An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae)
Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with...
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MDPI AG
2022-01-01
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| author | Jun He Zhongyu Yu Jiafu Jiang Sumei Chen Weimin Fang Zhiyong Guan Yuan Liao Zhenxing Wang Fadi Chen Haibin Wang |
| author_facet | Jun He Zhongyu Yu Jiafu Jiang Sumei Chen Weimin Fang Zhiyong Guan Yuan Liao Zhenxing Wang Fadi Chen Haibin Wang |
| author_sort | Jun He |
| collection | DOAJ |
| description | Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized <i>C. nankingense</i> autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-<i>copia</i> and Ty3-<i>gypsy</i> elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-<i>copia</i> and Ty3-<i>gypsy</i> were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae. |
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| last_indexed | 2024-03-09T23:19:59Z |
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| series | Plants |
| spelling | doaj.art-e4c626253956468d84c74e67490d97552023-11-23T17:29:55ZengMDPI AGPlants2223-77472022-01-0111331510.3390/plants11030315An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae)Jun He0Zhongyu Yu1Jiafu Jiang2Sumei Chen3Weimin Fang4Zhiyong Guan5Yuan Liao6Zhenxing Wang7Fadi Chen8Haibin Wang9State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaWhole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized <i>C. nankingense</i> autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-<i>copia</i> and Ty3-<i>gypsy</i> elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-<i>copia</i> and Ty3-<i>gypsy</i> were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.https://www.mdpi.com/2223-7747/11/3/315autopolyploidizationgenome duplicationevolution<i>Chrysanthemum</i>Asteraceae |
| spellingShingle | Jun He Zhongyu Yu Jiafu Jiang Sumei Chen Weimin Fang Zhiyong Guan Yuan Liao Zhenxing Wang Fadi Chen Haibin Wang An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae) Plants autopolyploidization genome duplication evolution <i>Chrysanthemum</i> Asteraceae |
| title | An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae) |
| title_full | An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae) |
| title_fullStr | An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae) |
| title_full_unstemmed | An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae) |
| title_short | An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of <i>Chrysanthemum nankingense</i> (Asteraceae) |
| title_sort | eruption of ltr retrotransposons in the autopolyploid genomes of i chrysanthemum nankingense i asteraceae |
| topic | autopolyploidization genome duplication evolution <i>Chrysanthemum</i> Asteraceae |
| url | https://www.mdpi.com/2223-7747/11/3/315 |
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