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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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f2b3d885a2084b59adf7f4f84a274cdb
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spelling	oai:doaj.org-article:f2b3d885a2084b59adf7f4f84a274cdb2021-12-02T16:08:23ZRapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax10.1038/s41598-017-08194-52045-2322https://doaj.org/article/f2b3d885a2084b59adf7f4f84a274cdb2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08194-5https://doaj.org/toc/2045-2322Abstract 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.Junki LeeNomar Espinosa WaminalHong-Il ChoiSampath PerumalSang-Choon LeeVan Binh NguyenWoojong JangNam-Hoon KimLi-zhi GaoTae-Jin YangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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
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.
format	article
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
title	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_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_sort	rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus panax
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/f2b3d885a2084b59adf7f4f84a274cdb
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Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax

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