edwards ◽  
Kate L Sanders ◽  
Alexander Suh ◽  
...  
Keyword(s):  
Horizontal Transfer ◽  
Comparative Research ◽  
Marine Species ◽  
Regulatory Elements ◽  
Ecological Niches ◽  
A Genome ◽  
Tangible Evidence ◽  
Jumping Genes ◽  
Genetic Novelty ◽  
Broad Scale

Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they can be exapted as coding and regulatory elements, or can promote genetic rearrangement. In so doing TEs act as a source of genetic novelty, hence understanding TE evolution within lineages is key in understanding adaptation to their environment. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. The few broad scale studies in Squamata which have been conducted found both the diversity and total number of TEs differs significantly across the entire order. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if this pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~15-25 Mya and have since rapidly diversified into 6 amphibious, ~60 marine and ~100 terrestrial species which fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three transferred into the ancestral hydrophiine likely from marine species. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.

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