Department of Biology, University of Missouri-Saint Louis, Saint Louis, Missouri, United States of America.
PLoS One. 2012;7(6):e38702. doi: 10.1371/journal.pone.0038702. Epub 2012 Jun 18.
Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum) and common or Proso millet (P. miliaceum). Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels.
多倍体为系统发育重建带来了挑战，因为需要识别和区分同源基因座。这可以通过使用低拷贝核标记来解决。 Panicum s.s. 是禾本科 Paniceae 族中的一个约有 100 种的属，分为五个节。许多物种已知是多倍体。 Panicum 多倍体中最著名的是柳枝稷（Panicum virgatum）和普通或小米（P. miliaceum）。柳枝稷位于 Virgata 节，与 P. tricholaenoides、P. amarum 和 P. amarulum 一起，而 P. miliaceum 则位于 sect. Panicum。我们已经从五个低拷贝核基因座和两个叶绿体基因座生成了序列数据，并阐明了 P. virgatum 的起源。我们发现，Virgata 和 Urvilleana 节的所有成员都是单一异源多倍化事件后的多样化结果。柳枝稷最接近的二倍体近亲来自中美洲和南美洲的 Rudgeana 节。在 Virgata 和 Urvilleana 节内，P. tricholaenoides 是其余物种的姊妹群。 Panicum racemosum 和 P. urvilleanum 形成一个分支，可能与 P. chloroleucum 是姊妹群。 P. amarum、P. amarulum 和低地和高地生态型的 P. virgatum 共同形成一个分支，其内部关系复杂。六倍体和八倍体植物可能是异源多倍体，P. amarum 和 P. amarulum 与 P. virgatum 共享基因组。八倍体 P. virgatum 植物是由不同的四倍体杂交形成的。我们表明，在一组复杂的多倍体中，多倍体先于多样化；因此，我们的数据表明，多倍体可能为多样化提供了原材料。此外，我们在柳枝稷的祖先中发现了两轮异源多倍化，并确定了其他可能是其更广泛基因库的一部分的物种。这对于为生物燃料开发该作物可能是相关的。
