Abstract
Background
Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily.
Objective
In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G. falcata.
Methods
Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species.
Results
Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (Glycine max) or its progenitor (Glycine soja).
Conclusions
We discuss that the GftoMITE1 family reveals a single rapid amplification in G. falcata and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.
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Data availability
All data are deposited in a publicly available repository with accession numbers.
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Acknowledgements
This work was partially supported by the TÜBİTAK Project ID 118O670. HYA has a fellowship from the 100/2000 YÖK Program and Ayhan Şahenk Foundation.
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A.L.T. conceived the study and designed the experiments. A.L.T., H.Y.A., and E.C.K. performed the experiments, conducted the data analysis, and wrote the paper. All authors read and approved the final manuscript.
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13258_2024_1519_MOESM3_ESM.xlsx
Supplementary file3 The physical location and coordinates of GftoMITE1 in the assembled whole genome of Glycine falcata (XLSX 960 KB)
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Yıldız Akkamış, H., Kaya, E.C. & Tek, A.L. Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine. Genes Genom (2024). https://doi.org/10.1007/s13258-024-01519-5
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DOI: https://doi.org/10.1007/s13258-024-01519-5