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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.

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