Prof. LI Jie and his team of Xishuangbanna Tropical Botanical Garden (XTBG) used two low-copy nuclear genes (LEAFY and RPB2) for phylogenetic analyses in Lauraceae. They aimed to assess the performance of the LEAFY second intron for phylogenetic reconstruction in Cinnamomum.

 The researchers cloned and sequenced the LEAFY gene for 63 Cinnamomum species and found two copies of the second intron within species of the diploid sect. Cinnamomum.  Although these two copies are very similar, they can be distinguished easily due to a specific ca. 47-bp segment that is missing in the “short sequence” copy. The “long sequence” copy performed well in phylogenetic analysis of Cinnamomum and is largely consistent with phylogenetic relationships based on internal transcribed spacer region sequences. In contrast, the “short sequence” copy was problematic for phylogenetic reconstruction and PCR-mediated recombination was detected in 20 of the 38 Cinnamomum species with two LEAFY copies. Thirty-one recombinants were discriminated and the breakpoints suggested by the programs RDP3 and GARD were distributed randomly along the recombination sequences.

 This study shows that duplication in low-copy nuclear genes and problems associated with PCR-mediated recombination need to be given more attention in phylogenetic studies.

  The study entitled “Phylogenetic utility of LEAFY gene in Cinnamomum (Lauraceae): Gene duplication and polymerase chain reaction-mediated recombination” has been published online in Journal of Systematics & Evolution.

 Contact

Prof.LI Jie Ph.D Ph.D Principal Investigator
Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
E-mail: jieli@xtbg.ac.cn