Xishuangbanna Tropical Botanical Garden, The Chinese Academy of Sciences, Kunming 650223, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China.
Royal Botanical Garden Edinburgh, Edinburg EH3 5LR, Scotland, United Kingdom.
Mol Phylogenet Evol. 2010 Apr;55(1):168-177. doi: 10.1016/j.ympev.2009.11.020. Epub 2009 Nov 27.
Molecular studies of six species from the ancient extant seed plant Cycas, covering a wide range of its morphological diversity and all major areas of distribution, revealed a high level of intra-individual polymorphism of the internal transcribed spacer (ITS1, 5.8S, and ITS2) region, indicative of incomplete nrDNA concerted evolution. Through a range of comparisons of sequence characteristics to functional cDNA ITS copies, including sequence length and substitution variation, GC content, secondary structure stability, the presence of a conserved motif in the 5.8S gene, and evolutionary rates, the PCR amplified divergent genomic DNA ITS paralogs were identified as either putative pseudogenes, recombinants or functional paralogs. This incomplete ITS concerted evolution may be linked to the high number of nucleolar organizer regions in the Cycas genome, and the incomplete lineage sorting due to recent species divergence in the genus. Based on the distribution of a 14 bp deletion, an early evolutionary origin of the pseudogenes is indicated, possibly predating the diversification of Cycas. Due to their early origin combined with the unconstraint evolution of the ITS region in pseudogenes, they accumulate high levels of homoplastic mutations. This leads to random relationships among the pseudogenes due to long-branch attractions, whereas the phylogenetic relationships inferred from the functional ITS paralogs grouped the sequences in species specific clades (except for C. circinalis and C. rumphii). The findings of our extensive study will have a wide significance, for the evolution of these molecular sequences, and their utilization as a major marker for reconstructing phylogenies.
对来自古老现存种子植物苏铁科的六个物种的分子研究，涵盖了其形态多样性的广泛范围和分布的所有主要区域，揭示了内部转录间隔区（ITS1、5.8S 和 ITS2）区域的个体内高度多态性，表明核 rDNA 协同进化不完全。通过对序列特征与功能 cDNA ITS 拷贝的一系列比较，包括序列长度和取代变异、GC 含量、二级结构稳定性、5.8S 基因中保守基序的存在以及进化率，鉴定出 PCR 扩增的分歧基因组 DNA ITS 同源物是假基因、重组体还是功能同源物。这种不完全的 ITS 协同进化可能与苏铁基因组中核仁组织区域的数量较多以及属内最近物种分歧导致的不完全谱系分选有关。基于 14 个碱基缺失的分布，表明假基因的早期进化起源，可能早于苏铁的多样化。由于它们的早期起源以及假基因中 ITS 区域的不受约束进化，它们积累了高水平的同形突变。这导致假基因之间由于长枝吸引而产生随机关系，而从功能 ITS 同源物推断出的系统发育关系将序列分组到物种特异性分支中（除了 C. circinalis 和 C. rumphii 之外）。我们广泛研究的结果将具有广泛的意义，因为这些分子序列的进化及其作为重建系统发育的主要标记的利用。
