A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni
Abstract
:1. Introduction
2. Materials and Methods
2.1. Construction, Screening and Sequencing of a Genomic Fosmid Library
2.2. Illumina Draft Genome of D. stevensoni
2.3. De Novo Identificiation of Ostracod TEs
2.4. Assessing Insertion Sites of TEs from Fosmid Data
2.5. Estimating Single-Copy Gene Content in Fosmid Sequence Data
2.6. Search for Remote Homologies
3. Results
3.1. TE Diversity, Substitution Levels and Abundance
3.2. TE Insertion Sites in Fosmids and Their Relationship to Telomeres and Coding Regions
3.3. Additional Domains in R4/Dong and Gypsy Retrotransposons
4. Discussion
4.1. Comparing Results from the Draft Genome and the Fosmid Library
4.2. TE Diversity and Substitution Levels
4.3. TE abundance
4.4. TE Insertion Sites
4.5. Assessing the Impact of Putatively Ancient Asexual Reproduction on TE Landscapes in Non-Marine Ostracods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Schön, I.; Rodriguez, F.; Dunn, M.; Martens, K.; Shribak, M.; Arkhipova, I.R. A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes 2021, 12, 401. https://doi.org/10.3390/genes12030401
Schön I, Rodriguez F, Dunn M, Martens K, Shribak M, Arkhipova IR. A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes. 2021; 12(3):401. https://doi.org/10.3390/genes12030401
Chicago/Turabian StyleSchön, Isa, Fernando Rodriguez, Matthew Dunn, Koen Martens, Michael Shribak, and Irina R. Arkhipova. 2021. "A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni" Genes 12, no. 3: 401. https://doi.org/10.3390/genes12030401
APA StyleSchön, I., Rodriguez, F., Dunn, M., Martens, K., Shribak, M., & Arkhipova, I. R. (2021). A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes, 12(3), 401. https://doi.org/10.3390/genes12030401