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Mitochondrial DNA B Resour
Mitochondrial DNA B Resour
Mitochondrial DNA. Part B, Resources
2380-2359
Taylor & Francis

10.1080/23802359.2024.2403410
2403410
Version of Record
Data Note
Plastome Report
The complete chloroplast genome sequence of Lilium saccatum S. Yun Liang (Liliaceae, Lilieae) and its phylogenetic analysis
X. Zhou et al.
Zhou Xuan a
Ma Jian-Hua b
Zhang Jun-Yi c
Luan Li b
Li Lin a
Gao Yun-Dong c
Feng Yu c
a Yajiang Clean Energy Ecological and Environment (Chengdu) Co., Ltd., Chengdu, China
b PowerChina Chengdu Engineering Corporation Limited, Chengdu, China
c CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2403410.

CONTACT Yun-Dong Gao gaoyd@cib.ac.cn
Yu Feng fengyu@cib.ac.cn CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P. O. Box 416, Chengdu 610041, China
16 9 2024
2024
16 9 2024
9 9 12231226
14 5 2024
5 9 2024
KnowledgeWorks Global Ltd.16 9 2024
published online in a building issue16 9 2024
© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
2024
The Author(s)
https://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

Abstract

Lilium saccatum is a species of ornamental plant found in southeastern Xizang, China. In the present study, the complete chloroplast (cp) genome of L. saccatum was sequenced using next-generation sequencing (NGS). The de novo assembled cp genome was 151,839 bp in length, including a pair of inverted repeat regions (IRs; 26,421 bp), a small single-copy region (SSC; 17,528 bp), and a large single-copy region (LSC; 81,469 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the cp genome was 37.0%. Phylogenetic analysis of 24 cp genomes revealed that L. saccatum was closely related to L. souliei. This study could provide fundamental information for the phylogenomics and utilization of Lilium.

Keywords

Chloroplast genome
Lilium saccatum
phylogeny
Second Tibetan Plateau Scientific Expedition and Research (STEP) 2019QZKK0301 2019QZKK0502 the National Plant Specimen Resource Center Project (NPSRC) E0117G1001 Wild Plants Sharing and Service Platform of Sichuan Province This study was supported by the Second Tibetan Plateau Scientific Expedition and Research (STEP) program [Grant No. 2019QZKK0301 and 2019QZKK0502], the National Plant Specimen Resource Center Project (NPSRC) [Grant No. E0117G1001], and Wild Plants Sharing and Service Platform of Sichuan Province.
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pmcIntroduction

Lilium saccatum S.Yun Liang 1987 is a herbaceous plant distributed in the southeastern Xizang Province, China (Liang 1987). The purple flowers of L. saccatum typically have bell-shaped, and the ovate or elliptic-lanceolate leaves are scattered, occasionally several in dense and subwhorled clusters (Liang and Minoru 2000). Lilies are popular ornamentals in gardens and landscapes for their beautiful flowers and evergreen foliage. With the rapid development of next-generation sequencing (NGS) technology, it is becoming easier to extract the information of organelle genomes. The chloroplast (cp) genome can provide valuable information for species identification, genetics, evolution, and phylogeny owing to its conserved genome structure and high substitution rates compared to other organelles of the plant (Daniell et al. 2021; Li et al. 2021; Zhang et al. 2022). To better understand the taxonomic and evolutionary relationships of Lilium, we assembled the complete cp genome of L. saccatum based on Illumina pair-end sequencing data (San Diego, CA).

Materials and methods

The samples of Lilium saccatum (Figure 1) were grown in the mountain slope regions of the southeastern Xizang Province, China (Milin County: 29°12′29.47″ N, 94°09′50.31″ E). Voucher specimens and fresh leaves of Lilium saccatum (voucher: GYD-1406; contact person: Bo Xu, xubo@cib.ac.cn) were deposited at the Herbarium of Chengdu Institute of Biology (CDBI). Total genomic DNA was extracted from silica-gel dried leaves through Plant DNA Isolation Kit (Cat. No. DE-06111, Foregene, Chengdu, China) and sequenced via Illumina paired-end technology (San Diego, CA). De novo assembly of the cp genome was carried out using GetOrganelle v1.7.2 (Jin et al. 2020), and the average coverage for the assembled cp genome was 3645.04× (Figure S1). The assembled cp genome was annotated using PGA (Qu et al. 2019) and manually corrected for the start and stop codons. The final genome map of L. saccatum was generated using CPGview (http://www.1kmpg.cn/cpgview). The phylogenetic analysis was constructed based on 24 complete cp genomes, including 23 species of Lilium and Fritillaria karelinii (Fisch.) Baker 1874 as outgroup species. Sequences were aligned via MAFFT v7.475 (Katoh and Standley 2013). A maximum-likelihood (ML) method for phylogenetic analysis was performed via IQ-Tree v.2.1.4 (Nguyen et al. 2015) with 2000 ultrafast bootstrap replicates. The resulted phylogenetic trees were visualized using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree). We also compared the singleton variable sites between L. saccatum and L. souliei (Franch.) Sealy 1950 by using DnaSP v6.12.03 (Rozas et al. 2017).

Figure 1. Photograph of Lilium saccatum (this unpublished photo, taken in Bomi County, Xizang Province, China by Mr. Shang-Hua Xia, is used with permission). Flower solitary, nodding and campanulate, tepals purple-red with dark spots adaxially.

Results

The cp genomes of Lilium saccatum and their sequenced raw data (GenBank number: OR353687; BioProject, SRA, and Bio-Sample numbers: PRJCA022586, CRR1005868, and SAMC3300505, respectively) were deposited in the NCBI (https://www.ncbi.nlm.nih.gov/) and CNCB (https://www.cncb.ac.cn/) database, respectively. The cp genome of L. saccatum was 151,839 bp in length; the quality control and read coverage depth map of the assembly of the cp genome are shown in Figure 2 and Figure S1. The overall GC content was 37.0%, which is higher than either large single-copy (LSC) regions (34.8%) or small single-copy (SSC) (30.6%) region, but lower than the inverted repeat (IR) (42.5%) region. It encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and four rRNAs. Introns were detected in 20 genes, where 16 genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) had a single intron, and two genes (clpP1 and pafI) had two introns (Figure S2). The trans-splicing gene rps12 had three unique exons (Figure S3). To clarify the system position of L. saccatum, we utilized a closely related genus species, Fritillaria karelinii, as outgroup and constructed ML tree based on 23 representative lilies, and the results showed that L. saccatum was closely clustered with L. souliei (Figure 3). Moreover, the aligned matrix of L. saccatum and L. souliei was 153,383 nucleotides in length with 565 singleton variable sites.

Figure 2. Chloroplast genome map of Lilium saccatum. The map was generated by CPGView. Genes located on the inner and outer of circle are transcribed clockwise and anticlockwise, respectively. The dark grey inner circle indicates GC content. Large single-copy (LSC), small single-copy (SSC), and inverted repeats (IRA and IRB) are indicated in the inner layer. The functional classification of the genes is provided in the bottom left corner.

Figure 3. The maximum-likelihood phylogeny obtained from 24 complete chloroplast sequences. The accession numbers of used sequences follow the species names, and the newly sequenced genome was shown in red font. The 23 species were Fritillaria karelinii (MG211818, outgroup) (Li et al. 2017), Lilium candidum (MK753244) (Lu et al. 2021), L. brownii (MK493294) (Du et al. 2017), L. formosanum (MK753244) (Lu et al. 2021), L. davidii (MW890008) (Li et al. 2021), L. pensylvanicum (MK493295) (Du et al. 2017), L. amabile (MT261159) (Do et al. 2020), L. concolor (MZ676707) (Du et al. 2017), L. pardalinum (MH029495) (Kim et al. 2018), L. superbum (KP462883) (Mennes et al. 2015), L. lophophorum (MK493298) (Du et al. 2017), L. nanum (MK493300) (Du et al. 2017), L. leucanthum (KY748299) (Du et al. 2017), L. nanum (MK493303) (Du et al. 2017), L. japonicum (MT261164) (Do et al. 2020), L. speciosum var. gloriosoides (MN509267) (Liu et al. 2019), L. henricii (MH029495) (Kim et al. 2018), L. medogense (OR797709) (Yuan and Gao 2024), L. saccatum (OR353687, this study), L. souliei (MW085076) (Li et al. 2021), L. amoenum (MT880912) (Do et al. 2020), L. bakerianum (KY748301) (Du et al. 2017), L. nepalense (MK493301) (Du et al. 2017), and L. taliense (KY009938) (Du et al. 2017).

Discussion and conclusions

In this study, we first reported the complete cp genome of Lilium saccatum, which was 151,839 bp in total length and had a typical quadripartite structure. A total of 113 unique genes were annotated in this plastome, which are not significantly different from other of published cp genomes in Lilium (Kim et al. 2017; Duan et al. 2022). The phylogeny reconstructed based on 23 complete cp genomes of Lilium reinforced the monophyly of this genus as a whole, which is consistent with previous studies (Du et al. 2017; Duan et al. 2022). Previous phylogenetic studies of the genus Lilium clarified L. saccatum was closely related to L. souliei based on cp gene sequences (Gao et al. 2013), and our phylogenetic results also reinforce this relationship. With the increase of sequenced species, the phylogenetic relationship on the genus Lilium will be clear. The complete cp genome of L. saccatum reported in this study is the first genomic resource for this species, a valuable resource for unraveling the evolutionary history of these high ornamental plants. Furthermore, our results provide a valuable resource for distribution, utilization, genetics, and phylogenetic studies of lilies.

Author contributions

XZ, YF, and YDG designed the study. JHM, JYZ, and L. Lin performed data analysis. XZ, JHM, and L. Li drafted the manuscript. YF revised the manuscript. All authors reviewed and approved the final manuscript.

Ethical approval

The collection of leaf samples conformed to the requirement of international ethics, which did not cause damage to the local environment. No endangered or protected species were involved in the study, and the collecting of the samples did not require specific permission from authorities.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are openly available in GenBank number OR353687 (https://www.ncbi.nlm.nih.gov/nuccore/0R353687) and the related BioProject, raw sequencing files in SRA, and the Bio-Sample number are PRJCA022586, CRR1005868, and SAMC3300505 (https://www.cncb.ac.cn/services), respectively.
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References

Baker JG. 1874. MR. J. G. Baker on Tulipeae. Bot J Linn Soc. 14 :268.
Daniell H, Jin S, Zhu XG, Gitzendanner MA, Soltis DE, Soltis PS. 2021. Green giant – a tiny chloroplast genome with mighty power to produce high‐value proteins: history and phylogeny. Plant Biotechnol J. 19 (3 ):430–447. doi:10.1111/pbi.13556.33484606
Do HDK, Kim C, Chase MW, Kim JH. 2020. Implications of plastome evolution in the true lilies (monocot order Liliales). Mol Phylogenet Evol. 148 :106818. doi:10.1016/j.ympev.2020.106818.32294543
Du Y, Bi Y, Yang F, Zhang M, Chen X, Xue J, Zhang X. 2017. Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses. Sci Rep. 7 (1 ):5751. doi:10.1038/s41598-017-06210-2.28720853
Duan Q, Liu F, Gui D, Fan W, Cui G, Jia W, Zhu A, Wang J. 2022. Phylogenetic analysis of wild species and the maternal origin of cultivars in the genus Lilium using 114 plastid genomes. Front Plant Sci. 13 :865606. doi:10.3389/fpls.2022.865606.35937320
Gao YD, Zhou S, He XJ. 2013. Lilium yapingense (Liliaceae), a new species from Yunnan, China, and its systematic significance relative to Nomocharis. Ann Bot Fennici. 50 (3 ):187–194. doi:10.5735/085.050.0311.
Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21 (1 ):241. doi:10.1186/s13059-020-02154-5.32912315
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30 (4 ):772–780. doi:10.1093/molbev/mst010.23329690
Kim HT, Zale PJ, Lim KB. 2018. Complete plastome sequence of Lilium pardalinum Kellogg (Liliaceae). Mitochondrial DNA B Resour. 3 (2 ):478–479. doi:10.1080/23802359.2018.1463826.33474211
Kim JH, Lee SI, Kim BR, Choi IY, Ryser P, Kim NS. 2017. Chloroplast genomes of Lilium lancifolium, L. amabile, L. callosum and L. philadelphicum: molecular characterization and their use in phylogenetic analysis in the genus Lilium and other allied genera in the order Liliales. PLOS One. 12 (10 ):e0186788. doi:10.1371/journal.pone.0186788.29065181
Li J, Cai J, Qin HH, Price M, Zhang Z, Yu Y, Xie DF, He XJ, Zhou SD, Gao XF. 2021. Phylogeny, age, and evolution of tribe Lilieae (Liliaceae) based on whole plastid genomes. Front Plant Sci. 12 :699226. doi:10.3389/fpls.2021.699226.35178055
Li S, Chang L, Zhang J. 2021. Advancing organelle genome transformation and editing for crop improvement. Plant Commun. 2 (2 ):100141. doi:10.1016/j.xplc.2021.100141.33898977
Li Y, Zhang Z, Lv G. 2017. The complete chloroplast genome of Fritillaria yuminensis, a rare and endangered species endemic to China. Mitochondrial DNA B Resour. 2 (2 ):913–914. doi:10.1080/23802359.2017.1413315.33474033
Liang SY, Minoru NT. 2000. Lilium Linnaeus. In: Wu ZY, Raven PH, Hong DY, editors. (2000) Flora of China. Vol. 24 . Beijing: Science Press; p. 135–149.
Liang SY. 1987. Lilium L. In: Wu ZY, editor. Flora Xizangica. Vol. 5 . Beijing: Science Press; p. 532–545.
Liu Y, Huang J, Moe TS, Khan MS, Xue J, Zhang X, Du Y. 2019. The complete chloroplast genome sequence of Lilium speciosum var. gloriosoides, an important breeding parent. Mitochondrial DNA B Resour. 5 (1 ):71–72. doi:10.1080/23802359.2019.1696245.33366427
Lu RS, Yang T, Chen Y, Wang SY, Cai MQ, Cameron KM, Li P, Fu CX. 2021. Comparative plastome genomics and phylogenetic analyses of Liliaceae. Bot J Linn Soc. 196 (3 ):279–293. doi:10.1093/botlinnean/boaa109.
Mennes CB, Lam VKY, Rudall PJ, Lyon SP, Graham SW, Smets EF, Merckx VSFT. 2015. Ancient Gondwana break-up explains the distribution of the mycoheterotrophic family Corsiaceae (Liliales). J Biogeogr. 42 (6 ):1123–1136. doi:10.1111/jbi.12486.
Nguyen LT, Schmidt HA, Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32 (1 ):268–274. doi:10.1093/molbev/msu300.25371430
Qu XJ, Moore MJ, Li DZ, Yi TS. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15 (1 ):50. doi:10.1186/s13007-019-0435-7.31139240
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol. 34 (12 ):3299–3302. doi:10.1093/molbev/msx248.29029172
Sealy JR. 1950. Nomocharis and Lilium. Kew Bull. 5 (2 ):273. doi:10.2307/4117245.
Yuan YM, Gao YD. 2024. Lilium liangiae, a new species in the genus Lilium (Liliaceae) that reveals parallel evolution within morphology. Front Plant Sci. 15 :1371237. doi:10.3389/fpls.2024.1371237.38601309
Zhang J-Y, Liao M, Cheng Y-H, Feng Y, Ju W-B, Deng H-N, Li X, Plenković-Moraj A, Xu B. 2022. Comparative chloroplast genomics of seven endangered Cypripedium species and phylogenetic relationships of Orchidaceae. Front Plant Sci. 13 :911702. doi:10.3389/fpls.2022.911702.35812969
