Complete plastome sequence of Lilium pardalinum Kellogg (Liliaceae)

Abstract

Lilium pardalinum Kellogg is native to the Pacific Coast of the United States, and grows in woodland near streams. In the present study, the complete plastome of L. pardalinum was sequenced. The plastome sequence is 151,969 bp long with a large single copy, a small single copy, and two inverted repeat regions of length 81,401, 17,346, and 26,611 bp, respectively. A total of 133 genes were identified, including 82 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 5 pseudogenes. Among the 5 pseudogenes, pseudo ndhF and ndhG genes were similar to that of L. washingtonianum and L. philadelphicum, respectively. Lilium pardalinum is sister to American lilies, except L. philadelphicum.

Keywords:

• Lilium pardalinum
• plastome
• phylogeny

The section Pseudolirium Endlicher of the genus Lilium consists of ca. 20 species inhabiting North America. 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. In the present study, the plastome of L. pardalinum was completely sequenced. The total genomic DNA was extracted from the fresh leaves of L. pardalinum using the DNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). Seeds of L. pardalinum were collected at Onion Meadow, Tulare County, California on 28 September 1989 and grew in Kyungpook University, Korea. The living material and DNA were stored in Kyungpook University, Korea. The total DNA was sequenced using HiSeq 2500 instrument (Illumina, San Diego, CA, USA). All genes were annotated using Geneious (Kearse et al. 2012) by comparing with the previously reported plastome sequences of Lilium species. The phylogenetic analysis was performed with the concatenated 78 genes using randomized axelerated maximum likelihood (RAxML) (Stamatakis 2014). The plastome sequences of 22 Lilium and 3 Fritillaria species were downloaded from the National Center for Biotechnology Information database.

The plastome sequence is 151,969 bp long and consists of a large single copy region (81,401 bp), a small single copy region (17,346 bp), and two inverted repeat regions (26,611 bp). A total of 133 genes were identified, including 82 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 5 pseudogenes.

The phylogenetic analysis showed that L. pardalinum and L. washingtonianum formed a clade, and they were sister to L. superbum of the section Pseudolirium (Figure 1). 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. Consequently, more phylogenetic studies will help us understand the relationship among the species of the genus Lilium.

Figure 1. Phylogenetic analysis with 78 genes using randomized axelerated maximum likelihood (RAxML). Lilium pardalinum and L. washingtonianum form a clade, and they are sister to L. superbum of the section Pseudolirium. However, L. philadelphicum, another species of the section Pseudolirium, is distant from rest of the section Pseudolirium. The numbers on the node and scale refer to bootstrap values and substitutions per site, respectively.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [Project No. NRF-2016R1D1A1B04932913] and Regional Subgenebank Support Program of Rural Development Administration, Korea [No. PJ013761].