The complete chloroplast genome sequence and phylogenetic analysis of the Bichetii grass Chlorophytum laxum (Asparagaceae).

Chlorophytum laxum of Asparagaceae is a valuable ornamental plant native to the tropical regions of Asia, Africa, and Australia. The plant also has medicinal properties and is used as source for folk medicine. Despite being commercially important, genetic studies of C. laxum are still limited. To expand the genomic information of this plant species, we sequenced, assembled, and characterized its complete chloroplast genome. The chloroplast genome was 153,678 bp in length, with a large single-copy region (83,225 bp) and a small single-copy region (18,031 bp) separated by a pair of inverted repeat regions (26,211 bp each). A total of 127 genes were predicted, including 81 protein-coding, 38 tRNA, and eight rRNA genes. The overall GC content was 37.3%. Based on current sampling size, phylogenetic analysis using the maximum likelihood based on the complete chloroplast genome sequence revealed that the relationship in Chlorophytum is well resolved; C. laxum was closely related to C. rhizopendulum.

The complete chloroplast genome sequence and phylogenetic analysis of Strobilanthes dalzielii (W.W.Sm.) Benoist 1935 (Acanthaceae).

Strobilanthes dalzielii of Acanthaceae is an herb species with potentially extensive applications for its pharmaceutical and ornamental values. Due to taxonomic complications and limited genetic information, the structural characteristics, and phylogenetic relationships of the S. dalzielii chloroplast genome were assembled and characterized here for the first time. The complete chloroplast genome of S. dalzielii was 144,580 bp in length. The genome is quadripartite in structure and consists of a large single-copy region (92,137 bp) and a small single-copy region (17,669 bp), which are separated by a pair of inverted repeats (each 17,387 bp). A total of 125 genes were annotated, including 80 protein-coding, 37 transfer RNA, and eight ribosomal RNA genes. The overall GC content was 36.4%. Phylogenetic analysis based on the complete chloroplast genome sequence of 21 taxa within the tribe Ruellieae of Acanthaceae using the maximum likelihood and Bayesian inference methods revealed that Strobilanthes diverged after Ruellia; S. dalzielii is closely related to S. tonkinensis. The genomic data obtained from this study will serve as valuable information to the species delimitation and genetic classification of Strobilanthes.

The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship.

Pandanus amaryllifolius of Pandanaceae, a plant native to Southeast Asia, has been domesticated for its health benefits and aromatic leaves. It is also used for phytoremediation and soil rehabilitation. However, genetic studies of this species are limited. This study aims to expand its genomic information by assembling and characterizing the complete chloroplast genome of P. amaryllifolius. The chloroplast genome, which was 157,839 bp long, contains a total of 133 genes, including 87 protein-coding (CDS), 38 tRNA, and eight rRNA genes. The overall G/C content was 37.7%. A phylogenetic analysis using 79 shared unique CDS revealed a monophyletic relationship in Pandanales. Based on the limited sampling size, Pandanus amaryllifolius was the first to diverge in Pandanaceae. The genomic data will be useful for future phylogenetic and evolutionary studies of Pandanaceae.

DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China.

Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.

Characterization of the complete plastid genome and phylogenetic analysis of Oreocharis argyreia var. angustifolia (Gesneriaceae).

Oreocharis argyreia var. angustifolia of Gesneriaceae is widely distributed in South China, including Guangdong, Guangxi, Hunan, and Jiangxi provinces. However, genetic information of this species is limited, further contributing to the taxonomic complications surrounding this species. Thus, in this study, we assembled and characterized the complete chloroplast genome of O. argyreia var. angustifolia as a genomic resource for future studies. The complete plastid genome was 154,675 bp in size, with a pair of inverted repeat regions of 25,329 bp each, separating the 85,977-bp large and 18,040-bp small single copy regions. A total of 131 genes were predicted, consisting of 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content was 37.6%. Phylogenetic analysis based on 79 shared unique CDS resulted in a fully resolved phylogenetic tree using both the maximum likelihood and Bayesian inference methods. Based on current circumscription, both methods indicated that Oreocharis is monophyletic; O. argyreia var. angustifolia diverged after O. chienii, which then followed by the divergence of the other three species included namely, O. continifolia, O. esquirolii, and O. mileensis. The genomic data obtained will be useful for future studies on the phylogenetics and evolution of Gesneriaceae.

Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea.

Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis 'Splendens'. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis 'Splendens'. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.

Complete Chloroplast Genome of Four Thai Native Dioscorea Species: Structural, Comparative and Phylogenetic Analyses.

The chloroplast genomes of Dioscorea brevipetiolata, D. depauperata, D. glabra, and D. pyrifolia are 153,370-153,503 bp in size. A total of 113 genes were predicted, including 79 protein-coding sequences (CDS), 30 tRNA, and four rRNA genes. The overall GC content for all four species was 37%. Only mono-, di-, and trinucleotides were present in the genome. Genes adjacent to the junction borders were similar in all species analyzed. Eight distinct indel variations were detected in the chloroplast genome alignment of 24 Dioscorea species. At a cut-off point of Pi = 0.03, a sliding window analysis based on 25 chloroplast genome sequences of Dioscorea species revealed three highly variable regions, which included three CDS (trnC, ycf1, and rpl32), as well as an intergenic spacer region, ndhF-rpl32. A phylogenetic tree based on the complete chloroplast genome sequence displayed an almost fully resolved relationship in Dioscorea. However, D. brevipetiolata, D. depauperata, and D. glabra were clustered together with D. alata, while D. pyrifolia was closely related to D. aspersa. As Dioscorea is a diverse genus, genome data generated in this study may contribute to a better understanding of the genetic identity of these species, which would be useful for future taxonomic work of Dioscorea.

Highly divergent regions in the complete plastome sequences of Aquilaria are suitable for DNA barcoding applications including identifying species origin of agarwood products.

Members of Aquilaria Lam. (Thymelaeaceae) are evergreen trees that are widely distributed in the Indomalesia region. Aquilaria is highly prized for its unique scented resin, agarwood, which is often the subject of unlawful trade activities. Survival of the tree is heavily threatened by destructive harvesting and agarwood poaching, leading to its protection under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Unfortunately, an efficient species identification method, which is crucial to aid in the conservation efforts of Aquilaria is lacking. Here, we described our search for a suitable specific DNA barcode for Aquilaria species using eight complete plastome sequences. We identified five highly variable regions (HVR) (matK-rps16, ndhF-rpl32, psbJ-petA, trnD, and trnT-trnL) in the plastomes. These regions were further analyzed using the neighbor-joining (NJ) method to assess their ability at discriminating the eight species. Coupled with in silico primer design, two potential barcoding regions, psbJ-petA and trnT-trnL, were identified. Their strengths in species delimitation were evaluated individually and in combination, via DNA barcoding analysis. Our findings showed that the combined dataset, psbJ-petA + trnT-trnL, effectively resolved members of the genus Aquilaria by clustering all species into their respective clades. In addition, we demonstrated that the newly proposed DNA barcode was capable at identifying the species of origin of six commercial agarwood samples that were included as unknown samples. Such achievement offers a new technical advancement, useful in the combat against illicit agarwood trades and in assisting the conservation of these valuable species in natural populations. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03479-1.

The complete chloroplast genome and phylogenetic analysis of Christella dentata (Forssk.) Brownsey & Jermy (Thelypteridaceae).

Christella dentata (Forssk.) Brownsey & Jermy (Thelypteridaceae) is endemic to the tropical and subtropical regions of Africa, Asia, and Asia Pacific. In this study, the complete chloroplast genome sequence of C. dentata was assembled using next-generation sequencing data. The complete chloroplast genome was 151,662 bp in length and had a typical quadripartite structure, which consisted of a small single-copy region (21,776 bp) and a large single-copy region (82,624 bp) that were separated by a pair of inverted repeats (23,631 bp each). A total of 131 genes were predicted, including 89 protein coding (CDS), 34 tRNA, and eight rRNA genes. The overall GC content of the chloroplast genome was 42.48%. Based on the concatenated shared unique CDS sequence dataset, phylogenetic analysis using both the maximum-likelihood and the Bayesian inference methods revealed that C. dentata is placed within Thelypteridaceae and is closely related to Christella appendiculata. Such genetic information would be useful for studies on the evolution pattern in ferns. The availability of chloroplast genome sequence for the species also paves the way to resolving the complicated relationship among members of Christella.

Characterization of the plastid genome of Cratoxylum species (Hypericaceae) and new insights into phylogenetic relationships.

To expand the genomic information of Hypericaceae, particularly on Cratoxylum, we characterized seven novel complete plastid genomes (plastomes) of five Cratoxylum and two of its allied taxa, including C. arborescens, C. formosum subsp. formosum, C. formosum subsp. pruniflorum, C. maingayi, C. sumatranum, Hypericum hookerianum, and Triadenum breviflorum. For Cratoxylum, the plastomes ranged from 156,962 to 157,792 bp in length. Genomic structure and gene contents were observed in the five plastomes, and were comprised of 128-129 genes, which includes 83-84 protein-coding (CDS), 37 tRNA, and eight rRNA genes. The plastomes of H. hookerianum and T. breviflorum were 138,260 bp and 167,693 bp, respectively. A total of 110 and 127 genes included 72 and 82 CDS, 34 and 37 tRNA, as well as four and eight rRNA genes. The reconstruction of the phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) trees based on the concatenated CDS and internal transcribed spacer (ITS) sequences that were analyzed separately have revealed the same topology structure at genus level; Cratoxylum is monophyletic. However, C. formosum subsp. pruniflorum was not clustered together with its origin, raising doubt that it should be treated as a distinct species, C. pruniflorum based on molecular evidence that was supported by morphological descriptions.

The complete chloroplast genome sequence of Durio oxleyanus (Malvaceae) and its phylogenetic position.

Durio oxleyanus (Griff) of Malvaceae is considered a natural heritage by the countries that produce it, including Peninsular Malaysia, Sumatra, and Borneo. Even though the species is regarded as a commercially valuable fruit, cultivation of this species is uncommon. The dwindling population of this species in the wild has put its survival in jeopardy. Conservation efforts are required for this species, which are limited. In this study, the complete chloroplast (cp) genome of D. oxleyanus was assembled and characterized as a genomic resource for conservation programs. The complete cp genome size was 164,831 bp in length, with a pair of inverted repeats of 23,782 bp each, separating the 96,446-bp large and the 20,823-bp small single copies. A total of 135 genes were predicted, which consisted of 90 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content was 35.8%. The phylogenetic analysis based on the maximum-likelihood and Bayesian inference methods revealed that D. oxleyanus is closely related to D. zibethinus. The genomic data obtained will be useful for future studies of Malvaceae's phylogenetics and evolution.

Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species.

In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997-152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae).

Owing to its attractive flower shape and color, Renanthera (Orchidaceae), comprising about 19 species, has significant ornamental value as a houseplant, in floral design and in landscape gardens. Two species of Renanthera are categorized as endangered and critically endangered in China's Red List and international trade in these orchids is currently strictly monitored by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). This paper reports on the de novo assembled and annotated plastome of four species of Renanthera; R. citrina, R. coccinea, R. imschootiana, and R. philippinensis. The length of the plastome sequences ranged from 144,673 bp (R. imschootiana) to 149,007 bp (R. coccinea) with GC content of 36.6-36.7%. The plastomes showed a typical quadripartite structure, including a large single-copy (84,241-86,404 bp), a small single-copy (11,468-12,167 bp), and a pair of inverted repeats (24,482-25,715 bp) regions. Of the 120 genes detected, 74 were protein coding, 38 were tRNA, and eight were rRNA genes. The plastome of Renanthera is rather conserved, but nucleotide variations that could distinguish them apart are noticeable-the total number of tandem repeats ranged from 62 (in R. imschootiana) to 74 (in R. citrina); while the number of long repeats ranged from 21 (in R. imschootiana and R. philippinensis) to 43 (in R. citrina). Three hypervariable regions (psbI-trnS-GCU, trnG-GCC, rpl32) were identified. Phylogenetic analyses based on the CDS using maximum likelihood (ML) and Bayesian inference (BI) revealed that Renanthera is closely related to Holcoglossum, Neofinetia, Pendulorchis, and Vanda. The relationship between the four species of Renanthera was fully resolved; a monophyletic clade was formed and R. coccinea was recorded as the first to diverge from the rest. The genetic data obtained from this study could serve as a useful resource for species identification in Renanthera as well as contribute to future research on the phylogenomics of Orchidaceae.

Molecular phylogenetic analyses based on the complete plastid genomes and nuclear sequences reveal Daphne (Thymelaeaceae) to be non-monophyletic as current circumscription.

The diverse members of the genus Daphne are prized for their fragrant flowers. Despite being promising ornamental plants in many countries, genetic information of Daphne is scarce. In this study, the plastomes of four species and one variety of Daphne were sequenced and analyzed. The plastomes were typical and contained a pair of inverted repeat (IR) regions that separated the large single-copy (LSC) region from the small single-copy (SSC) region. With a length ranging from 132,869 bp (D. genkwa) to 174,773 bp (D. championii), 106 to 141 genes were predicted. Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs, sequence variations, and mutational hotspots. Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic. Daphne genkwa was nested within the genus Wikstroemia, while D. championii was well resolved as sister to Edgeworthia. These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data. The conflicts on the molecular placement of D. championii and D. genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.

Comparative analysis of complete Ilex (Aquifoliaceae) chloroplast genomes: insights into evolutionary dynamics and phylogenetic relationships.

BACKGROUND: Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships. RESULTS: We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems. CONCLUSION: Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.

Wikstroemiafragrans (Thymelaeaceae, Daphneae), a new species from Mount Danxia, China based on morphological and molecular evidence.

A new species, Wikstroemiafragrans (Thymelaeaceae, Daphneae), from Danxiashan National Park, Shaoguan, Guangdong of China is described and illustrated. It is similar to the sympatric W.trichotoma, but can be differentiated easily from the latter by its shorter racemose inflorescences, yellowish green calyx tube, and smaller leaves. It also resembles the allopatric W.fargesii, but differs from it by its strigose-pubescent ovary and disk scale that is 2- or 3-dentate apically. Phylogenetic analysis using the nuclear DNA internal transcribed spacer (ITS) region revealed that W.fragrans falls within the Wikstroemia clade; based on current sampling, W.fragrans is closely-related to W.capitata. It is also the first species of Wikstroemia known to be endemic to the Danxia landform and is classified provisionally as Critically Endangered according to the IUCN Red List Categories and Criteria.

The complete chloroplast genome of Ormosia purpureiflora (Fabaceae).

Ormosia purpureiflora is endemic to China. It is named after its purple flowers. It is a small tree only up to 3 m. It has leathery leaves, racemose inflorescences. The seeds are elliptic and red in coat. It is only confined to Luofushan Provincial Nature Reserve in Huizhou of Guangdong Province. Herein, we first reported on its complete chloroplast genome sequence as genomic resource for conservation purposes. The chloroplast genome of O. purpureiflora was 173,364 bp in length, with a large single-copy region of 73,465 bp, a small single-copy region of 18,751 bp, and a pair of inverted repeat regions that were 40,574 bp each. A total of 90 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes were predicted, while 106 simple sequence repeats were recorded throughout the genome. Phylogenetic analysis revealed that O. purpureiflora was sister to O. emarginata.

Complete plastomes of six species of Wikstroemia (Thymelaeaceae) reveal paraphyly with the monotypic genus Stellera.

Wikstroemia (Thymelaeaceae) is a diverse genus that extends from Asia to Australia and has been recorded on the Hawaiian Islands. Despite its medicinal properties and resource utilization in pulp production, genetic studies of the species in this important genus have been neglected. In this study, the plastome sequences of six species of Wikstroemia were sequenced and analysed. The plastomes ranged in size between 172,610 bp (W. micrantha) and 173,697 bp (W. alternifolia) and exhibited a typical genome structure consisting of a pair of inverted repeat (IR) regions separated by a large single-copy (LSC) region and a small single-copy (SSC) region. The six plastomes were similar in the 138 or 139 genes predicted, which consisted of 92 or 93 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC contents were identical (36.7%). Comparative genomic analyses were conducted with the inclusion of two additional published species of Wikstroemia in which the sequence divergence and expansion of IRs in the plastomes were determined. When compared to the coding sequences (CDSs) of Aquilaria sinensis, five genes, namely, rpl2, rps7, rps18, ycf1 and ycf2, indicated positive selection in W. capitata. The plastome-based phylogenetic analysis inferred that Wikstroemia in its current state is paraphyletic to Stellera chamaejasme, while the ITS-based tree analyses could not properly resolve the phylogenetic relationship between Stellera and Wikstroemia. This finding rekindled interest in the proposal to synonymize Stellera with Wikstroemia, which was previously proposed but rejected due to taxonomic conflicts. Nevertheless, this study provides valuable genomic information to aid in the taxonomic implications and phylogenomic reconstruction of Thymelaeaceae.

Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars.

Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, P. odoratum and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivar were observed. For genetic aspect, the plastid genome of P. odoratum varies in length from 154,569 bp to 155,491 bp, containing a large single-copy region of 83,486-84,459 bp, a small single-copy region of 18,292-18,471 bp, and two inverted repeats of 26,302-26,370 bp. A total of 131 genes were predicted, including 85 protein-coding, 38 tRNA, and eight rRNA genes. Genome comparisons revealed a slight variation in the sequence across the five accessions, but two highly variable regions (trnC-petN and rpl32-trnL) were detected when comparing the four different cultivars. For the RAD-seq markers, a total of 33.64 Gb of clean data, with an average value of 1.08 Gb per sample, were analyzed for the presence of single nucleotide polymorphisms (SNPs). Well-resolved phylogenies of the P. odoratum cultivars are constructed; the nonmonophyletic relationship in the plastome-based phylogenetic trees, yet monophyletic form in the RAD-based linkage map suggested possibility of hybrid cultivar for P. odoratum "Dazhu" (GDDZ), which was further supported by morphological observations. Quality assessment based on the standards of the Chinese Pharmacopoeia on Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study recorded that PORs from P. odoratum "Zhongzhu" (GDZZ) met the minimum criteria for the acceptance as raw material for medicinal drug production. This study has provided insights on the morphological variations, genetic background, and medicinal qualities of P. odoratum cultivars that could be explored for future genetic improvement as well as breeding programs of P. odoratum for POR production.

The complete chloroplast genome of Walla Patta, Gyrinops walla (Thymelaeaceae), an agarwood-producing tree species from Sri Lanka.

Gyrinops walla is an important agarwood-producing tree and threatened species from Sri Lanka. Herein, we assembled and characterized the complete chloroplast (cp) genome of G. walla as a genomic resource for conservation purposes. The 175,130 bp long genome is comprised of 87,376 bp large single-copy (LSC) and 3316 bp small single-copy (SSC) regions, which are separated by two inverted repeat (IR) region, each with a size of 42,291 bp. A total of 140 genes were predicted for the cp genome, which includes 94 protein-coding, 38 tRNA, and eight rRNA genes. Phylogenetic analysis showed that G. walla is fully resolved in a sister position to Aquilaria in the family Thymelaeaceae. The data provided will be useful for study on the molecular phylogenetics and evolution of Thymelaeaceae in the future.