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 language | English (US) |
|---|---|
| Article number | 7353 |
| Journal | Scientific Reports |
| Volume | 8 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 1 2018 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
AU - Kim, Chang Kug
AU - Seol, Young Joo
AU - Perumal, Sampath
AU - Lee, Jonghoon
AU - Waminal, Nomar Espinosa
AU - Jayakodi, Murukarthick
AU - Lee, Sang Choon
AU - Jin, Seungwoo
AU - Choi, Beom Soon
AU - Yu, Yeisoo
AU - Ko, Ho Cheol
AU - Choi, Ji Weon
AU - Ryu, Kyoung Yul
AU - Sohn, Seong Han
AU - Parkin, Isobel
AU - Yang, Tae Jin
PY - 2018/12/1
Y1 - 2018/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85046847484&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85046847484&partnerID=8YFLogxK
U2 - 10.1038/s41598-018-25585-4
DO - 10.1038/s41598-018-25585-4
M3 - Article
AN - SCOPUS:85046847484
VL - 8
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
IS - 1
M1 - 7353
ER -