Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax
Abstract Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-g...
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Nature Portfolio
2017-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-017-08194-5 |
| _version_ | 1818856161017856000 |
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| author | Junki Lee Nomar Espinosa Waminal Hong-Il Choi Sampath Perumal Sang-Choon Lee Van Binh Nguyen Woojong Jang Nam-Hoon Kim Li-zhi Gao Tae-Jin Yang |
| author_facet | Junki Lee Nomar Espinosa Waminal Hong-Il Choi Sampath Perumal Sang-Choon Lee Van Binh Nguyen Woojong Jang Nam-Hoon Kim Li-zhi Gao Tae-Jin Yang |
| author_sort | Junki Lee |
| collection | DOAJ |
| description | Abstract Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8–4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39–52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23–35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America. |
| first_indexed | 2024-12-19T08:20:05Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-12-19T08:20:05Z |
| publishDate | 2017-08-01 |
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| series | Scientific Reports |
| spelling | doaj.art-f2b3d885a2084b59adf7f4f84a274cdb2022-12-21T20:29:25ZengNature PortfolioScientific Reports2045-23222017-08-01711910.1038/s41598-017-08194-5Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus PanaxJunki Lee0Nomar Espinosa Waminal1Hong-Il Choi2Sampath Perumal3Sang-Choon Lee4Van Binh Nguyen5Woojong Jang6Nam-Hoon Kim7Li-zhi Gao8Tae-Jin Yang9Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityAdvanced Radiation Technology Institute, Korea Atomic Energy Research InstituteDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityInstitution of Genomics and Bioinformatics, South China Agricultural UniversityDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityAbstract Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8–4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39–52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23–35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.https://doi.org/10.1038/s41598-017-08194-5 |
| spellingShingle | Junki Lee Nomar Espinosa Waminal Hong-Il Choi Sampath Perumal Sang-Choon Lee Van Binh Nguyen Woojong Jang Nam-Hoon Kim Li-zhi Gao Tae-Jin Yang Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax Scientific Reports |
| title | Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax |
| title_full | Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax |
| title_fullStr | Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax |
| title_full_unstemmed | Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax |
| title_short | Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax |
| title_sort | rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus panax |
| url | https://doi.org/10.1038/s41598-017-08194-5 |
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