Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years
Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years
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DOI：
10.1093/molbev/msn187
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发表时间：
2008-11-01
影响因子：
10.7
通讯作者：
Rieseberg, Loren H.
中科院分区：
文献类型：
--
作者：
Barker, Michael S.;Kane, Nolan C.;Rieseberg, Loren H.
在大约250，000种开花植物中，近十分之一是菊科（菊科）的成员，这是一个多样化的家族，几乎在除南极洲以外的所有大陆的每个栖息地都有发现。起源于始新世中期，菊科也是一个相对年轻的家族，在过去40万年中出现了显着的多样性。以前的细胞学和系统的调查表明，古多倍体可能发生在至少一个菊科谱系，但最近的基因组数据分析是模棱两可的。我们测试了古多倍体的证据，在家庭的进化史上使用最近可用的表达序列标签（EST）数据从菊科基因组计划。结合GenBank上的数据，我们分析了来自7属4族18个物种的近100万条EST。我们的分析显示，至少有三个古老的全基因组复制的菊科-古多倍体共享的所有分析的类群，并放置在家庭的起源附近的快速辐射之前，其部落和独立的基因组复制附近的基地的部落Mutisieae和Heliantheae。这些结果与先前的研究结果一致，暗示古多倍体在向日葵的进化和多样化。此外，我们观察到平行保留的重复基因的基础菊科基因组复制在所有部落，尽管分歧时间的33-38我在这些血统。这种保留模式也重复了Heliantheae复制的古生物。有趣的是，重复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，我们发现注释到结构成分或细胞组织的基因本体论类别在古生物中显着丰富，而与转录和其他调控功能相关的基因显着不足。我们的研究结果表明，古多倍性可以产生惊人的一致的签名，尽管广泛的谱系辐射和经常性的基因组重复的基因保留在植物基因组中，但这些模式有很大的不同较高的分类类别。
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.