Barker Michael S, Kane Nolan C, Matvienko Marta, Kozik Alexander, Michelmore Richard W, Knapp Steven J, Rieseberg Loren H
Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
Mol Biol Evol. 2008 Nov;25(11):2445-55. doi: 10.1093/molbev/msn187. Epub 2008 Aug 26.
Of the approximately 250,000 species of flowering plants, nearly one in ten are members of the Compositae (Asteraceae), a diverse family found in almost every habitat on all continents except Antarctica. With an origin in the mid Eocene, the Compositae is also a relatively young family with remarkable diversifications during the last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred in at least one Compositae lineage, but a recent analysis of genomic data was equivocal. We tested for evidence of paleopolyploidy in the evolutionary history of the family using recently available expressed sequence tag (EST) data from the Compositae Genome Project. Combined with data available on GenBank, we analyzed nearly 1 million ESTs from 18 species representing seven genera and four tribes. Our analyses revealed at least three ancient whole-genome duplications in the Compositae-a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes and independent genome duplications near the base of the tribes Mutisieae and Heliantheae. These results are consistent with previous research implicating paleopolyploidy in the evolution and diversification of the Heliantheae. Further, we observed parallel retention of duplicate genes from the basal Compositae genome duplication across all tribes, despite divergence times of 33-38 My among these lineages. This pattern of retention was also repeated for the paleologs from the Heliantheae duplication. Intriguingly, the categories of genes retained in duplicate were substantially different from those in Arabidopsis. In particular, we found that genes annotated to structural components or cellular organization Gene Ontology categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented. Our results suggest that paleopolyploidy can yield strikingly consistent signatures of gene retention in plant genomes despite extensive lineage radiations and recurrent genome duplications but that these patterns vary substantially among higher taxonomic categories.
在大约25万种开花植物中，近十分之一是菊科（菊科）的成员，菊科是一个多样化的科，除南极洲外，几乎在各大洲的每一个栖息地都能找到。菊科起源于始新世中期，也是一个相对年轻的科，在过去4000万年中经历了显著的多样化。先前的细胞学和系统学研究表明，至少在菊科的一个谱系中可能发生了古多倍体现象，但最近对基因组数据的分析并不明确。我们利用菊科基因组计划最近获得的表达序列标签（EST）数据，检测该科进化历史中古多倍体的证据。结合GenBank上可用的数据，我们分析了来自代表七个属和四个族的18个物种的近100万个EST。我们的分析揭示了菊科至少有三次古老的全基因组复制——所有分析类群共有的一次古多倍体化事件，发生在该科起源附近，就在其族快速分化之前，以及在Mutisieae族和向日葵族基部附近的独立基因组复制事件。这些结果与先前关于古多倍体在向日葵族进化和多样化中起作用的研究一致。此外，尽管这些谱系之间的分化时间为3300-3800万年，但我们观察到所有族中都平行保留了来自菊科基部基因组复制的重复基因。向日葵族复制产生的古同源基因也重复了这种保留模式。有趣的是，以重复形式保留的基因类别与拟南芥中的基因类别有很大不同。特别是，我们发现注释为结构成分或细胞组织基因本体类别的基因在古同源基因中显著富集，而与转录和其他调节功能相关的基因则显著减少。我们的结果表明，尽管存在广泛的谱系辐射和反复的基因组复制，但古多倍体仍能在植物基因组中产生惊人一致的基因保留特征，不过这些模式在较高分类类别中差异很大。
