Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion.
Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion.
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DOI：
10.1093/gbe/evv125
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发表时间：
2015-06-27
影响因子：
3.3
通讯作者：
Chaw SM
中科院分区：
文献类型：
--
作者：
Wu CS;Chaw SM
在被子植物中，已知基因转换可以减少质体基因组（质体体）的突变负荷。特别是，在反向重复（IR）区域比在单拷贝（SC）区域更频繁的基因转换导致这两个区域之间的替代率对比。然而，基因转化在裸子植物质体进化中的作用尚不清楚。苏铁是第二大裸子植物群。其质体的进化研究仅限于苏铁属，苏铁。在这项研究中，我们解决了三个问题。1)其他苏铁属的质体是否像以前在台湾苏铁质体中观察到的那样进化缓慢？2)它们的SC区和IR区取代率不同吗？3)苏铁质体中是否发生基因转化？如果是，它是at偏向还是gc偏向？对苏铁其他8属8种的质体体进行了测序。这些质体在基因组组织中是高度保守的。除银杏外，苏铁质体的同义和非同义取代率明显低于其他裸子植物，反映了它们在核苷酸突变中的进化停滞。在苏铁质体的IRs中，降低的替代率和gc偏倚突变与gc偏倚基因转换（gBGC）机制有关。进一步的研究表明，在苏铁中，gBGC能够纠正全质体突变。因此，本研究首次揭示了种子植物中的塑料gBGC。我们还提出了一个gBGC模型来解释苏铁质体的不同进化模式以及SC和IR区域的成分偏突变。
In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes.