ARS | Publication request: Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 14, 2011
Publication Date: September 14, 2011
Citation: Zheng, X., Hu, C., Spooner, D.M., Liu, J., Cao, J., Teng, Y. 2011. Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae). BMC Evolutionary Biology. 11:255.

Interpretive Summary: Pears are important commercial fruit crops with wild species useful for pear improvement through breeding. It is useful to know the wild relatives of cultivated pear to guide breeding efforts, and this study investigates these relationships (taxonomic relationships) by examining the DNA of gene regions technically called “Adh” and “LEAFY” of wild and cultivated pear. These studies showed that it was difficult to use these DNA data because there were different copies of these genes that made their comparison difficult. Despite these problems, we were able to select one of the LEAFY DNA sequences to investigate these relationships. This study is useful not only for the early results we have on relationships of wild and cultivated pear, but because it identified LEAFY as a useful gene region to use for future taxonomic studies.

Technical Abstract: The genus Pyrus includes some of the most important commercial fruit crops, including pears. There are long-standing alternative views on the origin of putative hybrids. Previous efforts have used the internal transcribed spacer region of nuclear ribosomal DNA (ITS) revealed a poorly resolved phylogeny. We here attempt to obtain a better phylogeny of Pyrus using introns of the low copy nuclear genes (LCNG) alcohol dehydrogenase (Adh) and LEAFY. Genomic sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus resulting from gene duplications. Only Adh1-1 was selected for phylogenetic reconstruction of 18 Pyrus species. Four paralogs representing Adh1-1 were further identified and all of them led to poorly resolved phylogenies due to low sequence divergence and inclusion of putative recombinants. For LEAFY, two major loci were identified, as expected, and only the second intron was used for phylogenetic analysis (LFY1int2, LFY2int2). LFY2int2 showed a relative high sequence divergence and led to a well resolved phylogeny, devoid of lineage sorting problems, congruent to previous phylogenetic reconstruction of Pyrus. These gene regions provided more useful information compared to ITS, but problems with paralogs, lineage sorting, pseudogenes, and putative recombinants made phylogenetic reconstruction of Pyrus difficult. Among the investigated nuclear gene regions, the second intron of LEAFY holds the greatest potential for phylogenetic reconstruction of Pyrus due to suitable sequence divergence and absence of lineage sorting.