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HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes
Open accessAbstract
Significance: Helitrons are unusual rolling-circle eukaryotic transposons with a remarkable ability to capture gene sequences, which makes them of considerable evolutionary importance. Because Helitrons lack typical transposon features, they are challenging to identify and are estimated to comprise at most 2% of sequenced genomes. Here, we describe HelitronScanner, a generalized tool for their identification based on a motif-extracting algorithm proposed initially in a study of natural languages. HelitronScanner overcomes the divergence of Helitron termini among species by using conserved nucleotides at potentially variable locations. Many new Helitrons were identified in all organisms examined, resulting in a major reassessment of their abundance in eukaryotic genomes. In maize, they make up >6% of the genome and are the most abundant DNA transposons identified.
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Cites
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
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RepeatModeler2 for automated genomic discovery of transposable element families
Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921046117 · Cited by 3,848
Improved maize reference genome with single-molecule technologies
Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C.-S., et al. (2017) · Nature · doi:10.1038/nature22971 · Cited by 1,210
van der Ven (2019) · doi:10.12688/f1000research · Cited by 599
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.046 · Cited by 578
Metadata
- Authors
- Xiong, W., He, L., Lai, J., Dooner, H. K., & Du, C.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2014-06-30
- Volume
- 111
- Issue
- 28
- Pages
- 10263-10268
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1980340421
- Cited by
- 272
- References
- 1
- FWCI
- 9.37
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Xiong, W., He, L., Lai, J., Dooner, H. K., & Du, C. (2014). HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1410068111
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