Kan Xian-Zhao, Wang Shan-Shan, Ding Xin, Wang Xiao-Quan
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China.
Mol Phylogenet Evol. 2007 Aug;44(2):765-77. doi: 10.1016/j.ympev.2007.05.004. Epub 2007 May 25.
Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.
核糖体DNA（nrDNA）被认为是推断许多分类水平上系统发育关系的重要工具。与被子植物中nrDNA快速的协同进化相比，裸子植物中nrDNA的协同进化缓慢，且ITS区域长度存在显著变异，尤其是在松科中。在此，我们研究了所有松科属nrDNA ITS区域的结构特征，包括亚重复序列组成、大小、GC含量和二级结构。结果表明，所有研究类群的ITS区域均包含亚重复单元，数量从2到9个不等，这些单元可分为两种类型，即不含基序（5'-GGCCACCCTAGTC）的较长亚重复序列（LSR）和含该基序的较短亚重复序列（SSR）。系统发育分析表明，一些SSR的同源性仍然可以被识别，这为nrDNA ITS的进化历史和松科系统发育提供了重要信息。特别是，在一些属中，相邻串联的SSR之间的关系并不比它们与较远的SSR之间的关系更密切，这可能意味着这些类群的ITS1区域发生了多种结构变异，如重组。本研究还发现，ITS1区域的GC含量与其序列长度和亚重复序列数量相关，并能提供一些系统发育信息，特别是支持云杉属、松属和银杉属之间的密切关系。此外，还发现了松科ITS1二级结构的几个特征：（1）该结构以几个延伸的发夹结构为主；（2）构型复杂性与亚重复序列数量呈正相关；（3）配对的亚重复序列在保守基序（5'-GGCCACCCTAGTC）处经常部分重叠，并形成一个长茎，而其他亚重复序列则自身折叠，使部分保守基序暴露在发夹环中。
