Identification of transcriptionally active transposons in Barley
Abstract Background 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 fa...
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | BMC Genomic Data |
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| Online Access: | https://doi.org/10.1186/s12863-023-01170-1 |
| _version_ | 1797636658606112768 |
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| author | Dongying Gao Emma Fox-Fogle |
| author_facet | Dongying Gao Emma Fox-Fogle |
| author_sort | Dongying Gao |
| collection | DOAJ |
| description | Abstract Background 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. Results We analyzed the barley full-length cDNA (FLcDNA) sequences 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. Conclusion 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 and other research. |
| first_indexed | 2024-03-11T12:37:11Z |
| format | Article |
| id | doaj.art-029588000df749eb823bba14cd1ef48f |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-03-11T12:37:11Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-029588000df749eb823bba14cd1ef48f2023-11-05T12:30:48ZengBMCBMC Genomic Data2730-68442023-11-0124111010.1186/s12863-023-01170-1Identification of transcriptionally active transposons in BarleyDongying Gao0Emma Fox-Fogle1Small Grains and Potato Germplasm Research Unit, USDA-ARSSmall Grains and Potato Germplasm Research Unit, USDA-ARSAbstract Background 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. Results We analyzed the barley full-length cDNA (FLcDNA) sequences 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. Conclusion 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 and other research.https://doi.org/10.1186/s12863-023-01170-1BarleyTransposonExpressionGenomeComparative analysis |
| spellingShingle | Dongying Gao Emma Fox-Fogle Identification of transcriptionally active transposons in Barley BMC Genomic Data Barley Transposon Expression Genome Comparative analysis |
| title | Identification of transcriptionally active transposons in Barley |
| title_full | Identification of transcriptionally active transposons in Barley |
| title_fullStr | Identification of transcriptionally active transposons in Barley |
| title_full_unstemmed | Identification of transcriptionally active transposons in Barley |
| title_short | Identification of transcriptionally active transposons in Barley |
| title_sort | identification of transcriptionally active transposons in barley |
| topic | Barley Transposon Expression Genome Comparative analysis |
| url | https://doi.org/10.1186/s12863-023-01170-1 |
| work_keys_str_mv | AT dongyinggao identificationoftranscriptionallyactivetransposonsinbarley AT emmafoxfogle identificationoftranscriptionallyactivetransposonsinbarley |