Chloroplast Markers Research Articles

Towards the identification of wild African date palms in Kerkennah Islands from Tunisia by morphometric and genetic analyses

Wild relatives constitute an invaluable resource for crop breeding and are key components to understand their domestication history. Date palm is one of the oldest fruit crops, cultivated for millennia for its nutritional value and major economic and symbolic role. Two strongly differentiated gene pools have been recognized as the Western gene pool in North Africa and the Eastern one in the Middle East. Although a wild population has been proposed in Oman for the Eastern genetic pool, no wild date palm from the Western one has been yet described. In Tunisia, the date palms of Kerkennah archipelago consisted of spontaneous uncultivated individuals that are promising candidates for putative wild date palms. Morphometric tools were applied to 1140 date palm seeds of 69 Kerkennah accessions and compared to previously defined reference morphotypes. The genetic diversity of Kerkennah accessions was also compared to date palm populations and three Phoenix species using 18 nuclear microsatellite and one chloroplastic minisatellite markers. Morphometric analyses of Kerkennah accessions revealed genotypes with round-shaped seeds, characteristic of wild Phoenix species. Genetic analyses showed that Kerkennah's date palm belonged to the Western gene pool and exhibited a larger diversity and allelic richness than the western cultivated ones, proving that they are more probably wild than ferals. Altogether, our results strongly suggest that the spontaneous date palms growing in the harsh environment of the Kerkennah archipelago are wild populations. This unique heritage long-time preserved from anthropogenic pressure, is likely to contain some of the ancestral genetic diversity that would be of great value for breeding and provides new information for the discovery of the origins of the date palm.

Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier.

DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.

Genetic diversity among local mango (Mangifera indica L.) germplasm using morphological, biochemical and chloroplast DNA barcodes analyses.

In this study, the genetic diversity of local mango (Mangifera indica L.) germplasm including 14 genotypes were evaluated by using morphological, biochemical markers and DNA barcoding technique. Morphological characterization is the first step towards utilizing these germplasm in crop improvement studies. The advanced chloroplast based DNA barcode method can be utilized to assess the genetic diversity and phylogenetic structure in such populations. The study was carried out during 2018-2019years to evaluate local mango germplasm including 14 diverse genotypes based on a number of morphological and biochemical traits and chloroplast DNA barcoding as well. The experiment was laid out in one way ANOVA design with fourteen germplasm indicated with indigenous collection number. Among local mango germplasm, IC 589756 was found to be the most promising with respect to high magnitudes of fruit length, fruit width, fruit weight, pulp weight, soluble solid content (SSC)/Acidity ratio, pH and low acidity followed by IC 589746 exhibiting the highest pulp percentage and SSC accompanied with lowest stone weight and stone percent as compared to the other genotypes. Further, the dendrogram and cluster analyses based on sequencing of chloroplast marker i.e., trnH- psbA and trnCD depicted the relationship among mango genotypes and clearly clustered them into two main clusters at a similarity coefficient 0.035 and 0.150, respectively. The first cluster includes only one genotype and cluster-II contains 13 genotypes. Particularly results revealed that DNA barcoding of local mango germplasm can assist not only in molecular identification but also help in elucidation of their phylogenetic relationship and thus important in maintaining biodiversity inventories.

Transfer of Millettia pachycarpa and M. entadoides to Derris (Fabaceae), supported by morphological and molecular data

Derris Lour. and Millettia Wight & Arn. are two genera of the tribe Millettieae (Fabaceae). The biggest difference between the two genera is that Derris has indehiscent, thin and winged pods, while Millettia has dehiscent, compressed and wingless pods, but some exceptions also exist. Because of their tardily dehiscent, inflated and wingless pods, two Asian liana species, Millettia pachycarpa Benth. and M. entadoides Z. Wei, were previously placed in Millettia sect. Macrospermae Dunn. However, their vegetative and floral characters, as well as the shape of seeds match with those of Derris very well. Phylogenetic analyses based on three chloroplast markers (trnK/matK, trnL-F IGS, and psbA-trnH IGS), and nuclear ITS/5.8S showed that the two species are nested within Derris, and separate from other samples of Millettia species with strong support. Therefore, the two species should be transferred from Millettia to Derris to maintain the monophyly of the latter, which inevitably results in an emendation of the generic circumscription of Derris. Due to the existence of Derris pachycarpa Merr., the second earliest valid epithet “taiwaniana” should be used for this taxon when transfering Millettia pachycarpa Benth. to Derris. Thus, a new combination, Derris taiwaniana (Hayata) Z.Q. Song, is proposed here. Millettia entadoides Z. Wei is recombined as Derris entadoides (Z. Wei) Z.Q. Song. The floral morphology of D. entadoides is described here for the first time, and it is reported as a new record from Thailand in this study.

Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae).

Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.

PHYLOGENETIC RELATIONSHIPS OF UKRAINIAN ACCESSIONS OF LATHYRUS VENETUS (MILL.) WOHLF. AND L. VERNUS (L.) BERNH. BASED ON THE ANALYSIS OF THE psbA-trnH REGION OF THE CHLOROPLAST GENOME

The member of the genus Lathyrus, L. venetus is listed in the Red Data Book of Ukraine as a vulnerable species. Estimation of L. venetus abundance is complicated by the prevalence of interspecies hybrids with L. vernus. These hybrid populations are often misidentified as populations of the L. venetus due to their morphological similarity. The study of genetic resources of L. venetus requires the use of molecular markers, both nuclear (to identify hybrid forms) and plastid (to determine the direction of hybridization) localization. One of the most promising chloroplast markers, the IGS region between the psbA and trnH genes, has not yet been sequenced for L. venetus and L. vernus. In this work, we evaluated the possibility of using the psbA-trnH region of the chloroplast genome to identify the parental forms of hybrids between L. venetus and L. vernus. We amplified and sequenced the psbA-trnH IGS for the collected in Ukraine accessions of L. venetus and L. vernus. For comparison, psbA-trnH sequences from the GenBank database were used that represent species from phylogenetically distant sections of the genus Lathyrus, as well as species of the Orobus section closely related to L. venetus and L. vernus. Based on the analysis of alignment of all sequences used, we found that the level of variability of psbA-trnH exceeds that of other chloroplast DNA regions used in phylogenetic studies of the genus Lathyrus. On the phylogenetic tree constructed by us, the genus Lathyrus forms a monophyletic group with high statistical support. The sequences analysis showed significant differences between the psbA-trnH IGS of L. venetus and L. vernus and confirmed the effectiveness of using this region for molecular identification of these species and for determining the direction of hybridization in the hybrid forms.

Not dead yet: Diatom resting spores can survive in nature for several millennia.

Understanding the adaptive capacities of species over long timescales lies in examining the revived recent and millennia-old resting spores buried in sediments. We show for the first time the revival, viability, and germination rate of resting spores of the diatom Chaetoceros deposited in sub-seafloor sediments from three ages (recent: 0 to 80 years; ancient: ~1250 (Medieval Climate Anomaly) and ~6600 (Holocene Thermal Maximum) calendar year before present. Recent and ancient Chaetoceros spores were revived to examine their viability and germination rate. Light and scanning electron microscopy and Sanger sequencing was done to identify the species. We show that ~6600 cal. year BP old Chaetoceros resting spores are still viable and that the vegetative reproduction in recent and ancient resting spores varies. The time taken to germinate is three hours to 2 to 3 days in both recent and ancient spores, but the germination rate of the spores decreased with increasing age. The germination rate of the recent spores was ~41% while that of the ancient spores were ~31% and ~12% for the ~1250 and ~6600 cal. year BP old resting spores, respectively. Based on the morphology of the germinated vegetative cells we identified the species as Chaetoceros muelleri var. subsalsum. Sanger sequences of nuclear and chloroplast markers identified the species as Chaetoceros muelleri. We identify a unique model system, Chaetoceros muelleri var. subsalsum and show that recent and ancient resting spores of the species buried in sediments in the Baltic Sea can be revived and used for long-term evolutionary studies.

Изучение биоразнообразия дикоросов рода Rosa L. в Казахстане и их молекулярно-генетическая идентификация

The reduction of biological diversity is one of the most important problems of the present time. Wild plants are not only a source of genetic resources but are also important for the economy. Species of the genus Rosa L are among the most significant wild-growing fruit plants in Kazakhstan. The genus rosehip (Rosa L.) belongs to the perennial plants of the Rosaceae family. More than 20 wild rosehip species grow in Kazakhstan. In modern plant growing, wild rose is used as a medicinal, food, and ornamental plant. Determination of the species composition, and its morphological and genetic characteristics is the basis for the rational use of plant resources. The aim of our research was to study the biodiversity of plants of the genus Rosa L. based on the morphological characteristics of plants and their molecular genotyping. In this study, we identified 6 plant species of the following genus: Rosa kokanica (REGEL) REGEL ex JUZ., Rosa spinosissima L., Rosa majalis Herrm. (Rosa cinnamomea L.), Rosa acicularis L., Rosa laxa Retz, Rosa canina L. by morphological characteristics and performed identification using the rbcL chloroplast marker. The data obtained can be used for a comparative study of the biodiversity of rosehip plants.

The origin of the genus Cannabis

Chloroplast markers (cp markers) are the useful instrument for cannabis (syn. hemp, Cannabis sativa L.) to study relationships of accessions between different geographic origins. In an alignment of three published plastomes 38 chloroplast polymorphisms were identified from which 8 cp markers were used to study relationships of 53 cannabis accessions by high-resolution-melting analyis (HRMA). The marker set could distinguish six haplotypes (‘A’ to ‘F’) in the cannabis collection, where haplotypes ‘A’ and ‘F’ dominated with 34% and 50% of the individuals, respectively. A majority of populations (37) were homogeneous regarding the haplotype, 12 accessions were constituted of two haplotypes and 4 accessions of three haplotypes. Most of the European fibre cultivars consisted of the ‘F’-type (e.g. ‘Fibrimon’, Fibrimon 21’, Juso 14’, ‘Fasamo’ and ‘Schurig’), some were mixed ‘A/F’-types (e.g. ‘Fibrimon 21’, ‘Superfibra’, ‘Lorrin 110’, ‘Futura’, ‘Havelländische’). The Italian ‘Carmagnola in Selezione’ was exceptional in being a pure ‘A’-type. In the heterogenous populations, expected heterozygosity ranged from 0.06 to 0.41. The populations were well differentiated by this marker set locating 79% of the variation among populations (AMOVA). By comparison with plastomes from the closest related genus Humulus, haplotype ‘B’ could be identified as haplotype of the common ancestor of both genera. The haplotype ‘B’ is rare with a frequency of only 4% in the populations analysed. Unfortunately, the true geographic origin of most samples was unclear. However, amongst all published plastomes, only two were classified as haplotype ‘B’, both pointing independently back to Yunnan province (China), indicating Yunnan as the region of origin of the genus Cannabis.

Using DNA metabarcoding to decipher the diet plant component of mammals from the Eastern Mediterranean region

Longevity of species populations depends largely on interactions among animals and plants in an ecosystem. Predation and seed dispersal are among the most important interactions necessary for species conservation and persistence, and diet analysis is a prerequisite tool to evaluate these interactions. Understanding these processes is crucial for identifying conservation targets and for executing efficient reforestation and ecological restoration. In this study, we applied a scat DNA metabarcoding technique using the P6-loop of thetrnL(UAA) chloroplastic marker to describe the seasonal plant diet composition of 15 mammal species from a highly biodiverse Lebanese forest in the Eastern Mediterranean. We also recovered plant seeds, when present, from the scats for identification. The mammal species belong to 10 families from 5 different orders. More than 133 plant species from 54 plant families were detected and identified. Species from the Rosaceae, Poaceae, Apiaceae, Fabaceae, Fagaceae and Berberidaceae families were consumed by the majority of the mammals and should be taken into consideration in future reforestation and conservation projects. Our results showed that the DNA metabarcoding approach provides a promising method for tracking the dietary plant components of a wide diversity of mammals, yielding key insights into plant-animal interactions inside Lebanon’s forests.

DNA Barcoding of Adiantum (Pteridaceae: Vittarioideae) in Puerto Rico

We used the chloroplast markers trnL-F and rbcL to construct a DNA barcode sequence library of Adiantum (Pteridaceae) from Puerto Rico. By conducting BLAST searches, the trnL-F marker was able to successfully determine specimens of six out of 10 species for which data were generated, and failed for four. For the nine species for which rbcL sequences were obtained, the BLAST search method was successful for three, partially successful for three, and a failure for three. Phylogenetic analyses of both markers were able to resolve and distinguish all sampled taxa, with the exception that sequences of A. latifolium and A. ×variopinnatum were recovered as an unresolved polytomy with A. petiolatum nested within it. The molecular data indicate that what has previously been determined as A. pyramidale on Jamaica, Cuba, Hispaniola, and Puerto Rico likely represents at least two distinct species, based on data from Cuba and Puerto Rico. We also report the presence of A. ×variopinnatum on Puerto Rico for the first time.

Phylogenetic position of Phlojodicarpus villosus (Apiaceae) based on ITS and trnH-psbA nucleotide sequences

The aim of our work was to obtain chloroplast (trnH-psbA) and nuclear (ITS1-ITS2) DNA nucleotide sequences and identify the phylogenetic position of Phlojodicarpus villosus (Apiaceae). This species of vascular plants is represented in the Urals by isolated relic populations and is included in the regional Red Data Books. There is no data on P. villosus nucleotide sequences in the international open genetic databases. We studied two herbarium specimens of P. villosus, one collected from the Ural part of its range in the Komi Republic (Northern Urals) and the second collected from the main part of its range in the Magadan Region (Kolyma Highlands). Combining nuclear and chloroplast markers made it possible to reliably determine phylogenetic position of P. villosus within the tribe Selineae (subfamily Apioideae, family Apiaceae). We found ITS1-ITS2 and trnH-psbA nucleotide sequences to be sufficiently informative to identify specimens of this genus. High polymorphism of P. villosus sequences obtained from different parts of its range (Northern Urals and Kolyma Highlands) and the presence of evolutionary events (deletions) require more detail study of P. villosus and other Phlojodicarpus taxa by DNA barcoding methods.

Establishing community-wide DNA barcode references for conserving mangrove forests in China

BackgroundMangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering ‘blue carbon’. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country’s coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification.ResultsTo investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances.ConclusionWe suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.

Discovery of a new species of Adder\u2019s tongue fern from India with comparative analysis of morphological and molecular attributes

Eusporangiate fern genus Ophioglossum L. is commonly known as Adder’s tongue fern as its fertile frond gives the appearance of snake tongue. A new species in this fern genus, O. trilokinathii belonging to Ophioglossaceae family has been discovered from the plateau region of Rajasthan State of northwestern India. The new species can be distinguished from other taxa of this genus by its smaller habit, subglobose-tuberous rhizome, basipetal emergence of young roots, aggregation of old decaying roots on rhizome apex, fertile stalk as well as spike short and thick, trophophylls in rosette, ovate or orbicular and a unique sporoderm sculpture pattern under SEM having broad reticulations with thick and raised muri enclosing large hexagonal or irregular areas on the distal and proximal faces of the spores hitherto unreported in any of the presently known taxa of Ophioglossum. In addition, comparative study of stomatal structure, foliar anatomy and nucleotide sequence data of its three chloroplast DNA markers (trnL-F, rbcL and psbA-trnH) was carried out. In view of all the attributes including habitat, ecology, morphology, foliar anatomy, stomatal features, palynology and molecular phylogenetic data, the present study suggests that the Ophioglossum specimen collected from plateau region of Rajasthan represents a hitherto undescribed species thereby warranting its establishment as O. trilokinathii sp. nov. A detailed comparative account of the new taxon with its allied species has also been provided.

Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan

The Adiantum pedatum complex is disjunctly distributed in North America and eastern Asia. In this study, we carried out a detailed morphological study based on 137 specimens representing the biogeographic diversity of this complex. The sequences of eight chloroplast markers of 35 samples were analyzed with maximum likelihood and Bayesian inference. The morphological and phylogenetic analyses support the recognition of a new species of the A. pedatum complex from Japan. We propose the new species as A. japonicum based on the examinations of specimens from Japan and the comparative analyses of the whole complex. This new species can be distinguished from A. pedatum by the erect rhizome and shows significant molecular differences from other species in this complex. A taxonomic description with detailed morphological characters of the new species is presented.

Around the world in 40 million years: Phylogeny and biogeography of Tecomeae (Bignoniaceae)

Intercontinental disjunct distributions can arise from vicariance, long distance dispersal, or both. Tecomeae (Bignoniaceae) are a nearly cosmopolitan clade of flowering plants providing us with an excellent opportunity to investigate global distribution patterns. While the tribe contains only about 57 species, it has achieved a distribution that is not only pantropical, but also extends into the temperate zones in both the Northern and Southern hemispheres. This distribution is similar to the distribution of its sister group, a clade of about 750 spp. that includes most remaining taxa in Bignoniaceae. To infer temporal and spatial patterns of dispersal, we generated a phylogeny of Tecomeae by gathering sequence data from chloroplast and nuclear markers for 41 taxa. Fossil calibrations were used to determine divergence times, and ancestral states were reconstructed to infer its biogeographic history. We found support for a South American origin and a crown age of the tribe estimated at ca. 40 Ma. Two dispersal events seem to have happened during the Eocene-Oligocene, one from South America to the Old World, and another from South America to North America. Furthermore, two other dispersal events seem to have taken place during the Miocene, one from North America to Asia, and another from Australia to South America. We suggest that intercontinental dispersal via land bridges and island hopping, as well as sweepstakes of long distance dispersal from the Eocene to the present explain the global distribution of Tecomeae.

Aenigmanu, a new genus of Picramniaceae from Western Amazonia

AbstractAn unusual tree was collected in the Manu National Park in Peru in 1973 and although recollected many times, remained unidentified for decades. Preliminary molecular analysis indicated that it belonged to the Picramniaceae, even though the vegetative features were discordant. Using the nuclear marker ITS and the chloroplast marker rbcL, sequences were analyzed using Bayesian inference and maximum likelihood methods. The molecular analyses and study of the morphology showed that it is a new genus and species of Picramniaceae, herein described as Aenigmanu alvareziae. We provide a full morphological description, illustrations, and a distribution map of the new taxon, as well as a revised key to the genera of Picramniaceae.

The genetic variation and relationship among the natural hybrids of Mangifera casturi Kosterm

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi’s genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

Bryoerythrophyllum campylocarpum (Müll.Hal.) H.A.Crum, a tropical and subtropical moss new to Ireland and Britain

ABSTRACT Introduction An unfamiliar member of the Pottiaceae discovered near Goginan in Cardiganshire, Wales, UK, was identified as Bryoerythrophyllum campylocarpum sensu lato. An earlier collection from a wood in East Cork, Ireland, was subsequently confirmed as belonging to the same species. This moss is primarily a tropical and subtropical species and is very rare in Europe. Methods Both the Irish and Welsh plants were initially identified by morphological comparison with herbarium specimens of Bryoerythrophyllum campylocarpum from other areas of its distribution. Identification was confirmed by assessment of molecular affinities using two chloroplast markers, rps4 and trnM–trnV. Key results and conclusions Molecular and morphological affinities are presented and discussed. Comparisons are made with similar species and notes on identification are presented. Bryoerythrophyllum campylocarpum, as currently circumscribed, is confirmed as a member of the Irish and British bryophyte floras; however, both the molecular and morphological variation of specimens attributed to this species suggest that it is a collective taxon comprising at least three lineages which will probably need to be described as species in the future. The possible origins of the Irish and Welsh plants are considered.

The complete chloroplast genome of a shrub species, Smilax glabra (Smilacaceae) from Guangdong, China

Smilax glabra is a perennial woody scandent shrub, of which the dried aerial tuber has been used as Chinese medicine. Here, we sequenced S. glabra and assembled its complete chloroplast (cp) genome. The genome is 157,889 bp in length and has a typical quadripartite structure. We annotated 131 genes, of which 84 were protein-coding genes, 37 were tRNAs and 8 were rRNA genes. Phylogenetic analysis of this genome with 26 representatives Liliales fully resolved S. glabra in a clade with S. china. The phylogenetic tree we constructed is largely consistent with recently published phylogenetic trees using both complete chloroplast genomes and marker gene sequences.