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

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

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

Original languageEnglish (US)
Article number7353
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018
Externally publishedYes

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Brassica
genome
diploidy
Brassica nigra
genomics
Raphanus sativus
Brassica rapa
Brassica juncea
Brassica oleracea
ribosomal DNA
dominance (genetics)
genetic relationships
chloroplast genome

ASJC Scopus subject areas

  • General

Cite this

Kim, C. K., Seol, Y. J., Perumal, S., Lee, J., Waminal, N. E., Jayakodi, M., ... Yang, T. J. (2018). Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. Scientific Reports, 8(1), [7353]. https://doi.org/10.1038/s41598-018-25585-4

Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. / Kim, Chang Kug; Seol, Young Joo; Perumal, Sampath; Lee, Jonghoon; Waminal, Nomar Espinosa; Jayakodi, Murukarthick; Lee, Sang Choon; Jin, Seungwoo; Choi, Beom Soon; Yu, Yeisoo; Ko, Ho Cheol; Choi, Ji Weon; Ryu, Kyoung Yul; Sohn, Seong Han; Parkin, Isobel; Yang, Tae Jin.

In: Scientific Reports, Vol. 8, No. 1, 7353, 01.12.2018.

Research output: Contribution to journalArticle

Kim, CK, Seol, YJ, Perumal, S, Lee, J, Waminal, NE, Jayakodi, M, Lee, SC, Jin, S, Choi, BS, Yu, Y, Ko, HC, Choi, JW, Ryu, KY, Sohn, SH, Parkin, I & Yang, TJ 2018, 'Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences', Scientific Reports, vol. 8, no. 1, 7353. https://doi.org/10.1038/s41598-018-25585-4
Kim, Chang Kug ; Seol, Young Joo ; Perumal, Sampath ; Lee, Jonghoon ; Waminal, Nomar Espinosa ; Jayakodi, Murukarthick ; Lee, Sang Choon ; Jin, Seungwoo ; Choi, Beom Soon ; Yu, Yeisoo ; Ko, Ho Cheol ; Choi, Ji Weon ; Ryu, Kyoung Yul ; Sohn, Seong Han ; Parkin, Isobel ; Yang, Tae Jin. / Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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AU - Jayakodi, Murukarthick

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AU - Choi, Ji Weon

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