藓纲（苔藓植物门）质体基因组中71 kb倒位的分布及其系统发育意义
Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta).
作者信息
Goffinet Bernard, Wickett Norman J, Werner Olaf, Ros Rosa Maria, Shaw A Jonathan, Cox Cymon J
机构信息
Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, University of Connecticut, Storrs, CT 06269-3043, USA.
出版信息
Ann Bot. 2007 Apr;99(4):747-53. doi: 10.1093/aob/mcm010. Epub 2007 Mar 2.
BACKGROUND AND AIMS
The recent assembly of the complete sequence of the plastid genome of the model taxon Physcomitrella patens (Funariaceae, Bryophyta) revealed that a 71-kb fragment, encompassing much of the large single copy region, is inverted. This inversion of 57% of the genome is the largest rearrangement detected in the plastid genomes of plants to date. Although initially considered diagnostic of Physcomitrella patens, the inversion was recently shown to characterize the plastid genome of two species from related genera within Funariaceae, but was lacking in another member of Funariidae. The phylogenetic significance of the inversion has remained ambiguous.
METHODS
Exemplars of all families included in Funariidae were surveyed. DNA sequences spanning the inversion break ends were amplified, using primers that anneal to genes on either side of the putative end points of the inversion. Primer combinations were designed to yield a product for either the inverted or the non-inverted architecture.
KEY RESULTS
The survey reveals that exemplars of eight genera of Funariaceae, the sole species of Disceliaceae and three generic representatives of Encalyptales all share the 71-kb inversion in the large single copy of the plastid genome. By contrast, the plastid genome of Gigaspermaceae (Funariales) is characterized by a gene order congruent with that described for other mosses, liverworts and hornworts, and hence it does not possess this inversion.
CONCLUSIONS
The phylogenetic distribution of the inversion in the gene order supports a hypothesis only weakly supported by inferences from sequence data whereby Funariales are paraphyletic, with Funariaceae and Disceliaceae sharing a common ancestor with Encalyptales, and Gigaspermaceae sister to this combined clade. To reflect these relationships, Gigaspermaceae are excluded from Funariales and accommodated in their own order, Gigaspermales order nov., within Funariideae.
背景与目的
模式分类群小立碗藓（葫芦藓科，苔藓植物门）质体基因组完整序列的最新组装显示，一个包含大部分大单拷贝区域的71 kb片段发生了倒位。这种占基因组57%的倒位是迄今为止在植物质体基因组中检测到的最大重排。尽管最初认为该倒位是小立碗藓的诊断特征，但最近发现它也是葫芦藓科相关属的两个物种质体基因组的特征，而在葫芦藓科的另一个成员中则不存在。该倒位的系统发育意义仍不明确。
方法
对葫芦藓科所有包含的科的代表样本进行了调查。使用与倒位假定端点两侧基因退火的引物，扩增跨越倒位断点末端的DNA序列。设计引物组合以产生倒位或非倒位结构的产物。
主要结果
调查显示，葫芦藓科八个属的代表样本、Disceliaceae的唯一物种以及Encalyptales的三个属代表在质体基因组的大单拷贝中都存在71 kb的倒位。相比之下，Gigaspermaceae（葫芦藓目）的质体基因组的基因顺序与其他苔藓、地钱和角苔所描述的一致，因此不具有这种倒位。
结论
基因顺序倒位的系统发育分布支持了一个仅由序列数据推断微弱支持的假说，即葫芦藓目是并系的，葫芦藓科和Disceliaceae与Encalyptales有共同祖先，而Gigaspermaceae是这个组合类群的姐妹类群。为了反映这些关系，Gigaspermaceae被排除在葫芦藓目之外，并在葫芦藓亚纲内归入其自己的目，即新目Gigaspermales。
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