Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

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A Comparative Analysis of L1 Retrotransposition Activities in Human Genomes Suggests an Ongoing Increase in L1 Number Despite an Evolutionary Trend Towards Lower Activity

10.21203/rs.3.rs-495389/v1 ◽

2021 ◽

Author(s):

Sawsan Sami Wehbi ◽

Heinrich zu Dohna

Keyword(s):

Cell Culture ◽

Population Dynamics ◽

Comparative Analysis ◽

Transposable Elements ◽

Human Population ◽

Population Level ◽

Evolutionary Trend ◽

Human Genomes ◽

Long Interspersed Nuclear Elements ◽

Insight Into

Abstract BackgroundLINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates.ResultsOur results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in L1s resulting from continuing retrotransposition. ConclusionsTogether, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

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A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity

Mobile DNA ◽

10.1186/s13100-021-00255-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sawsan Sami Wehbi ◽

Heinrich zu Dohna

Keyword(s):

Cell Culture ◽

Population Dynamics ◽

Comparative Analysis ◽

Transposable Elements ◽

Human Population ◽

Population Level ◽

Evolutionary Trend ◽

Human Genomes ◽

Long Interspersed Nuclear Elements ◽

Insight Into

Abstract Background LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates. Results Our results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in active L1s resulting from continuing retrotransposition. Conclusions Together, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

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Faculty Opinions recommendation of Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1019363.227450 ◽

2004 ◽

Author(s):

Philip Benfey

Keyword(s):

Arabidopsis Thaliana ◽

Comparative Analysis ◽

Transposable Elements ◽

Brassica Oleracea ◽

Related Species ◽

Genome Wide

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Faculty Opinions recommendation of Comparative analysis of bat genomes provides insight into the evolution of flight and immunity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717968901.793472443 ◽

2013 ◽

Author(s):

Peter Openshaw ◽

Monika Bajorek

Keyword(s):

Comparative Analysis ◽

Insight Into

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Motivation Configuration of Bluxury Tourism Behavior: An FsQCA Application

Cornell Hospitality Quarterly ◽

10.1177/19389655211014472 ◽

2021 ◽

pp. 193896552110144

Author(s):

Da Shi ◽

Bowen Yi ◽

Fangfang Shi ◽

Simone Satta

Keyword(s):

Comparative Analysis ◽

Complexity Theory ◽

Fuzzy Set ◽

Qualitative Comparative Analysis ◽

Complex Configuration ◽

Physical Factors ◽

Motivation Theory ◽

Main Motivation ◽

Push And Pull ◽

Insight Into

This study investigates the motivation configuration of bluxury tourism behavior. According to complexity theory and push and pull motivation theory, we establish a framework of complex configuration conditions, including push forces, pull forces, and constraints that lead to bluxury tourism. Based on fuzzy-set qualitative comparative analysis, we identified seven main motivation configurations of bluxury tourism behavior covering three core factors: physical factors, seeking/exploration in push forces, and intangible factors in pull forces. In addition, combinations of constraints in the configuration demonstrate various paths leading to bluxury tourism behavior. These findings provide unique insight into bluxury tourism participation.

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RESEARCH INTO THE METHODS OF ANALYSING THE PRODUCTIVITY INDICATORS OF TRANSPORT TERMINALS

Transport ◽

10.3846/1648-4142.2009.24.192-199 ◽

2009 ◽

Vol 24 (3) ◽

pp. 192-199 ◽

Cited By ~ 3

Author(s):

Ilona Jaržemskienė

Keyword(s):

Comparative Analysis ◽

Functional Dependence ◽

Data Envelopment ◽

Analysis Method ◽

Accurate Evaluation ◽

Feasible Alternative ◽

Productivity Indicators ◽

Insight Into ◽

Regressive Analysis

The measurement of terminal productivity is the issue of extreme importance to both terminal owners and management and customers. As the sector of transport is highly intensive in terms of investments into the infrastructure, the productivity of a terminal may play a crucial role in competing with other terminals. Productivity is defined in terms of inputs and output. The majority of the available studies, wherein this issue is addressed, are generally focused on the determination of functional dependence between inputs and output using the method of regressive analysis. The present article provides an insight into the Data Envelopment Analysis method as a tool for measuring productivity. This technique enables a rather accurate evaluation of terminal productivity by means of comparative analysis, which, in fact, appears to be the only feasible alternative in cases where statistic data required for performing regressive analysis is lacking.

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Conjugative plasmids: vessels of the communal gene pool

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0037 ◽

2009 ◽

Vol 364 (1527) ◽

pp. 2275-2289 ◽

Cited By ~ 244

Author(s):

Anders Norman ◽

Lars H. Hansen ◽

Søren J. Sørensen

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Significant Contribution ◽

Prokaryotic Genome ◽

Whole Genome ◽

Adaptive Traits ◽

Conjugative Plasmids ◽

Environmental Setting ◽

Genome Analyses ◽

Insight Into

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.

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