A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.
A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.
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基于大规模群体的细胞器泛基因组构建和系统发育分析揭示了甘蓝型油菜叶绿体和线粒体的遗传多样性和进化起源。
DOI：
10.1186/s12864-022-08573-x
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发表时间：
2022-04-30
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
背景异源四倍体油菜（Brassica napus L.）是世界上重要的油料作物。由于缺乏野生资源，油菜籽的起源至今仍不确定。尽管已有的遗传结构和系统发育研究主要集中在大群的细胞器核基因组上，但在全局模式下的细胞器基因组信息仍是未知的，这为B.油菜。在这里，基于1, 579 B的从头组装。利用全球范围内收集到的甘蓝型油菜材料，构建了甘蓝型油菜叶绿体和线粒体全基因组。napus的遗传多样性、系统发育关系等方面进行了研究。napus，B.拉帕湾结果利用线粒体特异性标记和不同的开放阅读框，在本研究群体中鉴定出4种主要的细胞质单倍型，分别对应于ap、pol、ole和cammitotypes，其中叶绿体基因组的结构比线粒体基因组保守，没有发生任何重排。叶绿体基因组中共检测到2，092个变异体，而线粒体基因组中仅检测到326个变异体，表明叶绿体基因组比线粒体基因组表现出更高水平的单碱基多态性。基于全基因组变异多样性分析，在叶绿体基因组上发现了11个不同细胞质单倍型间的遗传差异区域。系统发育树包括加入的B。rapa，B. oleracea，B. napus揭示了B. cam型和pol型均来源于B. rapa，而theole-type起源于B.值得注意的是，在B. rapapopulation和syntheticB. napus，表明B. rapam可能是nap-typeB的母系祖先。结论系统发育结果为植物细胞器基因组进化提供了新的视角。天然油菜种子至少含有4种细胞质单倍型，其中占优势的nap型可能起源于B.拉帕。此外，细胞器泛基因组和总体变异数据为油菜重要农艺性状的细胞质遗传分析提供了有用的资源，对油菜品种的培育和改良具有重要意义。
BackgroundAllotetraploid oilseed rape (Brassica napusL.) 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 ofBrassicanuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies ofB. napus. Here, based on de novo assemblies of 1,579B. napusaccessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes ofB. napus, and investigated the genetic diversity, phylogenetic relationships ofB. napus,B. rapaandB. oleracea.ResultsBased on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding thenap,pol,ole, andcammitotypes, 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 theB. rapa,B. oleracea, natural and synthetic populations ofB. napusrevealed multiple origins ofB. napuscytoplasm.Thecam-type andpol-type were both derived fromB. rapa,while theole-type was originated fromB. oleracea.Notably, thenap-type cytoplasm was identified in both theB. rapapopulation and the syntheticB. napus, suggesting thatB. rapamight be the maternal ancestor ofnap-typeB. napus.ConclusionsThe phylogenetic results provide novel insights into the organelle genomic evolution ofBrassicaspecies. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominantnap-type might be originated fromB. 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.
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