Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

Abstract The concept of U’s triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome)...

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Autores principales:	Chang-Kug Kim, Young-Joo Seol, Sampath Perumal, Jonghoon Lee, Nomar Espinosa Waminal, Murukarthick Jayakodi, Sang-Choon Lee, Seungwoo Jin, Beom-Soon Choi, Yeisoo Yu, Ho-Cheol Ko, Ji-Weon Choi, Kyoung-Yul Ryu, Seong-Han Sohn, Isobel Parkin, Tae-Jin Yang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e5ee3fece8a349868271b64d8c7b9835
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spelling	oai:doaj.org-article:e5ee3fece8a349868271b64d8c7b98352021-12-02T16:08:25ZRe-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences10.1038/s41598-018-25585-42045-2322https://doaj.org/article/e5ee3fece8a349868271b64d8c7b98352018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25585-4https://doaj.org/toc/2045-2322Abstract The concept of U’s triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2–6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U’s triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.Chang-Kug KimYoung-Joo SeolSampath PerumalJonghoon LeeNomar Espinosa WaminalMurukarthick JayakodiSang-Choon LeeSeungwoo JinBeom-Soon ChoiYeisoo YuHo-Cheol KoJi-Weon ChoiKyoung-Yul RyuSeong-Han SohnIsobel ParkinTae-Jin YangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chang-Kug Kim Young-Joo Seol Sampath Perumal Jonghoon Lee Nomar Espinosa Waminal Murukarthick Jayakodi Sang-Choon Lee Seungwoo Jin Beom-Soon Choi Yeisoo Yu Ho-Cheol Ko Ji-Weon Choi Kyoung-Yul Ryu Seong-Han Sohn Isobel Parkin Tae-Jin Yang Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
description	Abstract The concept of U’s triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2–6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U’s triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.
format	article
author	Chang-Kug Kim Young-Joo Seol Sampath Perumal Jonghoon Lee Nomar Espinosa Waminal Murukarthick Jayakodi Sang-Choon Lee Seungwoo Jin Beom-Soon Choi Yeisoo Yu Ho-Cheol Ko Ji-Weon Choi Kyoung-Yul Ryu Seong-Han Sohn Isobel Parkin Tae-Jin Yang
author_facet	Chang-Kug Kim Young-Joo Seol Sampath Perumal Jonghoon Lee Nomar Espinosa Waminal Murukarthick Jayakodi Sang-Choon Lee Seungwoo Jin Beom-Soon Choi Yeisoo Yu Ho-Cheol Ko Ji-Weon Choi Kyoung-Yul Ryu Seong-Han Sohn Isobel Parkin Tae-Jin Yang
author_sort	Chang-Kug Kim
title	Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
title_short	Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
title_full	Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
title_fullStr	Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
title_full_unstemmed	Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
title_sort	re-exploration of u’s triangle brassica species based on chloroplast genomes and 45s nrdna sequences
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/e5ee3fece8a349868271b64d8c7b9835
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Re-exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

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