Too good to be true: a genome specific distribution of a transposable element in soybean species

We discovered a novel DNA transposon element called GftoMITE1 integrated into the CenH3 gene in Glycine falcata. Interestingly, GftoMITE1 shows genome-specific distribution in wild perennial soybean species, regardless of ploidy, but is absent in cultivated soybean and its progenitor.
Too good to be true: a genome specific distribution of a transposable element in soybean species
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Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine - Genes & Genomics

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.

We are a small research lab working on plant chromosomes with emphasis on legumes at Niğde Ömer Halisdemir University, Türkiye. Our research is primarily driven by curiosity rather than the availability of research funding and performed by exceptionally dedicated and intelligent students.

Miniature inverted-repeat transposable elements (MITEs) are dispersed DNA transposon elements in the genome of eukaryotes. We discovered a novel MITE element called GftoMITE1 integrated into the centromere-specific histone H3 (CenH3) gene in the Glycine falcata (Figure 1). 

Figure 1. A comparison of the morphology of flowers, seed pods and seeds in cultivated soybean (Glycine max) and its wild relative (Glycine falcata)

 

We identified a total of ~460 MITEs distributed between 10 and 33 copies in each of 20 chromosomes of G. falcata. Their distribution has been mostly in the subtelomere regions, possibly favoring the gene-rich regions along the chromosomes. To better understand the GftoMITE1 dynamics and presence in other Glycine species,  we extended our analysis to include annual and perennial, domesticated and wild, diploid and polyploid Glycine species (Figure 2). Interestingly, GftoMITE1 shows genome-specific distribution in wild perennial soybean species but is absent in cultivated soybean and its progenitor species. While diploid wild species harbor their own genome-specific GftoMITE1 homologs, polyploids contain both homologs derived from the ancestral genomes and preserved in the extant genomes after the polyploidization event. 

Figure 2.
Figure 2. A phylogenetic tree showing the genome specific distribution of GftoMITE1 in Glycine species. Each species is shown with the ploidy level, chromosome number and genome assignment.

Furthermore, we think this discovery may have potential implications for gene regulation and soybean breeding as an effective genetic marker for germplasm utilization in the future. The remaining questions may be whether a) our findings are truly valid in a wider genome coverage, any point we missed b) if true, other MITE families also show similar genome specificity in Glycine species, c) more importantly, other organisms in different taxa show same level of specific distribution at species level in comparison to domesticated and wild relatives, even with polyploid members. So, we now have more questions than the answers with our publication.

Our research is published in Genes & Genomics Special Issue—Retrotransposons and DNA Transposons: Insights into Evolutionary Genomics—organized by Editor Prof. Kyudong Han. If you want to read our work, follow the link above.  

Please feel free to contact me at altek2@gmail.com if you have any questions or comments about the work.

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