Submitted to: BMC Genomic Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2023
Publication Date: 11/4/2023
Citation: Gao, D., Fox-Fogle, E.G. 2023. Identification of transcriptionally active transposons in barley. BMC Genomic Data. (2023) 24:64. https://doi.org/10.1186/s12863-023-01170-1.
Interpretive Summary: The barley genome is very big (~5.1 Gb) and highly repetitive as it consists of large amount of transposons or 'jumping genes'. The movement of transposons may cause mutations and affect the host's fitness, thus the host cells have evolved some mechanisms to suppress these repetitive elements. However, transposons can also be used to develop new tools for crop improvement and to create novel and valuable variations. In this study, we conducted computational and molecular analysis and identified six newly expressed transposons in barley. Genome-wide transposon comparisons revealed the recent activity of three transposon families. Thus far, active transposons are poorly understood and the gene-tagging system in barley was developed from the maize transposons. Our efforts provide important resource for addressing the transposon activities and for developing genetic tools for barley improvement and other related studies.
Technical Abstract: The genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants. We analyzed the barley full-length cDNA (FLcDNA) database and detected 71 unique FLcDNAs exhibiting significant sequence similarity to the extant transposase proteins. These FLcDNAs were then used to search against the genome of a malting barley cultivar ‘Morex’, seven new intact transposons were identified. Sequence alignments indicated that six intact transposons contained the entire FLcDNAs whereas another one served as 3’ untranslated region (3’ UTR) of a barley gene. Our reverse transcription-PCR (RT-PCR) experiment further confirmed the expression of these six transposons and revealed their differential expression. We conducted genome-wide transposon comparisons and detected polymorphisms of three transposon families between the genomes of ‘Morex’ and other three genotypes including the wild barley (Hordeum spontaneum, B1K-04-12) and two cultivated barley varieties, ‘Golden Promise’ and ‘Lasa Goumang’. Lastly, we screened the transcripts of all annotated barley genes and found that some transposons may serve as the coding regions (CDSs) or UTRs of barley genes.We identified six newly expressed transposons in the barley genome and revealed the recent mobility of three transposon families. Our efforts provide a valuable resource for understanding the effects of transposons on barley genome evolution and for developing novel molecular tools for barley genetic improvement.