Wang Baosheng, Ding Zhuoya, Liu Wei, Pan Jin, Li Changbao, Ge Song, Zhang Daming
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, PR China.
BMC Evol Biol. 2009 Oct 14;9:250. doi: 10.1186/1471-2148-9-250.
Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process.
Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis.
C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids.
多倍体化是植物进化中的一个重要过程，但其机制及时空过程仍知之甚少。稻属药用野生稻复合体是稻属中的一个多倍体复合体，它不仅涵盖了多种倍性水平，而且其多倍体在亚洲、非洲、澳大利亚和美洲呈现泛热带地理分布格局，其中关键的C基因组见证了整个多倍体化过程，因此可以作为研究这些问题的典型例子。
通过系统发育分析、分子钟分析以及使用基因组特异性探针的荧光原位杂交技术，追溯药用野生稻复合体中C基因组的进化历史，本研究揭示了基因组关系、多倍体形成和分化时间以及二倍体化过程。结果表明，C基因组与B基因组在约480万年前分离，随后是一系列C基因组二倍体的物种形成事件（约180 - 90万年前），这些二倍体随后参与了连续的多倍体化事件，在约90万年前形成了CCDD四倍体，并在约30 - 60万年前逐步形成了BBCC四倍体。在BBCC四倍体斑点野生稻中鉴定出了B基因组与C基因组之间的基因组间易位。通过C基因组特异性探针观察到三个CCDD物种之间明显的荧光原位杂交（FISH）模式。B基因组在形成BBCC四倍体马拉普扎野生稻之前发生了修饰。
该复合体中所有多倍体物种共有的C基因组经历了不同的进化历史，特别是在多倍体化之后，例如BBCC中的基因组间交换和CCDD四倍体中的基因组入侵。它在480万年前与B基因组分化，然后参与了从90万年前到30万年前的四倍体形成过程，并通过跨大陆的远距离扩散而非本研究中提出的替代分布（考虑到大陆分裂比C基因组物种辐射早得多）传播到间断大陆的热带地区。我们还发现可靠证据表明，亚洲一个已灭绝的BB二倍体物种可能是其同域四倍体的直接基因组供体。
