Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution
Abstract
:1. Introduction
2. Materials and Methods
2.1. Transposable Elements Reference Construction
2.2. Identification and Annotation of Transposable Elements
2.3. Transposable Element Loads and Expansion Analyses
2.4. Reconstructing the Phylogenetic Tree
2.5. Time-Calibrated Phylogeny
2.6. Fitting Multiple Phylogenetic Comparative Models
2.7. Phylogenetically Independent Contrasts
2.8. Ancestral State Reconstruction of Transposable Element Loads
2.9. Identifying Shifts of Transposable Element Loads Change Rates in the Phylogeny
2.10. Transposable Element Protein Annotation
2.11. The Phylogenetic Analyses of LTRs in LEPIDOPTERA
2.12. Horizontal Transposable Element Transfer
2.13. Analysis of Transposable Elements Distribution in Arthropods
2.14. The ArTEdb Database
3. Results
3.1. Construction of Transposable Element References
3.2. Transposable Element Loads Vary Greatly in Arthropods
3.2.1. Transposable Element Loss is Prevalent in Hymenoptera
3.2.2. Recent LTR Expansion in T. urticae
3.2.3. Lepidopterans Have Diversified Transposable Elements Subfamilies and Large Transposable Elements Loads
3.2.4. The Evolutionary History of LTRs in Lepidoptera
3.2.5. Non-LTR Transposable Elements Contribute More to Arthropods with Larger Genomes
3.3. The Expansion and Contraction of Transposable Elements in Arthropods
3.4. Transposable Element Loads are Significantly Correlated with Genome Sizes
3.5. Horizontal Transposable Element Transfer in Arthropods
3.6. The ArTEdb
4. Discussion
4.1. A New Database of High-Quality Transposable Element References for Arthropods
4.2. Why Does the Transposable Element Loads Can Be So Different Across Arthropod Species?
4.3. The Contribution of HTTs to the Transposable Element Repertoire in Arthropod Genomes
4.4. Adaptive Transposable Element Insertions in Arthropods
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Class | Order | Species | Genome Sizes † | TE Reference Sequences | ||
---|---|---|---|---|---|---|
RB/RM/LTR | RTE/DTE/UnC | Total | ||||
Insecta | Diptera | Drosophila melanogaster | 144 Mb | 147/79/8 | 159/47/28 | 234 |
Lepidoptera | Spodoptera frugiperda | 358 Mb | 1/475/12 | 263/190/35 | 488 | |
Bombyx mori‡ | 460 Mb | 92/546/183 | 552/232/37 | 821 | ||
Papilio xuthus | 244 Mb | 41/319/60 | 248/151/21 | 420 | ||
Melitaea cinxia | 390 Mb | 0/763/17 | 433/299/48 | 780 | ||
Hymenoptera | Bombus terrestris | 249 Mb | 6/520/12 | 241/267/30 | 538 | |
Apis cerana | 228 Mb | 0/86/1 | 28/49/10 | 87 | ||
Apis mellifera | 250 Mb | 6/136/1 | 35/98/10 | 143 | ||
Hemiptera | Acyrthosiphon pisum | 542 Mb | 331/752/75 | 326/796/36 | 1158 | |
Nilaparvata lugens | 1.14 Gb | 0/1,136/230 | 872/419/75 | 1366 | ||
Orthoptera | Locusta migratoria | 5.6 Gb | 1028/1182/56 | 1144/1018/104 | 2266 | |
Arachnida | Trombidiformes | Tetranychus urticae | 90 Mb | 10/122/73 | 105/86/14 | 205 |
Araneae | Acanthoscurria geniculata | 7.2 Gb | 0/1857/167 | 967/982/75 | 2024 | |
Scorpiones | Mesobuthus martensii | 925 Mb | 39/1260/101 | 476/843/81 | 1400 |
TE Subfamilies | Correlation Coefficient | P | Corrected P |
---|---|---|---|
LINE/L2 | 0.868 | 1.20 × 10−4 | 3.01 × 10−3 |
SINE/Unclassified | 0.784 | 1.51 × 10−3 | 3.18 × 10−2 |
LINE/Unclassified | 0.760 | 2.55 × 10−3 | 4.85 × 10−2 |
DNA/Unclassified | 0.756 | 2.79 × 10−3 | 5.02 × 10−2 |
DNA/TcMar | 0.728 | 4.75 × 10−3 | 8.07 × 10−2 |
LTR/Copia | 0.724 | 5.14 × 10−3 | 8.22 × 10−2 |
DNA/hAT | 0.654 | 1.53 × 10−2 | 2.13 × 10−1 |
LINE/CR1 | 0.644 | 1.75 × 10−2 | 2.13 × 10−1 |
LINE/RTE | 0.652 | 1.57 × 10−2 | 2.13 × 10−1 |
LTR/Unclassified | 0.654 | 1.52 × 10−2 | 2.13 × 10−1 |
LTR/Pao | 0.644 | 1.76 × 10−2 | 2.13 × 10−1 |
DNA/Ginger | 0.559 | 4.72 × 10−2 | 4.25 × 10−1 |
LINE/I | 0.511 | 7.45 × 10−2 | 5.96 × 10−1 |
DNA/CMC | 0.489 | 8.97 × 10−2 | 6.28 × 10−1 |
DNA/Academ | 0.419 | 1.54 × 10−1 | 9.23 × 10−1 |
LINE/Dong-R4 | 0.403 | 1.73 × 10−1 | 9.23 × 10−1 |
DNA/Harbinger | 0.358 | 2.30 × 10−1 | 9.23 × 10−1 |
DNA/PiggyBac | 0.371 | 2.12 × 10−1 | 9.23 × 10−1 |
LINE/Jockey | 0.394 | 1.83 × 10−1 | 9.23 × 10−1 |
LINE/R1 | 0.351 | 2.40 × 10−1 | 9.23 × 10−1 |
LTR/Gypsy | 0.382 | 1.98 × 10−1 | 9.23 × 10−1 |
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Wu, C.; Lu, J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes 2019, 10, 338. https://doi.org/10.3390/genes10050338
Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes. 2019; 10(5):338. https://doi.org/10.3390/genes10050338
Chicago/Turabian StyleWu, Changcheng, and Jian Lu. 2019. "Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution" Genes 10, no. 5: 338. https://doi.org/10.3390/genes10050338
APA StyleWu, C., & Lu, J. (2019). Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes, 10(5), 338. https://doi.org/10.3390/genes10050338