Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
Hubei Hongshan Laboratory, Wuhan, 430070, China.
BMC Genomics. 2022 Apr 30;23(1):339. doi: 10.1186/s12864-022-08573-x.
Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.
Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.
The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.
异源四倍体油菜（甘蓝型油菜）是一种重要的世界产油作物。由于缺乏野生资源，油菜的起源仍不确定。尽管已经对包括甘蓝型油菜在内的大组甘蓝型核基因组进行了某些遗传结构和系统发育研究，但全球范围内细胞器基因组信息在很大程度上仍然未知，这为油菜的系统发育研究提供了独特的材料。在这里，我们基于全球收集的 1579 个油菜品系的从头组装，构建了油菜的叶绿体和线粒体泛基因组，并研究了油菜、白菜和甘蓝的遗传多样性和系统发育关系。
基于独特的标记和线粒体变体 ORFs，我们在四个主要细胞质单倍型群体中鉴定出了 nap、pol、ole 和 cam 型，其中叶绿体基因组的结构比线粒体基因组更保守，没有任何重排。叶绿体基因组共检测到 2092 个变异，而线粒体基因组只有 326 个，表明叶绿体基因组的单碱基多态性水平高于线粒体基因组。基于全基因组变异多样性分析，在不同细胞质单倍型的叶绿体基因组上鉴定出 11 个遗传差异区。包含白菜、甘蓝、油菜自然和合成群体的系统发育树揭示了油菜细胞质的多种起源。cam 型和 pol 型均来自白菜，而 ole 型则起源于甘蓝。值得注意的是，nap 型细胞质在白菜群体和合成油菜中均有发现，这表明白菜可能是 nap 型油菜的母本祖先。
系统发育结果为芸薹属植物细胞器基因组进化提供了新的见解。野生油菜至少包含四个细胞质单倍型，其中占主导地位的 nap 型可能起源于白菜。此外，细胞器泛基因组和总体变异数据为分析油菜细胞质遗传相关的农艺重要性状提供了有用的资源，这将极大地促进油菜品种的培育和改良。
