Recent Advances in Transposable Elements-Based Genetic Diversity Assessment, Discovery, and Analysis

A special issue of BioTech (ISSN 2673-6284).

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 8321

Special Issue Editor


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Guest Editor
Institute of Biotechnology, University of Helsinki, Biocentre 3, P.O. Box 65, Viikinkaari 1, 00014 Helsinki, Finland
Interests: genomics and evolution; biology of mobile elements; applications as markers for biodiversity and breeding; identification of mobile elements; bioinformatics (string searching and complexity analysis, search of repeats, DNA alignment and assembly, PCR primer/probe design)
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Special Issue Information

Dear colleague,

Transposable elements are very common mobile genetic elements that are composed of several classes and make up the majority of eukaryotic genomes. The movement and accumulation of mobile genetic elements have been a major force in the formation of the genes and genomes of nearly all organisms. As dispersed and ubiquitous mobile elements, their life cycle of replicative transposition leads to genome rearrangements that affect cellular function. Both the overall structure of mobile genetic elements and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Transposable elements are important drivers of species diversity, and they exhibit great variety in the structure, size, and mechanisms of transposition, making them important putative actors in genome evolution.

Various applications have been developed to exploit polymorphisms in transposable element insertion patterns, using high-throughput applications and bioinformatics.

This Special Issue will focus on the utilization and application of transposable element-based throughput techniques developed and assesses the analysis of genetic diversity, including (but not limited to) the following issues:

high-throughput, next generation sequencing and bioinformatic tools, nucleic acid amplification and microarray techniques to DNA marker applications, genome-wide profiling for transposable element analysis of repetitive elements, discovery and comparative analysis of transposable elements, mobile element and host genome evolution.

We welcome the following article types: original research, reviews, computational tools and opinions.

Prof. Dr. Ruslan Kalendar
Guest Editor

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Keywords

  • Mobile element and host genome evolution
  • DNA rearrangements affect cellular function
  • Mobile genetic elements in biotechnological methods
  • DNA marker applications, genome-wide profiling for transposable element
  • Comparative analyses of transposable elements and computational tools
  • High-throughput DNA methylation analysis of repetitive elements
  • Discovery and analysis of transposable elements

Published Papers (2 papers)

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Research

19 pages, 2437 KiB  
Article
Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.
by Oxana Khapilina, Ainur Turzhanova, Alevtina Danilova, Asem Tumenbayeva, Vladislav Shevtsov, Yuri Kotukhov and Ruslan Kalendar
BioTech 2021, 10(4), 23; https://doi.org/10.3390/biotech10040023 - 13 Oct 2021
Cited by 10 | Viewed by 4336
Abstract
Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a [...] Read more.
Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology. Full article
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17 pages, 9264 KiB  
Article
Retrotransposons and the Evolution of Genome Size in Pisum
by T. H. Noel Ellis and Alexander V. Vershinin
BioTech 2020, 9(4), 24; https://doi.org/10.3390/biotech9040024 - 26 Nov 2020
Cited by 2 | Viewed by 3057
Abstract
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of [...] Read more.
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes. Full article
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