On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements
Abstract
:1. Introduction
2. Transposable Elements: Classification and Mechanisms of Transposition
3. How Population Dynamics and Intrinsic Properties of Genomes Shape TEs Polymorphisms
3.1. The Role of Purifying Selection and Demography
3.2. Non-Equilibrium between Transposition and Loss
3.3. Transposition and Variable Rates of Recombination
3.4. Coevolutionary Dynamics
4. Transposable Elements as a Source of Adaptation
4.1. Evidence for Positive Selection on TEs and SNPs
4.2. Quantifying Positive Selection on TEs
4.3. Studying Balancing Selection on TEs
4.4. Limitations and Future Improvements
5. The Role of Selfish Elements in Genomic Conflicts: Impact in Natural Populations
6. Future Directions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Name of the Method | Purpose | Link | Reference |
---|---|---|---|
Popoolation_TE2 | TE detection in pooled designs | https://sourceforge.net/p/popoolation-te2/wiki/Home/ | [156] |
T-LEX2 | Detection of polymorphic TEs from short reads | http://petrov.stanford.edu/cgi-bin/Tlex.html | [157] |
STEAK | Detection of polymorphic TEs from short reads | https://github.com/applevir/STEAK | [158] |
TIDAL | Detection of polymorphic TEs from short reads | http://www.bio.brandeis.edu/laulab/Tidal_Fly/Tidal_Fly_Home.html | [159] |
MELT | Detection of polymorphic TEs from short reads | http://melt.igs.umaryland.edu/ | [153] |
LoRTE | Detection of polymorphic TEs from PacBio sequencing | http://www.egce.cnrs-gif.fr/?p=6422 | [160] |
ITIS | Detection of polymorphic TEs from short reads | https://github.com/Chuan-Jiang/ITIS | [161] |
TEMP | Detection of polymorphic TEs from short reads | https://github.com/JialiUMassWengLab/TEMP | [162] |
Mobster | Detection of polymorphic TEs from short reads | http://sourceforge.net/projects/mobster/ | [163] |
Tangram | Detection of polymorphic TEs from short reads | https://github.com/jiantao/Tangram | [164] |
RetroSeq | Detection of polymorphic TEs from short reads | https://github.com/tk2/RetroSeq | [165] |
RelocaTE2 | Detection of polymorphic TEs from short reads | https://github.com/JinfengChen/RelocaTE2 | [166] |
McClintock | Combination of several methods into a single pipeline | https://github.com/bergmanlab/mcclintock | [167] |
Invade | Population genomics modeling (forward-in-time) incorporating coevolution with piRNA clusters | https://sourceforge.net/p/te-tools/code/HEAD/tree/sim3p/ | [104] |
SLIM3 | Population genomics modeling (forward-in-time) | https://messerlab.org/slim/ | [79] |
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Bourgeois, Y.; Boissinot, S. On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements. Genes 2019, 10, 419. https://doi.org/10.3390/genes10060419
Bourgeois Y, Boissinot S. On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements. Genes. 2019; 10(6):419. https://doi.org/10.3390/genes10060419
Chicago/Turabian StyleBourgeois, Yann, and Stéphane Boissinot. 2019. "On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements" Genes 10, no. 6: 419. https://doi.org/10.3390/genes10060419