Phylogenetic study of Ipomoeeae (Convolvulaceae) based on chromosome painting

Abstract Background: The phylogenetic relationships for Ipomoeeae species are incongruence in previous studies. Comparative chromosome painting (CCP) can provide valuable information for phylogenetic relationships among species. Results: In this study, 31 Ipomoea species were analyzed by oligo-based chromosome painting (CP) technique to better understand their phylogenetic relationships. The results indicated that the distribution patterns of oligo probes in three species with 28 chromosomes were significantly different from the other species with 30 chromosomes. Therefore, we proposed that the difference of chromosome number should be foremost factor in determining the phylogenetic relationships among species and the previous division of two large clades in Ipomoeeae wasn’t supported. The division of smaller clades within the Astripomoeinae in Ipomoeeae was generally supported with a few exceptions, whereas the division of smaller clades within Argyreiinae wasn’t resolved by our CP results. In addition, species relationship for the species belonging to same smaller clade with same CP pattern was further resolved by physical mapping of the 5S and 45S rDNA using fluorescence in situ hybridization (FISH) technique. Conclusions: This study is the first phylogenetic analysis of Ipomoea species based on CP technique. Our results provide intuitive and reliable resolution of phylogenetic relationships for 31 Ipomoea species and demonstrate the validity of oligo-based CCP analysis in phylogenetic study.