Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Aug 4;12(8):1190.
doi: 10.3390/life12081190.

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

Nicole S Paulat  1 , Erin McGuire  2 , Krishnamurthy Subramanian  2   3 , Austin B Osmanski  1 , Diana D Moreno-Santillán  1 , David A Ray  1 , Jinchuan Xing  2   3
Affiliations

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

Nicole S Paulat et al. Life (Basel). .

Abstract

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.

Keywords: genome evolution; insertion preference; transposable elements.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of species in this study (based on [32]). Bat suborder is shown at far right, and family is indicated by three-letter abbreviations: Phy = Phyllostomidae, Mol = Molossidae, Ves = Vespertilionidae, Rhi = Rhinolophidae, Pte = Pteropodidae.
Figure 2
Figure 2
The number of annotated TEs for each species. Young: elements < 25 Mys old; Old: elements > 40 Mys old; Intermediate: elements between 25 and 40 Mys old. Species abbreviations: MyoMyo: My. myotis; MyoLuc: My. lucifugus; PipKuh: Pi. kuhlii; MolMol: Mo. molossus, PhyDis: Ph. discolor; RihFer: Rh. ferrumequinum; RouAeg: Ro. aegyptiacus.
Figure 3
Figure 3
Size distribution of TEs in each species. The x-axis represents TE size (bps) on a log10 scale. Species abbreviations: MyoMyo: My. myotis; MyoLuc: My. lucifugus; PipKuh: Pi. kuhlii; MolMol: Mo. molossus, PhyDis: Ph. discolor; RihFer: Rh. ferrumequinum; RouAeg: Ro. aegyptiacus.
Figure 4
Figure 4
Relationship between TEs and genic features. Results from the Jaccard, absolute distance, and relative distance tests for old (A) and young (B) TEs. Minimum cutoff of 100 bp length for TE insertion, and 10,000 insertions per element per species. Attraction is indicated in blue, repulsion in red, no-significant in grey, and not-tested in white. Species abbreviations: MyoMyo: My. myotis; MyoLuc: My. lucifugus; PipKuh: Pi. kuhlii; MolMol: Mo. molossus, PhyDis: Ph. discolor; RihFer: Rh. ferrumequinum; RouAeg: Ro. aegyptiacus.
See this image and copyright information in PMC

References

    1. McClintock B. Chromosome organization and genic expression. Cold Spring Harb. Symp. Quant. Biol. 1951;16:13–47. doi: 10.1101/SQB.1951.016.01.004. - DOI - PubMed
    1. Plasterk R.H. The origin of footprints of the Tc1 transposon of Caenorhabditis elegans. EMBO J. 1991;10:1919–1925. doi: 10.1002/j.1460-2075.1991.tb07718.x. - DOI - PMC - PubMed
    1. Jiang N., Bao Z., Zhang X., Eddy R.S., Wessler R.S. Pack-MULE transposable elements mediate gene evolution in plants. Nature. 2004;431:569–573. doi: 10.1038/nature02953. - DOI - PubMed
    1. Sen S.K., Han K., Wang J., Lee J., Wang H., Callinan A.P., Dyer M., Cordaux R., Liang P., Batzer A.M. Human genomic deletions mediated by recombination between Alu elements. Am. J. Hum. Genet. 2006;79:41–53. doi: 10.1086/504600. - DOI - PMC - PubMed
    1. Xing J., Zhang Y., Han K., Salem A.H., Sen K.S., Huff D.C., Zhou Q., Kirkness F.E., Levy S., Batzer A.M., et al. Mobile elements create structural variation: Analysis of a complete human genome. Genome Res. 2009;19:1516–1526. doi: 10.1101/gr.091827.109. - DOI - PMC - PubMed

LinkOut - more resources