Abstract
Lilium dauricum Ker Gawler is a wild lily species that belongs to section Sinomartagon and is one of the ancestors of the Asiatic hybrid lilies. Unique traits such as disease resistance and early flowering make L. dauricum a desirable resource for interspecific hybridization. However, in Korea, the natural resources of L. dauricum are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of L. dauricum was generated using Illumina paired-end sequencing technology, and its structure was compared with that of other Lilium species. The chloroplast genome was 152,063 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (26,492 bp) separated by a large (81,485 bp) and small (17,584 bp) single-copy (SC) region. The genome encodes 131 different genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis strongly supported the relationship of L. dauricum with other members of Sinomartagon and Martagon lilies.
Keywords: Chloroplast genome, Lilium dauricum, phylogenetic analysis
Introduction
Lilium dauricum Ker Gawler (genus Lilium) is a perennial bulb-producing flowering plant known for its high degree of resistance to Fusarium oxysporum var lilii, and exhibits early flowering, making it a valuable genitor for both interspecific and intersectional hybridizationhybridisation (Löffler et al. 1996). In Korea, the considerable economic value of L. dauricum has led to its overexploitation, causing a severe reduction in the size of its natural population.
Here, we report on the complete chloroplast (cp) genome sequence of L. dauricum. Plant material collected from Odesan Mountain, Gangwon-do, South Korea (37.46.42N, 128.36.02E) under accession number 2015-10 high-throughput sequencing was performed using an Illumina HiSeq 4000 platform. The raw reads were quality trimmed by Trimmomatic (Bolger et al. 2014), and high-quality reads were assembled by the Newbler assembler. The representative cp contigs were extracted, ordered, and merged into a single draft sequence by comparing with the already available cp genomes of Lilium species. The structural features and genes were predicted using the DOGMA program (Wyman et al. 2004), manual curation based on BLAST searches and ARTEMIS software (Rutherford et al. 2000). We have submitted the assembled and annotated sequence to GenBank under the accession number MK879804.
To ascertain the phylogenetic status of L. dauricum, the complete cp genome of 15 species in the family Liliaceae, including 11 representative species from the genus Lilium and two species each from Fritillaria and Cardiocrinum, and that of Smilax china as an outgroup were selected. A neighbour-joining (NJ) tree was constructed with Mega 6.0 using 1000 bootstrap replicates (Tamura et al. 2013) clustered the Lilium species into two groups. One group comprised sections Sinomartagon (L. cernuum, L. lancifolium, L. amabile, and L. dauricum), Martagon (L. hansonii and L. tsingtauense) and Leucolirion (L. brownii and L. longiflorum). Another group comprised Sinomartagon (L. fargesii) and Leucolirion (L. henryi and L. leucanthum) (Figure 1). Fritillaria and Cardiocrinum were placed in a distinct cluster, and Lilium and Fritillaria were strongly supported as sister taxa. L. dauricum together with sections Sinomartagon (L. cernuum, L. lancifolium, L. amabile, and L. dauricum) and Martagon (L. hansonii and L. tsingtauense) formed a monophyletic clade with a high bootstrap value, indicating a close relationship among these species.
Figure 1.
Molecular phylogenetic tree of the Liliaceae family based on the complete cp genome of 16 species.
Acknowledgements
We thank Mr. Choi Ki-Man, Gangwon Nature Environment Research Park (Gangwon-do), who kindly provided the sample.
Author contributions
MK and IYC conceived and designed the project and edited the manuscript. RVR contributed to the data analysis and drafted the manuscript. KP and IYC prepared the sample materials and analysed the data. All authors read and approved the final manuscript.
Disclosure statement
No potential conflict of interest was reported by the authors.
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