A novel mutator-like transposable elements with unusual structure and recent transpositions in barley (Hordeum vulgare)

Authors: Gao, Dongying; Caspersen, Ann; Hu, Gongshe; Bockelman, Harold; Chen, Xianming

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/3/2022
Publication Date: 5/23/2022
Citation: Gao, D., Caspersen, A.M., Hu, G., Bockelman, H.E., Chen, X. 2022. A novel mutator-like transposable elements with unusual structure and recent transpositions in barley (Hordeum vulgare). Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.904619.
DOI: https://doi.org/10.3389/fpls.2022.904619

Interpretive Summary: Due to its relatively smaller genome size, diploid genome, and other unique features, barley has emerged as a model to understand the molecular functions of genes in wheat and other important cereals. Transposons are mobile elements that can move in host genome and cause gene mutations, thus provide valuable resources for functional genomics and other studies. The mutator-like transposable elements (MULEs) represent one of the most mutagenic plant transposon families. However, no active MULE was reported in barley. We analyzed the barley genome and identified a new mutator transposon Hvu_Abermu which is abundantly present in barley and shows unusual sequence structure as it contains three open reading frames (ORFs). We also found homologous sequences of the transposon in many dicots and monocots including wheat and other cereals. Phylogenetic analysis revealed that the new transposon family was separated from the previously reported active MULEs. We conducted genome-wide comparisons between the barley pan genomes and detected polymorphic Hvu_Abermu transposons between different barley genomes. The new transposon identified in this study offers some clues about barley genome evolution, it can also be used to develop molecular markers and other genetic tools for barley and other crops.

Technical Abstract: Mutator-like transposable elements (MULEs) represent a unique superfamily of DNA transposons as they can capture host genes and cause higher frequency of mutations in some eukaryotes. Despite their essential roles in plant evolution and functional genomics, MULEs are not fully understood yet in many important crops including barley (Hordeum vulgare). In this study, we analyzed the barley genome and identified a new mutator transposon Hvu_Abermu. This transposon is present at extremely high copy number in barley and shows unusual structure as it contains three open reading frames (ORFs) including one ORF (ORF1) encoding mutator transposase protein and one ORF (ORFR) showing opposite transcriptional orientation. We identified homologous sequences of Hvu_Abermu in both monocots and dicots and grouped them into a large mutator family named Abermu. Abermu transposons from different species share significant sequence identity, but they exhibit distinct sequence structures. Unlike the transposase proteins which are highly conserved between Abermu transposons from different organisms, the ORFR-encoded proteins are quite different from distant species. Phylogenetic analysis indicated that Abermu transposons shared closer evolutionary relationships with the maize MuDR transposon than other reported MULEs. We also found phylogenetic incongruence for the Abermu transposons identified in rice and its wild species implying the possibility of horizontal transfer of transposon. Further comparison indicated that over 200 barley genes contain Abermu-related sequences. We analyzed the barley pan genomes and detected polymorphic Hvu_Abermu transposons between the sequenced 23 wild and cultivated barley genomes. Our efforts identified a novel mutator transposon and revealed its recent transposition activity, which may help to develop genetic tools for barley and other crops.