Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA

Abstract

We present a comprehensive phylogeny derived from nuclear ribosomal DNA (nrDNA) for 214 samples representing 98 species and five varieties, including 44 species and five varieties native to China. Our collection of 25 species and five varieties (44 samples) covering all five sections of the genus (Comber) distributed in China also were included in the internal transcribed spacer (ITS) database. This study incorporates previous research with an emphasis on Chinese species, including the controversial subsection, Sinomartagon 5c Comber. In the phylogenetic tree obtained by maximum parsimony (PAUP) and maximum likelihood (RAxML) analyses, the samples were divided into four major groups. Our results suggest that the subsection (subsect.) 5c Comber should be classified into the true subsect. 5c and the section (sect.) Lophophorum. And the latter was divided into three subsections (subsect. Lophophorum I, subsect. Lophophorum II, and subsect. Lophophorum III). Based on molecular phylogenetic analysis and fluorescence in situ hybridization, we report that L. henryi and L. rosthornii are closely related, and we propose their classification into subsect. Leucolirion 6a. Our results support Comber's subdivision of sect. Leucolirion, which was primarily based on bulb color. Chinese species were divided into five sections: sect. Martagon, sect. Archelirion, sect. Leucolirion, sect. Sinomartagon, and sect. Lophophorum. These findings contribute to our understanding of the phylogeny, origin, and classification of Lilium.

Complete plastome sequence of Lilium pardalinum Kellogg (Liliaceae)

“…However, these three species were distantly related to L. philadelphicum. This polyphyly of the section Pseudolirium has been reported by previous studies (Hayashi and Kawano 2000;Lee et al 2011); however, certain studies have supported that the section Pseudolirium forms a clade (Nishikawa et al 2001;Du et al 2014). However, our result does not imply that L. philadelphicum should be distinguished from other Pseudolirium species because there are still taxonomic gaps and questions on the misidentification of samples.…”

“…This section was considered to be very closely related to section Martagon because of whorled leaves (Comber 1949;Lighty 1968). However, the most recent phylogenetic analyses using molecular markers indicated that both the sections are distantly related (Hayashi and Kawano 2000;Lee et al 2011;Gao et al 2013;Du et al 2014). Lilium pardalinum Kellogg belongs to the section Pseudolirium and is native to the Pacific Coast of the United States, growing in woodland near streams (McRae et al 1998).…”

“…In contrast to certain species in the same section, L. pardalinum has been successfully used for intersectional hybridization of the genus Lilium (van Tuyl and Arens 2010). However, sectional delimitation based on morphological and geographical characters of the genus Lilium has been controversial because the recent phylogenetic studies have not strongly supported the sectional classification of the genus Lilium (Hayashi and Kawano 2000;Du et al 2014). Therefore, the genetic studies of Lilium species are necessary for systematics and prospective breeding of the genus Lilium.…”

Genetic variability and diversity of the main resources of lily assessed via phenotypic characters, pollen morphology, and ISSR markers

“…Inter-simple sequence repeats (ISSR) are among the most useful DNA markers that have overcome most of these limitations, and have been efficiently and widely used in current studies addressing the genetic variability and diversity of plants and crops (Taheri et al, 2012;Karimi et al, 2014). At present, only a few studies have examined the diversity of Lilium species using molecular markers, including RAPD (Huang et al, 2009), ITS (Sultana et al, 2011;Du et al, 2014a) and ISSR (Guo et al, 2011;Xi et al, 2012;Zhao et al, 2014;Cui et al, 2014).…”

“…Despite this taxonomic system, it is difficult to classify several species of Lilium based on morphological traits alone, given that some traits are shared by distantly related species (Nishikawa et al, 1999;Du et al, 2014a). Taxonomists and botanists have gradually recognized the importance of pollen morphology in clarifying the classification of Lilium.…”