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Article

Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality

1
Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
2
Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
3
Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
*
Authors to whom correspondence should be addressed.
Academic Editor: Kyudong Han
Life 2022, 12(8), 1190; https://doi.org/10.3390/life12081190
Received: 1 July 2022 / Revised: 1 August 2022 / Accepted: 2 August 2022 / Published: 4 August 2022
(This article belongs to the Special Issue Genomic Impact of Transposable Elements)
Bat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past ~40 million years. Each also exhibits its own target site preferences (sometimes shared with other TEs) that impact where they are likely to insert when mobilizing. Therefore, bats provide a great resource for understanding the diversity of TE insertion patterns. To gain insight into how these diverse TEs impact genome structure, we performed comparative spatial analyses between different TE classes and genomic features, including genic regions and CpG islands. Our results showed a depletion of all TEs in the coding sequence and revealed patterns of species- and element-specific attraction in the transcript. Trends of attraction in the distance tests also suggested significant TE activity in regions adjacent to genes. In particular, the enrichment of small, non-autonomous TE insertions in introns and near coding regions supports the hypothesis that the genomic distribution of TEs is the product of a balance of the TE insertion preference in open chromatin regions and the purifying selection against TEs within genes. View Full-Text
Keywords: transposable elements; genome evolution; insertion preference transposable elements; genome evolution; insertion preference
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    Doi: 10.7282/00000212
    Link: https://doi.org/10.7282/00000212
    Description: Bat_TE_7Species.tar.gz: Genome annotation files for seven bat species Folder content: CGI: CpG Island definition files in bed format. Gene: Gene annotation files in gtf format. RepeatMasker: Transposable element annotation files in Repeatmasker output format. mammal_library.fa.gz: mammalian TE consensus library This TE library is a combination of mammalian TE sequences that were available from RepBase as well as those which were manually curated by the Zoonomia project.
MDPI and ACS Style

Paulat, N.S.; McGuire, E.; Subramanian, K.; Osmanski, A.B.; Moreno-Santillán, D.D.; Ray, D.A.; Xing, J. Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality. Life 2022, 12, 1190. https://doi.org/10.3390/life12081190

AMA Style

Paulat NS, McGuire E, Subramanian K, Osmanski AB, Moreno-Santillán DD, Ray DA, Xing J. Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality. Life. 2022; 12(8):1190. https://doi.org/10.3390/life12081190

Chicago/Turabian Style

Paulat, Nicole S., Erin McGuire, Krishnamurthy Subramanian, Austin B. Osmanski, Diana D. Moreno-Santillán, David A. Ray, and Jinchuan Xing. 2022. "Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality" Life 12, no. 8: 1190. https://doi.org/10.3390/life12081190

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