Low-copy nuclear genes in plants are a rice source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstructions at all taxonomical levels, especially where universal markers such as cpDNA and nrDNA are unable to generate a strong phylogenetic hypothesis. Low-copy nuclear genes, however, remain underused in plant phylogenetic studies due to practical and theoretical complications in unraveling evolutionary dynamics of a nuclear gene family. The lack of the universal markers or universal PCR primers of low-copy nuclear genes has also hampered their phylogenetic utility. It has recently become clear that low-copy nuclear genes are particularly helpful in resolving close interspecific relationships and in reconstructing allopolyploidization in plants. Gene markers that are widely, if not universal, useful have begun to emerge. Although utilizing low-copy nuclear genes usually requires extra lab work such as designing PCR primers, PCR-cloning, and/or Southern blotting, rapid accumulation of gene sequences in the databases and advances in cloning techniques have continued to make such studies less labor-intensive. The growing number of theoretical studies devoted to the gene tree and species tree problem began to build a solid foundation for reconstructing complex plant phylogenies based on multiple gene trees. It is also increasingly realized that fast evolving introns of the low-copy nuclear genes will provide much needed phylogenetic information around the species boundary, and allow us to address fundamental questions concerning processes of plant speciation.

Key words: low-copy nuclear genes, phylogeny