THE ITS REGION OF NUCLEAR RIBOSOMAL DNA - A VALUABLE SOURCE OF EVIDENCE ON ANGIOSPERM PHYLOGENY
THE ITS REGION OF NUCLEAR RIBOSOMAL DNA - A VALUABLE SOURCE OF EVIDENCE ON ANGIOSPERM PHYLOGENY
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DOI：
10.2307/2399880
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发表时间：
1995-01-01
影响因子：
1.9
通讯作者：
DONOGHUE, MJ
中科院分区：
文献类型：
--
作者：
BALDWIN, BG;SANDERSON, MJ;DONOGHUE, MJ
18 S-26 S核核糖体DNA（nrDNA）的内转录间隔区（ITS）已被证明是被子植物系统发育研究的有用特征来源。该区域的两个间隔区ITS-1和ITS-2（每个< 300 bp）可以很容易地通过PCR扩增，并使用通用引物进行测序，甚至可以从植物标本的DNA中进行。尽管两个间隔区的拷贝数很高，但由于快速协同进化，ITS旁系同源物的近一致性允许在许多物种中对合并的PCR产物进行直接测序。不同的旁系同源，如果检测到，需要克隆，但可能提供一种手段，获得多个估计的生物体关系和确定放置的根在一个独立的外群的考虑。在已报道的研究中，ITS序列之间的变异主要归因于点突变。相对较小比例的位点受到足够相似以保留足够信号用于系统发育分析的序列之间的插入或缺失（indels）的影响。在这些限制内，序列比对通常是明确的，除了在明显较低的结构约束的小区域。系统发育分析的组合数据集，从两个间隔，在检查，产生更大的分辨率和内部支持比分析的基础上，单独的间隔树。基于每个间隔区中有用字符的数量少，同时分析的这种有益效果并不令人惊讶。这种效应也表明间隔区数据的高度互补性，与大多数密切相关的被子植物中ITS-1和ITS-2的大小、序列变异性和G + C含量的相似性雅阁。非独立的ITS位点的进化参与intracer RNA碱基配对可能会发生，考虑到可能的功能限制，但初步的二级结构分析的ITS-2的Calycadenia（菊科）没有明确的证据，补偿间隔突变。正如预期的那样，ITS序列变异的水平，适合系统发育分析中发现在不同的分类学水平的家庭，这取决于血统。ITS分子进化的表观速率与植物的生活型大致相关，就像叶绿体DNA（cpDNA）数据一样，但这种观察的原因尚不清楚。ITS特征通过以下方式提高了我们对几个类群被子植物进化的理解：（1）证实了早期的意外发现，（2）解决了其他数据集之间的冲突，（3）提高了物种关系的分辨率，或（4）提供了网状进化的直接证据。在一个谱系中，祖先多态性的杂交或排序可以使基于任何类型的进化证据（包括ITS或cpDNA序列）的树的解释复杂化，特别是在缺乏来自相同生物体的至少一个独立的系统发育数据集的情况下。需要从核基因组的系统发育标记，以补充快速增长的cpDNA数据的身体，使ITS区植物系统学家的一个特别宝贵的资源。
The internal transcribed spacer (ITS) region of 18S-26S nuclear ribosomal DNA (nrDNA) has proven to be a useful source of characters for phylogenetic studies in many angiosperm families. The two spacers of this region, ITS-1 and ITS-2 (each < 300 bp), can be readily amplified by PCR and sequenced using universal primers, even from DNAs of herbarium specimens. Despite high copy numbers of both spacers, the near uniformity of ITS paralogues, attributed to rapid concerted evolution, allows direct sequencing of pooled PCR products in many species. Divergent paralogues, where detected, require cloning, but may offer a means of obtaining multiple estimates of organismal relationships and of determining placement of the root in a phylogeny independent of outgroup considerations. In reported studies, variation between ITS sequences is mostly attributable to point mutations. A relatively minor proportion of sites is affected by insertions or deletions (indels) among sequences that are similar enough to have retained sufficient signal for phylogenetic analysis. Within these limits, sequence alignment is generally unambiguous except in small regions of apparently lower structural constraint. Phylogenetic analyses of combined data sets from both spacers, where examined, yield trees with greater resolution and internal support than analyses based on either spacer alone. This beneficial effect of simultaneous analysis is not surprising based on the low number of useful characters in each spacer. This effect also suggests high complementarity of spacer data, in accord with similarity in size, sequence variability, and G + C content of ITS-1 and ITS-2 in most investigated groups of closely related angiosperms. Non-independent evolution of ITS sites involved in intraspacer RNA base-pairing may occur, given possible functional constraints, but preliminary secondary structure analyses of ITS-2 in Calycadenia (Asteraceae) show no definite evidence of compensatory spacer mutations. As expected, levels of ITS sequence variation suitable for phylogenetic analysis are found at various taxonomic levels within families, depending on the lineage. The apparent rates of ITS molecular evolution are roughly correlated with plant life-form, as with chloroplast DNA (cpDNA) data, but reasons for this observation are unclear. ITS characters have improved our understanding of angiosperm phylogeny in several groups by (1) corroborating earlier unexpected findings, (2) resolving conflicts between other data sets, (3) improving resolution of species relationships, or (4) providing direct evidence of reticulate evolution. Hybridization or sorting of ancestral polymorphism in a lineage can complicate interpretation of trees based on any type of evolutionary evidence, including ITS or cpDNA sequences, particularly in the absence of at least one independent phylogenetic data set from the same organisms. The need for phylogenetic markers from the nuclear genome, to complement the rapidly growing body of cpDNA data, makes the ITS region a particularly valuable resource for plant systematists.