Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
Key Laboratory of Crop Quality Improvement of Anhui Province, Anhui Academy of Agricultural Sciences, Crop Research Institute, Hefei, Anhui, 230031, China.
Plant J. 2021 Dec;108(5):1456-1472. doi: 10.1111/tpj.15522. Epub 2021 Oct 13.
The architecture and genetic diversity of mitogenome (mtDNA) are largely unknown in cultivated soybean (Glycine max), which is domesticated from the wild progenitor, Glycine soja, 5000 years ago. Here, we de novo assembled the mitogenome of the cultivar 'Williams 82' (Wm82_mtDNA) with Illumina PE300 deep sequencing data, and verified it with polymerase chain reaction (PCR) and Southern blot analyses. Wm82_mtDNA maps as two autonomous circular chromosomes (370 871-bp Chr-m1 and 62 661-bp Chr-m2). Its structure is extensively divergent from that of the mono-chromosomal mitogenome reported in the landrace 'Aiganhuang' (AGH_mtDNA). Synteny analysis showed that the structural variations (SVs) between two genomes are mainly attributed to ectopic and illegitimate recombination. Moreover, Wm82_mtDNA and AGH_mtDNA each possess six and four specific regions, which are absent in their counterparts and likely result from differential sequence-loss events. Mitogenome SV was further studied in 39 wild and 182 cultivated soybean accessions distributed world-widely with PCR/Southern analyses or a comparable in silico analysis. The results classified both wild and cultivated soybeans into five cytoplasmic groups, named as GSa-GSe and G1-G5; 'Williams 82' and 'Aiganhuang' belong to G1 and G5, respectively. Notably, except for members in GSe and G5, all accessions carry a bi-chromosomal mitogenome with a common Chr-m2. Phylogenetic analyses based on mtDNA structures and chloroplast gene sequences both inferred that G1-G3, representing >90% of cultigens, likely inherited cytoplasm from the ancestor of domestic soybean, while G4 and G5 likely inherited cytoplasm from wild soybeans carrying GSa- and GSe-like cytoplasm through interspecific hybridization, offering new insights into soybean cultivation history.
栽培大豆（Glycine max）的线粒体基因组（mtDNA）结构和遗传多样性在很大程度上是未知的，它是由 5000 年前的野生祖先大豆（Glycine soja）驯化而来。在这里，我们使用 Illumina PE300 深度测序数据从头组装了栽培品种‘Williams 82’（Wm82_mtDNA）的线粒体基因组，并通过聚合酶链反应（PCR）和 Southern blot 分析进行了验证。Wm82_mtDNA 图谱为两个自主的圆形染色体（370871-bp Chr-m1 和 62661-bp Chr-m2）。它的结构与在地方品种‘Aiganhuang’（AGH_mtDNA）中报道的单染色体线粒体基因组有很大的不同。同线性分析表明，两个基因组之间的结构变异（SVs）主要归因于异位和非同源重组。此外，Wm82_mtDNA 和 AGH_mtDNA 各有六个和四个特定区域，在其对应物中不存在，可能是由于不同的序列缺失事件造成的。通过 PCR/Southern 分析或类似的计算机分析，进一步研究了来自全球的 39 个野生和 182 个栽培大豆品系中的线粒体基因组 SV。结果将野生和栽培大豆分为五个细胞质组，命名为 GSa-GSe 和 G1-G5；‘Williams 82’和‘Aiganhuang’分别属于 G1 和 G5。值得注意的是，除了 GSe 和 G5 中的成员外，所有品系都携带一个具有共同 Chr-m2 的双染色体线粒体基因组。基于 mtDNA 结构和叶绿体基因序列的系统发育分析都推断，G1-G3，代表了 >90%的栽培品种，可能从栽培大豆的祖先那里继承了细胞质，而 G4 和 G5 可能通过种间杂交从携带 GSa-和 GSe 样细胞质的野生大豆中继承了细胞质，为大豆栽培历史提供了新的见解。
