scholarly journals Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Olga Raskina
Keyword(s):  
Transposable Elements ◽  
Mobile Element ◽  
Plant Genome ◽  
Aegilops Speltoides ◽  
Genome Architecture ◽  
Different Types ◽  
In The Wild ◽  
Species Specific ◽  
Current Species

Repetitive DNA—specifically, transposable elements (TEs)—is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

scholarly journals Transposable elements and gene expression during the evolution of amniotes

2018 ◽  
Author(s):  
Lu Zeng ◽  
Stephen M. Pederson ◽  
R. Daniel Kortschak ◽  
David L. Adelson
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Regulation Of Gene Expression ◽  
Specific Gene ◽  
Evolutionary Novelty ◽  
Regulatory Motifs ◽  
Bearded Dragon ◽  
Different Types ◽  
Developmental Gene Regulation ◽  
Species Specific

AbstractBackgroundTransposable elements (TEs) are primarily responsible for the changes in genome sequences that occur over time within and between species. TEs themselves evolve, with clade specific LTR/ERV, LINEs and SINEs responsible for the bulk of species specific genomic features. Because TEs can contain regulatory motifs, they can be exapted as regulators of gene expression. While TE insertions can provide evolutionary novelty for the regulation of gene expression, their overall impact on the evolution of gene expression is unclear. Previous investigators have shown that tissue specific gene expression in amniotes is more similar across species than within species, supporting the existence of conserved developmental gene regulation. In order to understand how species specific TE insertions might affect the evolution/conservation of gene expression, we have looked at the association of gene expression in six tissues with TE insertions in six representative amniote genomes (human, opossum, platypus, anole lizard, bearded dragon and chicken).ResultsWe have used a novel bootstrapping approach to minimise the conflation of effects of repeat types on gene expression. We compared the expression of orthologs containing different types of recent TE insertions to orthologs that contained older TE insertions and found significant differences in gene expression associated with TE insertions. Likewise, we compared the expression of non-ortholog genes containing different types of recent TE insertions to non-orthologs with older TE insertions and found significant differences in gene expression associated with TE insertions. As expected TEs were associated with species-specific changes in gene expression, but the magnitude and direction of change of expression changes were unexpected. Overall, orthologs containing clade specific TEs were associated with lower gene expression, while in non-orthologs, non clade-specific TEs were associated with higher gene expression. Exceptions were SINE elements in human and chicken, which had an opposite association with gene expression compared to other species.ConclusionsOur observed species-specific associations of TEs with gene expression support a role for TEs in speciation/response to selection by species. TEs do not exhibit consistent associations with gene expression and observed associations can vary depending on the age of TE insertions. Based on these observations, it would be prudent to refrain from extrapolating these and previously reported associations to distantly related species.

scholarly journals How to be a great dad: Parental care in a flock of greater flamingo (Phoenicopterus roseus)

2017 ◽  
Author(s):  
Camillo Sandri ◽  
Vittoria Vallarin ◽  
Carolina Sammarini ◽  
Barbara Regaiolli ◽  
Alessandra Piccirillo ◽  
...  
Keyword(s):  
Parental Care ◽  
Bird Species ◽  
Ex Situ ◽  
Controlled Environment ◽  
Science Literature ◽  
Nest Protection ◽  
In The Wild ◽  
Species Specific ◽  
Greater Flamingos

The zoo-science literature on flamingos, and avian species in general, is lacking. However, this kind of research is important to improve the knowledge on these species and to improve their ex-situ and in-situ conservation. The aims of the present study were to assess the welfare of a captive colony of greater flamingo hosted at Parco Natura Viva, an Italian zoological garden, through ethological parameters and to improve the knowledge on this species in zoological gardens. In particular, the present study investigated and compared the parental care of females and males in 35 breeding pairs of greater flamingos. For each pair, we collected data on the parental care behaviour of both females and males, recording their position in relation to the nest (near the nest, on the nest, away from the nest) and the behavioural category that was performed. The main results were that males spent more time than females on the nest and near it and were more aggressive toward other flamingos. Therefore, male flamingos seem to be more involved in incubation duties and nest protection than females. Greater flamingos of this study performed species-specific behaviours. Both parents were involved in parental care and displayed all the activities reported in the wild. Therefore, the study flock of greater flamingos seems to be in a good welfare. This kind of research is important not only to expand the knowledge on bird species such as flamingos, but also to improve their husbandry and breeding in controlled environment.

scholarly journals How to be a great dad: Parental care in a flock of greater flamingo (Phoenicopterus roseus)

2017 ◽  
Author(s):  
Camillo Sandri ◽  
Vittoria Vallarin ◽  
Carolina Sammarini ◽  
Barbara Regaiolli ◽  
Alessandra Piccirillo ◽  
...  
Keyword(s):  
Parental Care ◽  
Bird Species ◽  
Ex Situ ◽  
Controlled Environment ◽  
Science Literature ◽  
Nest Protection ◽  
In The Wild ◽  
Species Specific ◽  
Greater Flamingos

The zoo-science literature on flamingos, and avian species in general, is lacking. However, this kind of research is important to improve the knowledge on these species and to improve their ex-situ and in-situ conservation. The aims of the present study were to assess the welfare of a captive colony of greater flamingo hosted at Parco Natura Viva, an Italian zoological garden, through ethological parameters and to improve the knowledge on this species in zoological gardens. In particular, the present study investigated and compared the parental care of females and males in 35 breeding pairs of greater flamingos. For each pair, we collected data on the parental care behaviour of both females and males, recording their position in relation to the nest (near the nest, on the nest, away from the nest) and the behavioural category that was performed. The main results were that males spent more time than females on the nest and near it and were more aggressive toward other flamingos. Therefore, male flamingos seem to be more involved in incubation duties and nest protection than females. Greater flamingos of this study performed species-specific behaviours. Both parents were involved in parental care and displayed all the activities reported in the wild. Therefore, the study flock of greater flamingos seems to be in a good welfare. This kind of research is important not only to expand the knowledge on bird species such as flamingos, but also to improve their husbandry and breeding in controlled environment.

scholarly journals Supernumerary B Chromosomes and Plant Genome Changes: A Snapshot of Wild Populations of Aegilops speltoides Tausch (Poaceae, Triticeae)

2020 ◽  
Vol 21 (11) ◽  
pp. 3768 ◽  
Author(s):  
Imad Shams ◽  
Olga Raskina
Keyword(s):  
B Chromosomes ◽  
Plant Genome ◽  
Aegilops Speltoides ◽  
Genomic Component ◽  
Dna Damage And Repair ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers ◽  
Number Dynamics ◽  
Species Specific ◽  
The Impact

In various eukaryotes, supernumerary B chromosomes (Bs) are an optional genomic component that affect their integrity and functioning. In the present study, the impact of Bs on the current changes in the genome of goatgrass, Aegilops speltoides, was addressed. Individual plants from contrasting populations with and without Bs were explored using fluorescence in situ hybridization. In parallel, abundances of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons (TEs), and the species-specific Spelt1 tandem repeat (TR) in vegetative and generative spike tissues were estimated by real-time quantitative PCR. The results revealed: (i) ectopic associations between Bs and the regular A chromosomes, and (ii) cell-specific rearrangements of Bs in both mitosis and microgametogenesis. Further, the copy numbers of TEs and TR varied significantly between (iii) genotypes and (iv) different spike tissues in the same plant(s). Finally, (v) in plants with and without Bs from different populations, genomic abundances and/or copy number dynamics of TEs and TR were similar. These findings indicate that fluctuations in TE and TR copy numbers are associated with DNA damage and repair processes during cell proliferation and differentiation, and ectopic recombination is one of the mechanisms by which Bs play a role in genome changes.

scholarly journals Co-opted transposons help perpetuate conserved higher-order chromosomal structures

2018 ◽  
Author(s):  
Mayank NK Choudhary ◽  
Ryan Z Friedman ◽  
Julia T Wang ◽  
Hyo Sik Jang ◽  
Xiaoyu Zhuo ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Binding Site ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Genome Architecture ◽  
3D Genome ◽  
Domain Structures ◽  
Architectural Proteins ◽  
Mammalian Genomes ◽  
Species Specific

ABSTRACTTransposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include architectural proteins—such as CTCF, RAD21 and SMC3—that are involved in tethering chromatin loops and marking domain boundaries. The 3D organization of the mammalian genome is intimately linked to its function and is remarkably conserved. However, the mechanisms by which these structural intricacies emerge and evolve have not been thoroughly probed. Here we show that TEs contribute extensively to both the formation of species-specific loops in humans and mice via deposition of novel anchoring motifs, as well as to the maintenance of conserved loops across both species via CTCF binding site turnover. The latter function demonstrates the ability of TEs to contribute to genome plasticity and reinforce conserved genome architecture as redundant loop anchors. Deleting such candidate TEs in human cells leads to a collapse of such conserved loop and domain structures. These TEs are also marked by reduced DNA methylation and bear mutational signatures of hypomethylation through evolutionary time. TEs have long been considered a source of genetic innovation; by examining their contribution to genome topology, we show that TEs can contribute to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture globally, revealing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation.One-sentence summaryCo-option of transposable elements maintains conserved 3D genome structures via CTCF binding site turnover in human and mouse.

scholarly journals How to be a great dad: parental care in a flock of greater flamingo (Phoenicopterus roseus)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3404 ◽  
Author(s):  
Camillo Sandri ◽  
Vittoria Vallarin ◽  
Carolina Sammarini ◽  
Barbara Regaiolli ◽  
Alessandra Piccirillo ◽  
...  
Keyword(s):  
Parental Care ◽  
Bird Species ◽  
Social Needs ◽  
Ex Situ ◽  
Nest Protection ◽  
Zoo Animals ◽  
In The Wild ◽  
Species Specific ◽  
Greater Flamingos

In the last years, studies on captive greater flamingos have increased. Research on zoo animals is important to improve the knowledge on these species and to improve their ex-situ and in-situ conservation. The aim of the present study was to investigate the parental behaviour of a captive colony of greater flamingo hosted at Parco Natura Viva, an Italian zoological garden, to improve the knowledge on this species in zoos. In particular, the present study investigated and compared the parental care of females and males in 35 breeding pairs of greater flamingos. For each pair, we collected durations of parental care behaviour of both females and males, recording their position in relation to the nest (near the nest, on the nest, away from the nest) and individual and social behaviours performed. First, both partners were involved in parental care and displayed species-specific behaviours reported in the wild. The main results were that males spent more time than females on the nest (P = 0.010) and near it (P = 0.0001) and were more aggressive toward other flamingos than females, both when sitting on the nest (P = 0.003) and when near the nest (P = 0.0003). Therefore, male flamingos seem to be more involved in incubation duties and nest protection than females. This kind of research is important not only to expand the knowledge on bird species such as flamingos, but also to improve their husbandry and breeding in controlled environment. Indeed, understanding animal behaviour allows us to gain insights into their individual and social needs, addressing potential animal welfare issues.

Pb Electrodeposition in the Presence of Chlorine Ions on Cu(100): An in Situ Optical Reflectivity Difference Study

2003 ◽  
Vol 781 ◽  
Author(s):  
J. Gray ◽  
W. Schwarzacher ◽  
X.D. Zhu
Keyword(s):  
Oblique Incidence ◽  
Opposite Sign ◽  
Bulk Phase ◽  
Phase Layer ◽  
Optical Reflectivity ◽  
Scan Rate ◽  
Different Types ◽  
Chlorine Ions ◽  
High Overpotentials

AbstractWe studied the initial stages of the electrodeposition of Pb in the presence of chlorine ions on Cu(100), using an oblique-incidence optical reflectivity difference (OIRD) technique. The OI-RD results reveal that immediately following the underpotential deposition (UPD) of the first Pb monolayer, two different types of bulk-phase films grow depending upon the magnitude of overpotential and cyclic voltammetry (CV) scan rate. At low overpotentials and/or slow scan rates, we propose that a bulk-phase Pb film grows on top of the UPD monolayer. At high overpotentials and/or fast scan rates, either a PbO, PbCl2, or a rough Pb bulk-phase layer grows on top of the UPD layer such that the reflectivity difference signal from such a film has an opposite sign.

THE ESSENTIAL CONTRIBUTION OF CAPTIVE SUMATRAN ELEPHANT IN ELEPHANT TRAINING CENTER, WAY KAMBAS NATIONAL PARK FOR WILDLIFE GENETICS CONSERVATION

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Elly Lestari Rustiati ◽  
Priyambodo Priyambodo ◽  
Yanti Yulianti ◽  
Eko Agus Srihanto ◽  
Dian Neli Pratiwi ◽  
...  
Keyword(s):  
National Park ◽  
In Situ Conservation ◽  
Training Center ◽  
Conservation Effort ◽  
In The Wild ◽  
Wildlife Genetics ◽  
Way Kambas National Park ◽  
Human Conflict ◽  
Essential Contribution

Way Kambas National Park (WKNP) is home of five protected big mammals including sumatran elephants.  It shares its border with 22 of 37 villages surrounding the national park.  Understanding their existence in the wild is a priority, and  wildlife genetics is a crucially needed. Besides poaching and habitat fragmentation, wildlife-human conflict is one big issue.  Elephant Training Center (ETC) in WKNP is built for semi in-situ conservation effort on captive sumatran elephants that mainly have conflict histories with local people.  Participative observation and bio-molecular analysis were conducted to learn the importance of captive Sumatran elephant for conservation effort.  Through captive sumatran elephants, database and applicable methods are expected to be developed supporting the conservation of their population in the wild.  Participative observation and molecular identification was carried on captive sumatran elephants in ETC, WKNP under multiple year Terapan grant of Ministry of Research and Technology Higher Education, Indonesia. Gene sequence and cytological analyses showed that the captive sumatran elephants are closely related and tend to be domesticated.  Translocation among ETC to avoid inbreeding, and maintaining the captive sumatran elephant as natural as possible are highly recommended. Developing genetic database can be a reference for both captive and wild sumatran elephants.

scholarly journals Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

2021 ◽  
Vol 22 (13) ◽  
pp. 6783
Author(s):  
Renata Orłowska ◽  
Katarzyna A. Pachota ◽  
Wioletta M. Dynkowska ◽  
Agnieszka Niedziela ◽  
Piotr T. Bednarek
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Point Mutations ◽  
Mobile Elements ◽  
Dna Demethylation ◽  
Plant Genome

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

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