scholarly journals Evolutionary study of the 412/mdg1 lineage of the Ty3/gypsy group of LTR retrotransposons in Diptera

2020 ◽  
Author(s):  
Natasha Avila Bertocchi ◽  
Fabiano Pimentel Torres ◽  
Maríndia Deprá ◽  
Vera Lúcia da Silva Valente
Keyword(s):  
Drosophila Melanogaster ◽  
Evolutionary History ◽  
Ribonuclease H ◽  
Tsetse Flies ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Long Terminal Repeats ◽  
Gypsy Group ◽  
History Of ◽  
Small Orfs

AbstractLTR-retrotransposons are structurally similar to retroviruses, as they possess the enzymes reverse transcriptase, Ribonuclease H, integrase, proteinase, and the gag gene and are flanked by long terminal repeats (LTRs). The 412/mdg1 lineage, belonging to the Ty3/Gypsy group, consists of the TEs 412, mdg1, stalker, pilgrim, and blood. The 412/mdg1 lineage is distinguished from the others in the gypsy group in that it has small ORFs at the beginning of the TE and is highly similar to the pol ORF among the TEs that make up the lineage. In this study, our aim was to elucidate the evolutionary history of the 412/mdg1 lineage in the 127 dipteran genomes available to date, and the characteristics of the sequences in each genome. We used the canonical TE 412 probe described in Drosophila melanogaster as the query. We found sequences homologous to the 412/mdg1 lineage restricted to the suborder Brachycera. These sequences are widely distributed in drosophilids but are also present in other groups of flies. We note the presence of the 412/mg1 lineage in tsetse flies (Glossina). Furthermore, our results showed an elaborate evolutionary history for the pol ORF in the 412/mdg1 lineage of the LTR-Retrotransposon.

scholarly journals Evolutionary History of LTR Retrotransposon Chromodomains in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Anton Novikov ◽  
Georgiy Smyshlyaev ◽  
Olga Novikova
Keyword(s):  
Evolutionary History ◽  
Higher Plants ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Moss Species ◽  
Plant Genomes ◽  
Group I ◽  
Wide Range ◽  
History Of ◽  
Computer Based

Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.

scholarly journals copia-, gypsy- and LINE-Like Retrotransposon Fragments in the Mitochondrial Genome of Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 579-585 ◽  
Author(s):  
Volker Knoop ◽  
Michael Unseld ◽  
Joachim Marienfeld ◽  
Petra Brandt ◽  
Sabine Sünkel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Mitochondrial Genome ◽  
Evolutionary History ◽  
Nuclear Genome ◽  
Plant Mitochondrial Genome ◽  
Gypsy Group ◽  
History Of

Abstract Several retrotransposon fragments are integrated in the mitochondrial genome of Arabidopsis thaliana. These insertions are derived from all three classes of nuclear retrotransposons, the Tyl/copia, Ty3/gypsy- and non-LTR/LINE-families. Members of the Ty3/gypsy group of elements have not yet been identified in the nuclear genome of Arabidopsis. The varying degrees of similarity with nuclear elements and the dispersed locations of the sequences in the mitochondrial genome suggest numerous independent transfer-insertion events in the evolutionary history of this plant mitochondrial genome. Overall, we estimate remnants of retrotransposons to cover ≥5% of the mitochondrial genome in Arabidopsis.

scholarly journals Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Mobile DNA ◽  
2013 ◽  
Vol 4 (1) ◽  
pp. 5 ◽  
Author(s):  
Farid Benachenhou ◽  
Göran O Sperber ◽  
Erik Bongcam-Rudloff ◽  
Göran Andersson ◽  
Jef D Boeke ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Long Terminal Repeats ◽  
History Of ◽  
Terminal Repeats

scholarly journals A Sister Lineage of Sampled Retroviruses Corroborates the Complex Evolution of Retroviruses

2020 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Evolutionary History ◽  
Rna Viruses ◽  
Phylogenetic Analyses ◽  
Ribonuclease H ◽  
Genome Architecture ◽  
Major Lineage ◽  
Wide Range ◽  
History Of ◽  
Negative Sense ◽  
Complex Evolutionary History

Abstract The origin and deep history of retroviruses remain mysterious and contentious, largely because the diversity of retroviruses is incompletely understood. Here, we report the discovery of lokiretroviruses, a novel major lineage of retroviruses, within the genomes of a wide range of vertebrates (at least 137 species), including lampreys, ray-finned fishes, lobe-finned fishes, amphibians, and reptiles. Lokiretroviruses share a similar genome architecture with known retroviruses, but display some unique features. Interestingly, lokiretrovirus Env proteins share detectable similarity with fusion glycoproteins of viruses within the Mononegavirales order, blurring the boundary between retroviruses and negative sense single-stranded RNA viruses. Phylogenetic analyses based on reverse transcriptase demonstrate that lokiretroviruses are sister to all the retroviruses sampled to date, providing a crucial nexus for studying the deep history of retroviruses. Comparing congruence between host and virus phylogenies suggests lokiretroviruses mainly underwent cross-species transmission. Moreover, we find that retroviruses replaced their ribonuclease H and integrase domains multiple times during their evolutionary course, revealing the importance of domain shuffling in the evolution of retroviruses. Overall, our findings greatly expand our views of the diversity of retroviruses, and provide novel insights into the origin and complex evolutionary history of retroviruses.

scholarly journals Restriction map variation at the adh locus of Drosophila melanogaster in inverted and noninverted chromosomes.

Genetics ◽  
1988 ◽  
Vol 119 (1) ◽  
pp. 135-140
Author(s):  
M Aguade
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
Evolutionary History ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Restriction Map ◽  
Allozyme Polymorphism ◽  
Length Polymorphisms ◽  
History Of ◽  
Restriction Site Polymorphisms

Abstract Restriction map variation among 39 Standard and 40 In(2L)t chromosomes extracted from a Spanish natural population of Drosophila melanogaster was investigated for a 2.7-kb region encompassing the Adh locus with ten four-cutter restriction enzymes. A total of 20 polymorphisms were detected, representing 15 restriction site polymorphisms, 4 length polymorphisms and the allozyme polymorphism. Variation at the DNA level was compared among St-Adh(F), St-Adh(S) and t-Adh(S) chromosomes. t-Adh(S) chromosomes show a higher level of variation than St-Adh(F) chromosomes. This suggests that In(2L)t arose before the fast/slow allozyme divergence in the evolutionary history of D. melanogaster.

scholarly journals Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster

PLoS Genetics ◽  
2020 ◽  
Vol 16 (11) ◽  
pp. e1009110
Author(s):  
Priscilla A. Erickson ◽  
Cory A. Weller ◽  
Daniel Y. Song ◽  
Alyssa S. Bangerter ◽  
Paul Schmidt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
North America ◽  
Evolutionary History ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Complex Trait ◽  
Hybrid Swarm ◽  
Evolutionary Patterns ◽  
Hybrid Swarms ◽  
History Of

Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them to exploit favorable seasons and avoid unfavorable ones. Local adapation can result in variation in seasonal responses, but the genetic basis and evolutionary history of this variation remains elusive. Many insects, including Drosophila melanogaster, are able to undergo an arrest of reproductive development (diapause) in response to unfavorable conditions. In D. melanogaster, the ability to diapause is more common in high latitude populations, where flies endure harsher winters, and in the spring, reflecting differential survivorship of overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined the genetic basis and evolutionary history of ovarian diapause. We exposed outbred females to different temperatures and day lengths, characterized ovarian development for over 2800 flies, and reconstructed their complete, phased genomes. We found that diapause, scored at two different developmental cutoffs, has modest heritability, and we identified hundreds of SNPs associated with each of the two phenotypes. Alleles associated with one of the diapause phenotypes tend to be more common at higher latitudes, but these alleles do not show predictable seasonal variation. The collective signal of many small-effect, clinally varying SNPs can plausibly explain latitudinal variation in diapause seen in North America. Alleles associated with diapause are segregating in Zambia, suggesting that variation in diapause relies on ancestral polymorphisms, and both pro- and anti-diapause alleles have experienced selection in North America. Finally, we utilized outdoor mesocosms to track diapause under natural conditions. We found that hybrid swarms reared outdoors evolved increased propensity for diapause in late fall, whereas indoor control populations experienced no such change. Our results indicate that diapause is a complex, quantitative trait with different evolutionary patterns across time and space.

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