Tank D C, Sang T
Department of Botany and Plant Pathology, Michigan State University, East Lansing, Michigan 48824, USA.
Mol Phylogenet Evol. 2001 Jun;19(3):421-9. doi: 10.1006/mpev.2001.0931.
The nuclear-encoded chloroplast-expressed glycerol-3-phosphate acyltransferase (GPAT) gene has been found to be single-copy in a number of angiosperm families. In this study we investigated the phylogenetic utility of the GPAT gene at the interspecific level using the genus Paeonia (Paeoniaceae) as an example. An approximately 2.3- to 2.6-kb fragment of the GPAT gene, containing a large intron of more than 2 kb, was amplified, cloned, and sequenced from 19 accessions representing 13 Paeonia species. The GPAT gene phylogeny inferred by parsimony analysis supported interspecific relationships that were previously unresolved, suggesting that large introns of low-copy nuclear genes are particularly informative in the resolution of close relationships at low taxonomic levels. Whereas the GPAT phylogeny is largely congruent with the previous phylogenetic hypothesis of Paeonia, it shows a significant discordance involving the paraphyly of section Paeonia. Given evidence of an ancient duplication and the subsequent silencing of one GPAT locus in P. anomala, this discordance is most likely the result of paralogy. Two distinct genomic clones containing partial GPAT genes were isolated from P. anomala. The GPAT sequence from one clone corresponded to the functional copy of the gene, and the second genomic clone was determined to contain a GPAT pseudogene. The insertion of a retrotransposon in an intron of this pseudogene may have been responsible for the silencing of this GPAT locus in P. anomala. This study suggests that, although it is unlikely that universal nuclear gene markers free from paralogy are usually available, low-copy nuclear genes can be very useful in plant phylogenetic reconstruction, especially at low taxonomic levels, as long as the evolutionary dynamics of the genes are carefully examined.
核编码的叶绿体表达甘油-3-磷酸酰基转移酶（GPAT）基因在许多被子植物科中已被发现是单拷贝的。在本研究中，我们以芍药属（芍药科）为例，研究了GPAT基因在种间水平上的系统发育效用。从代表13个芍药物种的19个材料中扩增、克隆并测序了GPAT基因约2.3至2.6 kb的片段，该片段包含一个超过2 kb的大内含子。通过简约分析推断的GPAT基因系统发育支持了先前未解决的种间关系，这表明低拷贝核基因的大内含子在解决低分类水平的密切关系方面特别有信息价值。虽然GPAT系统发育在很大程度上与先前芍药属的系统发育假设一致，但它显示出与芍药组的并系性存在显著不一致。鉴于在块根芍药中存在一个古老的重复事件以及随后一个GPAT位点的沉默证据，这种不一致很可能是旁系同源性的结果。从块根芍药中分离出两个包含部分GPAT基因的不同基因组克隆。来自一个克隆的GPAT序列对应于该基因的功能拷贝，而第二个基因组克隆被确定包含一个GPAT假基因。该假基因一个内含子中反转录转座子的插入可能导致了块根芍药中这个GPAT位点的沉默。这项研究表明，虽然通常不太可能获得无旁系同源性的通用核基因标记，但只要仔细研究基因的进化动态，低拷贝核基因在植物系统发育重建中非常有用，特别是在低分类水平上。
