Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels
Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (<i>Fragaria x ananassa</i>) is one of the most important fruit crops, and its octoploid genome was formed through several rounds...
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MDPI AG
2023-11-01
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| Series: | International Journal of Molecular Sciences |
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| author | Keliang Lyu Jiajing Xiao Shiheng Lyu Renyi Liu |
| author_facet | Keliang Lyu Jiajing Xiao Shiheng Lyu Renyi Liu |
| author_sort | Keliang Lyu |
| collection | DOAJ |
| description | Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (<i>Fragaria x ananassa</i>) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the <i>Fragaria</i> genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (<i>F. viridis</i>) to 60.07% (<i>F. nilgerrensis</i>) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the <i>Fragaria</i> genomes (20.16% to 34.94%), particularly in <i>F. iinumae</i> (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between <i>Fragaria</i> species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that <i>F. vesca</i> and <i>F. iinumae</i> are likely the diploid ancestors of the cultivated strawberry, but not <i>F. viridis</i>. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution. |
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| id | doaj.art-ca7923b2b0f740d6af9a65ea5c9d00cc |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T01:50:15Z |
| publishDate | 2023-11-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ca7923b2b0f740d6af9a65ea5c9d00cc2023-12-08T15:17:45ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-11-0124231693510.3390/ijms242316935Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy LevelsKeliang Lyu0Jiajing Xiao1Shiheng Lyu2Renyi Liu3College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaHaixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaCollege of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaHaixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaTransposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (<i>Fragaria x ananassa</i>) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the <i>Fragaria</i> genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (<i>F. viridis</i>) to 60.07% (<i>F. nilgerrensis</i>) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the <i>Fragaria</i> genomes (20.16% to 34.94%), particularly in <i>F. iinumae</i> (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between <i>Fragaria</i> species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that <i>F. vesca</i> and <i>F. iinumae</i> are likely the diploid ancestors of the cultivated strawberry, but not <i>F. viridis</i>. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.https://www.mdpi.com/1422-0067/24/23/16935<i>Fragaria</i>cultivated strawberrytransposable elements (TEs)genome evolutionlong terminal repeat retrotransposons (LTR-RTs) |
| spellingShingle | Keliang Lyu Jiajing Xiao Shiheng Lyu Renyi Liu Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels International Journal of Molecular Sciences <i>Fragaria</i> cultivated strawberry transposable elements (TEs) genome evolution long terminal repeat retrotransposons (LTR-RTs) |
| title | Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels |
| title_full | Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels |
| title_fullStr | Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels |
| title_full_unstemmed | Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels |
| title_short | Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels |
| title_sort | comparative analysis of transposable elements in strawberry genomes of different ploidy levels |
| topic | <i>Fragaria</i> cultivated strawberry transposable elements (TEs) genome evolution long terminal repeat retrotransposons (LTR-RTs) |
| url | https://www.mdpi.com/1422-0067/24/23/16935 |
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