A Molecular Phylogeny of Lilium in the Internal Transcribed Spacer Region of Nuclear Ribosomal DNA

Abstract

Phylogenetic relationships among 55 species of Lilium, Cardiocrinum giganteum, and Nomocharis saluenensis were inferred from nucleotide sequence variations in the internal transcribed spacer (ITS) regions of 18S-25S nuclear ribosomal DNA. The phylogeny derived from ITS sequences estimated using maximum-likelihood methods indicated that (1) most of the species construct their own clade according to the classification based on morphological features at the section level; (2) section Daurolirion is not independent of Sinomartagon, and it is appropriate to integrate two sections as Sinomartagon; (3) it is appropriate that L. henryi and L. bulbiferum are classified into subsection 6a and Sinomartagon-Daurolirion, respectively; (4) subsection 6b is much closer to Sinomartagon than subsection 6a and Archelirion, and it arose directly from Sinomartagon; and (5) Lilium is much closer to Nomocharis than Cardiocrinum. Phylogenetic estimation using sequences of the ITS region is suitable at the levels of genus, section, and most of subsection.

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

“…1 in Van Tuyl et al (2000)). Despite this, both sections mostly co-occur within eastern Asia (i.e., areas A and B) (Liang and Tamura, 2000) and the close relationship between them has been suggested in previous phylogenetic studies (Nishikawa et al, 1999(Nishikawa et al, , 2001Hayashi and Kawano, 2000).…”

“…2 and 3). Species within the clade were first united by Liang (1980) and their close relationship has been supported by previous molecular systematic and karyotype studies (Nishikawa et al, 1999(Nishikawa et al, , 2001Gao et al, 2012). Members of this group shared funnel schaped flowers with narrow tubes, as well as white bulbs (Liang, 1980;Liang and Tamura, 2000).…”

“…In addition to the new sequences generated for this study, 55 ITS sequences and 43 matK sequences of Lilium used in previous studies were initially obtained from Genbank or directly from the authors (Nishikawa et al, 1999;Rønsted et al, 2005;_ Ikinci et al, 2006;Rešetnik et al, 2007;Nishikawa et al, unpublished). However, we followed Harpke and Peterson (2008) and removed six of the sequences obtained from GenBank (accession numbers: AB020439, AB020448, AB020450, AB020470, AM292432, AM292419) as possible pseduogenes because of variations within one or more of the three highly conserved motifs of 5.8S.…”

“…The boundaries of ITS were determined by comparing the aligned sequences with previously published Lilium sequences (Nishikawa et al, 1999(Nishikawa et al, , 2001. The boundaries of matK were decided by comparing with sequences of Lilium obtained from Genbank.…”

“…Since then, evidence from molecular phylogenetic studies shows that Nomocharis may be nested within Lilium and supports redefining Lilium to include Nomocharis (Nishikawa et al, 1999(Nishikawa et al, , 2001Hayashi and Kawano, 2000;Lee et al, 2011;Gao et al, 2012). In most previous phylogenetic studies, sampling of Nomocharis was limited to one or two species and authors asserted that additional sampling was needed before making taxonomic revisions (Nishikawa et al, 1999(Nishikawa et al, , 2001Hayashi and Kawano, 2000;Rønsted et al, 2005). Most recently, Gao et al (2012) reconstructed the phylogeny of Lilium and Nomocharis using two molecular markers and including six species of Nomocharis.…”