Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome

TPMGD: A genomic database for the traditional medicines in Pakistan

Objective

In Pakistan, traditional medicines are an important component of the medical system, with numerous varieties and great demands. However, due to the scattered resources and the lack of systematic collection and collation, adulteration of traditional Pakistani medicine (TPM) is common, which severely affects the safety of their medicinal use and the import and export trades. Therefore, it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of TPM.

Methods

We collected and organized the information on 128 TPMs with regard to their medicinal parts, efficacy, usage, and genetic material, based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine: Pharmaceutical Codex. The genetic information of TPM is summarized from national center for biotechnology information (NCBI) and global pharmacopoeia genome database (GPGD). Furthermore, we utilized bioinformatics technology to supplement the chloroplast genome (cp-genome) data of 12 TPMs. To build the web server, we used the Linux + Apache + MySQL + PHP (LAMP) system and constructed the webpage on a PHP: Hypertext Preprocessor (PHP) model view controller (MVC) framework.

Results

We constructed a new genomic database, the traditional Pakistani medicine genomic database (TPMGD). This database comprises five entries, namely homepage, medicinal species, species identification, basic local alignment search tool (BLAST), and download. Currently, TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs, including 140 cytochrome c oxidase subunit I (COI) sequences and 119 mitochondrial genome sequences from Bombyx mori, 1 396 internal transcribed spacer 2 (ITS2) sequences and 1 074 intergenic region (psbA-trnH) sequences specific to 92 and 83 plant species, respectively. Additionally, TPMGD includes 199 cp-genome sequences of 82 TPMs.

Conclusion

TPMGD is a multifunctional database that integrates species description, functional information inquiry, genetic information storage, molecular identification of TPM, etc. The database not only provides convenience for TPM information queries but also establishes the scientific basis for the medication safety, species identification, and resource protection of TPM.

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences

BACKGROUND

Lasianthus species are widely used in traditional Chinese folk medicine with high medicinal value. However, source materials and herbarium specimens are often misidentified due to morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Lasianthus species. To improve the molecular methods for distinguishing among Lasianthus species, we report the complete chloroplast (CP) genomes of Lasianthus attenuatus, Lasianthus henryi, Lasianthus hookeri, Lasianthus sikkimensis, obtained via high-throughput Illumina sequencing.

RESULTS

These showed CP genomes size of 160164-160246 bp and a typical quadripartite structure, including a large single-copy region (86675-86848 bp), a small single-copy region (17177-17326 bp), and a pair of inverted repeats (28089-28135 bp). As a whole, the gene order, GC content and IR/SC boundary structure were remarkably similar among of the four Lasianthus CP genomes, the partial gene length and IR, LSC and SSC regions length are still different. The average GC content of the CP genomes was 36.71-36.75%, and a total of 129 genes were detected, including 83 different protein-coding genes, 8 different rRNA genes and 38 different tRNA genes. Furthermore, we compared our 4 complete CP genomes data with publicly available CP genome data from six other Lasianthus species, and we initially screened eleven highly variable region fragments were initially screened. We then evaluated the identification efficiency of eleven highly variable region fragments and 5 regular barcode fragments. Ultimately, we found that the optimal combination fragment' ITS2 + psaI-ycf4' could authenticated the Lasianthus species well. Additionally, the results of genome comparison of Rubiaceae species showed that the coding region is more conservative than the non-coding region, and the ycf1 gene shows the most significant variation. Finally, 49 species of CP genome sequences belonging to 16 genera of the Rubiaceae family were used to construct phylogenetic trees.

CONCLUSIONS

Our research is the first to analyze the chloroplast genomes of four species of Lasianthus in detail and we ultimately determined that the combination fragment' ITS2 + psaI-ycf4' is the optimal barcode combination for identifying the genus of Lasianthus. Meanwhile, we gathered the available CP genome sequences from the Rubiaceae and used them to construct the most comprehensive phylogenetic tree for the Rubiaceae family. These investigations provide an important reference point for further studies in the species identification, genetic diversity, and phylogenetic analyses of Rubiaceae species.

The complete chloroplast genome of Tabebuia rosea (Bignoniaceae)

Tabebuia rosea is a world-renowned woody plant with colorful flowers in full bloom. In addition to its high ornamental value, it also has ecological and medicinal value. In this study, the complete circular chloroplast genome of T. rosea was reconstructed and annotated using Illumina sequencing. The chloroplast genome was 158,919 bp in size with GC content of 38.21%, including a large single-copy region of 85,823 bp, a small single-copy region of 12,816 bp, and a pair of inverted repeats of 30,140 bp. It encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Based on current available chloroplast genome sequences, the phylogenetic analysis indicated that T. rosea was clustered with T. nodosa and H. chrysanthus. This study provided insights into the evolutionary relationships among different species of Bignoniaceae.

Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation

The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.

Comparative and phylogenetic analysis of the complete chloroplast genomes of 10 Artemisia selengensis resources based on high-throughput sequencing

BACKGROUND

Artemisia selengensis, classified within the genus Artemisia of the Asteraceae family, is a perennial herb recognized for its dual utility in culinary and medicinal domains. There are few studies on the chloroplast genome of A. selengensis, and the phylogeographic classification is vague, which makes phylogenetic analysis and evolutionary studies very difficult.

RESULTS

The chloroplast genomes of 10 A. selengensis in this study were highly conserved in terms of gene content, gene order, and gene intron number. The genome lengths ranged from 151,148 to 151,257 bp and were typical of a quadripartite structure with a total GC content of approximately 37.5%. The chloroplast genomes of all species encode 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Due to the contraction and expansion of the inverted repeats (IR), the overlap of ycf1 and ndhF genes occurred at the inverted repeats B (IRB) and short single copy sequence (SSC) boundaries. According to a codon use study, the frequent base in the chloroplast genome of A. selengensis' third codon position was A/T. The number of SSR repeats was 42-44, most of which were single nucleotide A/T repeats. Sequence alignment analysis of the chloroplast genome showed that variable regions were mainly distributed in single copy regions, nucleotide diversity values of 0 to 0.009 were calculated by sliding window analysis, 8 mutation hotspot regions were detected, and coding regions were more conserved than non-coding regions. Analysis of non-synonymous substitution (Ka) and synonymous substitution (Ks) revealed that accD, rps12, petB, and atpF genes were affected by positive selection and no genes were affected by neutral selection. Based on the findings of the phylogenetic analysis, Artemisia selengensis was sister to the genus Artemisia Chrysanthemum and formed a monophyletic group with other Artemisia genera.

CONCLUSIONS

In this research, the present study systematically compared the chloroplast genomic features of A. selengensis and provided important information for the study of the chloroplast genome of A. selengensis and the evolutionary relationships among Asteraceae species.

Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships

BACKGROUND

Dactylicapnos is a climbing herbaceous vine, distributed from the Himalayas to southwestern China, and some of the species have important medicinal values. However, the chloroplast genomes of Dactylicapnos have never been investigated. In this study, chloroplast genomes of seven Dactylicapnos species covering all three sections and one informal group of Dactylicapnos were sequenced and assembled, and the detailed comparative analyses of the chloroplast genome structure were provided for the first time.

RESULTS

The results showed that the chloroplast genomes of Dactylicapnos have a typical quadripartite structure with lengths from 172,344 bp to 176,370 bp, encoding a total of 133-140 genes, containing 88-94 protein-coding genes, 8 rRNAs and 37-39 tRNAs. 31 codons were identified as relative synonymous codon usage values greater than one in the chloroplast genome of Dactylicapnos genus based on 80 protein-coding genes. The results of the phylogenetic analysis showed that seven Dactylicapnos species can be divided into three main categories. Phylogenetic analysis revealed that seven species form three major clades which should be treated as three sections.

CONCLUSIONS

This study provides the initial report of the chloroplast genomes of Dactylicapnos, their structural variation, comparative genomic and phylogenetic analysis for the first time. The results provide important genetic information for development of medical resources, species identification, infrageneric classification and diversification of Dactylicapnos.

Chloroplast genomes in seven Lagerstroemia species provide new insights into molecular evolution of photosynthesis genes

Lagerstroemia indica is an important commercial tree known for the ornamental value. In this study, the complete chloroplast genome sequence of Lagerstroemia indica "Pink Velour" (Lagerstroemia "Pink Velour") was 152,174 bp in length with a GC content of 39.50%. It contained 85 protein coding genes (PCGs), 37 tRNAs, and 8 rRNA genes. 207 simple sequence repeats (SSRs) and 31 codons with relative synonymous codon (RSCU)value > 1 were detected. Phylogenetic analysis divided 10 Lagerstroemia species into evolutionary branches of clade A and clade B. We conducted a comparative analysis of Lagerstroemia "Pink Velours" complete chloroplast genome with the genomes of six closely related Lagerstroemia species from different origins. The structural features of all seven species were similar, except for the deletion of ycf1 nucleobases at the JSA boundary. The large single-copy (LSC) and the small single-copy (SSC) had a higher sequence divergence than the IR region, and 8 genes that were highly divergent (trnK-UUU, petN, psbF, psbJ, ndhE, ndhD, ndhI, ycf1) had been identified and could be used as molecular markers in future studies. High nucleotide diversity was present in genes belonging to the photosynthesis category. Mutation of single nucleic acid was mainly influenced by codon usage. The value percentage of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) in 6 Lagerstroemia species revealed that more photosynthesis genes have Ka or Ks only in Lagerstroemia fauriei, Lagerstroemia limii, and Lagerstroemia subcostata. These advances will facilitate the breeding of closely related Lagerstroemia species and deepen understanding on climatic adaptation of Lagerstroemia plants.

Characterization of the chloroplast genome of Gleditsia species and comparative analysis

The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8-75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", and "rpl32-trnL" in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.

Phylogenetics Study to Compare Chloroplast Genomes in Four Magnoliaceae Species

Magnoliaceae, a family of perennial woody plants, contains several endangered species whose taxonomic status remains ambiguous. The study of chloroplast genome information can help in the protection of Magnoliaceae plants and confirmation of their phylogenetic relationships. In this study, the chloroplast genomes were sequenced, assembled, and annotated in Woonyoungia septentrionalis and three Michelia species (Michelia champaca, Michelia figo, and Michelia macclurei). Comparative analyses of genomic characteristics, repetitive sequences, and sequence differences were performed among the four Magnoliaceae plants, and phylogenetic relationships were constructed with twenty different magnolia species. The length of the chloroplast genomes varied among the four studied species ranging from 159,838 bp (Woonyoungia septentrionalis) to 160,127 bp (Michelia macclurei). Four distinct hotspot regions were identified based on nucleotide polymorphism analysis. They were petA-psbJ, psbJ-psbE, ndhD-ndhE, and rps15-ycf1. These gene fragments may be developed and utilized as new molecular marker primers. By using Liriodendron tulipifera and Liriodendron chinense as outgroups reference, a phylogenetic tree of the four Magnoliaceae species and eighteen other Magnoliaceae species was constructed with the method of Shared Coding Sequences (CDS). Results showed that the endangered species, W. septentrionalis, is relatively genetically distinct from the other three species, indicating the different phylogenetic processes among Magnoliaceae plants. Therefore, further genetic information is required to determine the relationships within Magnoliaceae. Overall, complete chloroplast genome sequences for four Magnoliaceae species reported in this paper have shed more light on phylogenetic relationships within the botanical group.

Comparative Analysis of the Chloroplast Genome of Sicyos angulatus with Other Seven Species of Cucurbitaceae Family

Sicyos angulatus (SA) is an annual plant from the Cucurbitaceae family that is native to the eastern part of North America. This study aims to assemble and annotate the chloroplast genome of S. angulatus, and then compare it with plastomes of the other species representing the Cucurbitaceae family. The chloroplast genome size of S. angulatus is 154,986 bp, including a pair of inverted repeats (IR) of 26,276 bp, and small single-copy region (SSC) of 18,079 bp and large single-copy region (LSC) of 84,355 bp. Compared to other Cucurbitaceae species, the chloroplast genome of S. angulatus is almost 4222 bp smaller than the plastome Gynostemma pentaphyllum. All other seven species have an identical set of tRNA (37), except Citrullus laevigata, which contains 36 tRNA. The IRa/LSC junction in all eight species is located upstream of rpl2 and downstream of trnH gene. Moreover, variation in the size of the gene and the presence of pseudogene ycf1 has been seen because of the IR contraction and expansion. The highest number of tandem repeats was seen in G. pentaphyllum, and then Corynocarpus leavigata. The sequence divergence analysis and topology of the phylogenetic tree indicate that S. angulatus is more similar to genus Citrullus as compared to genus Gynostemma. These findings contribute to developing the genomic marker for the purpose of future genetic studies.

First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species

Hedysarum is one of the largest genera in the Fabaceae family, mainly distributed in the Northern Hemisphere. Despite numerous molecular studies on the genus Hedysarum, there is still a lack of research aimed at defining the specific characteristics of the chloroplast genome (cp genome) of the genus. Furthermore, the interrelationships between sections in the genus based on the cp genome have not yet been studied. In this study, comprehensive analyses of the complete cp genomes of six Hedysarum species, corresponding to sections Multicaulia, Hedysarum, and Stracheya were conducted. The complete cp genomes of H. drobovii, H. flavescens, and H. lehmannianum were sequenced for this study. The cp genomes of six Hedysarum species showed high similarity with regard to genome size (except for H. taipeicum), gene sequences, and gene classes, as well as the lacking IR region. The whole cp genomes of the six species were found to contain 110 genes ranging from 121,176 bp to 126,738 bp in length, including 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. In addition, chloroplast SSRs and repetitive sequence regions were reported for each species. The six Hedysarum species shared 7 common SSRs and exhibited 14 unique SSRs. As well, three highly variable genes (clpP, accD, and atpF) with high Pi values were detected among protein-coding genes. Furthermore, we conducted phylogenetic analyses using the complete cp genomes and 76 protein-coding genes of 14 legume species, including the seven Hedysarum species. The results showed that the Hedysarum species form a monophyletic clade closely related to the genera Onobrychis and Alhagi. Furthermore, both of our phylogenetic reconstructions showed that section Stracheya is more closely related to section Hedysarum than to section Multicaulia. This study is the first comprehensive work to investigate the genome characteristics of the genus Hedysarum, which provides useful genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.

Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae)

Species of Tanaecium (Bignonieae, Bignoniaceae) are lianas distributed in the Neotropics and centered in the Amazon. Members of the genus exhibit exceptionally diverse flower morphology and pollination systems. Here, we sequenced, assembled, and annotated 12 complete and four partial chloroplast genomes representing 15 Tanaecium species and more than 70% of the known diversity in the genus. Gene content and order were similar in all species of Tanaecium studied, with genome sizes ranging between 158,470 and 160,935 bp. Tanaecium chloroplast genomes have 137 genes, including 80-81 protein-coding genes, 37 tRNA genes, and four rRNA genes. No rearrangements were found in Tanaecium plastomes, but two different patterns of boundaries between regions were recovered. Tanaecium plastomes show nucleotide variability, although only rpoA was hypervariable. Multiple SSRs and repeat regions were detected, and eight genes were found to have signatures of positive selection. Phylogeny reconstruction using 15 Tanaecium plastomes resulted in a strongly supported topology, elucidating several relationships not recovered previously and bringing new insights into the evolution of the genus.

Differentiation of Lingxiaohua and Yangjinhua by chloroplast genome sequencing and DNA barcoding markers

Lingxiaohua (Campsis Flos, Campsis grandiflora (Thunb.) K. Schum) is a medicinal herb used for promoting diuresis and treating blood-related disorders by the promotion of blood circulation. It also possesses anti-inflammatory and antioxidative properties. This non-poisonous plant is frequently confused with poisonous Yangjinhua (Daturae Metelis Flos, Datura metel Linnaeus) in the market, resulting in serious anticholinergic poisoning. The confusion of these two herbs is due to the similarity in their appearances. In our study, we compared the complete chloroplast genomes of the two plants and found that they are very different in terms of their gene content and gene arrangement. There were also significant differences in the number and repeating motifs of microsatellites and complex repeats. We used universal primers for the amplification of rbcL, matK, psbA-trnH, and ITS2 regions and successfully differentiated the two plants. Furthermore, we designed two pairs of primers based on the nucleotide differences in chloroplast genomes at the rps14 and rpoC1 regions to provide additional authentication markers. The universal primers and specific primers when used together can accurately discriminate Lingxiaohua and Yangjinhua.

Evolutionary Comparison of the Complete Chloroplast Genomes in Convallaria Species and Phylogenetic Study of Asparagaceae

The genus Convallaria (Asparagaceae) comprises three herbaceous perennial species that are widely distributed in the understory of temperate deciduous forests in the Northern Hemisphere. Although Convallaria species have high medicinal and horticultural values, studies related to the phylogenetic analysis of this genus are few. In the present study, we assembled and reported five complete chloroplast (cp) sequences of three Convallaria species (two of C. keiskei Miq., two of C. majalis L., and one of C. montana Raf.) using Illumina paired-end sequencing data. The cp genomes were highly similar in overall size (161,365–162,972 bp), and all consisted of a pair of inverted repeats (IR) regions (29,140–29,486 bp) separated by a large single-copy (LSC) (85,183–85,521 bp) and a small single-copy (SSC) region (17,877–18,502 bp). Each cp genome contained the same 113 unique genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene content, gene order, AT content and IR/SC boundary structure were nearly identical among all of the Convallaria cp genomes. However, their lengths varied due to contraction/expansion at the IR/LSC borders. Simple sequence repeat (SSR) analyses indicated that the richest SSRs are A/T mononucleotides. Three highly variable regions (petA-psbJ, psbI-trnS and ccsA-ndhD) were identified as valuable molecular markers. Phylogenetic analysis of the family Asparagaceae using 48 cp genome sequences supported the monophyly of Convallaria, which formed a sister clade to the genus Rohdea. Our study provides a robust phylogeny of the Asparagaceae family. The complete cp genome sequences will contribute to further studies in the molecular identification, genetic diversity, and phylogeny of Convallaria.

Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae)

The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai-Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.

Taxonomy, comparative genomics of Mullein (Verbascum, Scrophulariaceae), with implications for the evolution of Verbascum and Lamiales

BACKGROUND

The genus Verbascum L. (Scrophulariaceae) is distributed in Africa, Europe, and parts of Asia, with the Mediterranean having the most species variety. Several researchers have already worked on the phylogenetic and taxonomic analysis of Verbascum by using ITS data and chloroplast genome fragments and have produced different conclusions. The taxonomy and phylogenetic relationships of this genus are unclear.

RESULTS

The complete plastomes (cp) lengths for V. chaixii, V. songaricum, V. phoeniceum, V. blattaria, V. sinaiticum, V. thapsus, and V. brevipedicellatum ranged from 153,014 to 153,481 bp. The cp coded 114 unique genes comprising of 80 protein-coding genes, four ribosomal RNA (rRNA), and 30 tRNA genes. We detected variations in the repeat structures, gene expansion on the inverted repeat, and single copy (IR/SC) boundary regions. The substitution rate analysis indicated that some genes were under purifying selection pressure. Phylogenetic analysis supported the sister relationship of (Lentibulariaceae + Acanthaceae + Bignoniaceae + Verbenaceae + Pedaliaceae) and (Lamiaceae + Phyrymaceae + Orobanchaceae + Paulowniaceae + Mazaceae) in Lamiales. Within Scrophulariaceae, Verbascum was sister to Scrophularia, while Buddleja formed a monophyletic clade from (Scrophularia + Verbascum) with high bootstrap support values. The relationship of the nine species within Verbascum was highly supported.

CONCLUSION

Based on the phylogenetic results, we proposed to reinstate the species status of V. brevipedicellatum (Engl.) Hub.-Mor. Additionally, three genera (Mazus, Lancea, and Dodartia) placed in the Phyrymaceae family formed a separate clade within Lamiaceae. The classification of the three genera was supported by previous studies. Thus, the current study also suggests the circumscription of these genera as documented previously to be reinstated. The divergence time of Lamiales was approximated to be 86.28 million years ago (Ma) (95% highest posterior density (HPD), 85.12-89.91 Ma). The complete plastomes sequence data of the Verbascum species will be important for understanding the Verbascum phylogenetic relationships and evolution in order Lamiales.

The analysis of genetic structure and characteristics of the chloroplast genome in different Japanese apricot germplasm populations

BACKGROUND

Chloroplast (cp) genomes are generally considered to be conservative and play an important role in population diversity analysis in plants, but the characteristics and diversity of the different germplasm populations in Japanese apricot are still not clear.

RESULTS

A total of 146 cp genomes from three groups of wild, domesticated, and bred accessions of Japanese apricot were sequenced in this study. The comparative genome analysis revealed that the 146 cp genomes were divided into 41 types, and ranged in size from 157,886 to 158,167 bp with a similar structure and composition to those of the genus Prunus. However, there were still minor differences in the cp genome that were mainly caused by the contraction and expansion of the IR region, and six types of SSR in which mono-nucleotide repeats were the most dominant type of repeats in the cp genome. The genes rpl33 and psbI, and intergenic regions of start-psbA, rps3-rpl22, and ccsA-ndhD, showed the highest nucleotide polymorphism in the whole cp genome. A total of 325 SNPs were detected in the 146 cp genomes, and more than 70% of the SNPs were in region of large single-copy (LSC). The SNPs and haplotypes in the cp genome indicated that the wild group had higher genetic diversity than the domesticated and bred groups. In addition, among wild populations, Southwest China, including Yunnan, Tibet, and Bijie of Guizhou, had the highest genetic diversity. The genetic relationship of Japanese apricot germplasm resources in different regions showed a degree of correlation with their geographical distribution.

CONCLUSION

Comparative analysis of chloroplast genomes of 146 Japanese apricot resources was performed to analyze the used to explore the genetic relationship and genetic diversity among Japanese apricot resources with different geographical distributions, providing some reference for the origin and evolution of Japanese apricot.

Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus

The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89−104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.

Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships

BACKGROUND

Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time.

RESULTS

The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA-atpF and rps2-rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds.

CONCLUSION

In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.

Comparative Analysis of Chloroplast Genome Structure and Phylogenetic Relationships Among Six Taxa Within the Genus Catalpa (Bignoniaceae)

Species within the Genus Catalpa are mostly semievergreen or deciduous trees with opposite or whorled leaves. C. bungei, C. fargesii f. duclouxii and C. fargesii are sources of traditional precious wood in China, known as the “kings of wood”. Due to a lack of phenotypic and molecular studies and insufficient sequence information, intraspecific morphological differences, common DNA barcodes and partial sequence fragments cannot clearly reveal the phylogenetic or intraspecific relationships within Catalpa. Therefore, we sequenced the complete chloroplast genomes of six taxa of the genus Catalpa and analyzed their basic structure and evolutionary relationships. The chloroplast genome of Catalpa shows a typical tetrad structure with a total length ranging from 157,765 bp (C. fargesii) to 158,355 bp (C. ovata). The length of the large single-copy (LSC) region ranges from 84,599 bp (C. fargesii) to 85,004 bp (C. ovata), that of the small single-copy (SSC) region ranges from 12,662 bp (C. fargesii) to 12,675 bp (C. ovata), and that of the inverted repeat (IR) regions ranges from 30,252 bp (C. fargesii) to 30,338 bp (C. ovata). The GC content of the six chloroplast genomes were 38.1%. In total, 113 unique genes were detected, and there were 19 genes in IR regions. The 113 genes included 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Five hypervariable regions (trnH-psbA, rps2-rpoC2, rpl22, ycf15-trnl-CAA and rps15) were identified by analyzing chloroplast nucleotide polymorphisms, which might be serve as potential DNA barcodes for the species. Comparative analysis showed that single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were highly diverse in the six species. Codon usage patterns were highly similar among the taxa included in the present study. In addition to the stop codons, all codons showed a preference for ending in A or T. Phylogenetic analysis of the entire chloroplast genome showed that all taxa within the genus Catalpa formed a monophyletic group, clearly reflecting the relationships within the genus. This study provides information on the chloroplast genome sequence, structural variation, codon bias and phylogeny of Catalpa, which will facilitate future research efforts.

Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications

Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.

Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.)

The Albizia julibrissin chloroplasts have a classical chloroplast genome structure, containing 93 coding genes and 34 non-coding genes. Our research provides basic data for plant phylogenetic evolutionary studies. There is limited genomic information available for the important Chinese herb Albizia julibrissin Durazz. In this study, we constructed the chloroplast (Cp) genome of A. julibrissin. The length of the assembled Cp genome was 175,922 bp consisting of four conserved regions: a 5145 bp small single-copy (SSC) region, a 91,323 bp large single-copy (LSC) region, and two identical length-inverted repeat (IR) regions (39,725 bp). This Cp genome included 34 non-coding RNAs and 93 unique genes, the former contains 30 transfer and 4 ribosomal RNA genes. Gene annotation indicated some of the coding genes (82) in the A. julibrissin Cp genome classified in the Leguminosae family, with some to other related families (11). The results show that low GC content (36.9%) and codon bias towards A- or T-terminal codons may affect the frequency of gene codon usage. The sequence analysis identified 30 forward, 18 palindrome, and 1 reverse repeat > 30 bp length, and 149 simple sequence repeats (SSR). Fifty-five RNA editing sites in the Cp of A. julibrissin were predicted, most of which are C-to-U conversions. Analysis of the reverse repeat expansion or contraction and divergence area between several species, including A. julibrissin, was performed. The phylogenetic tree revealed that A. julibrissin was most closely related to Albizia odoratissima and Albizia bracteata, followed by Samanea saman, forming an evolutionary branch with Mimosa pudica and Leucaena trichandra. The research results are helpful for breeding and genetic improvement of A. julibrissin, and also provide valuable information for understanding the evolution of this plant.

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis

Most Alpinia species are valued as foods, ornamental plants, or plants with medicinal properties. However, morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Alpinia species. Difficulties in species identification have led to confusion in the sale and use of Alpinia for medicinal use. To mine resources and improve the molecular methods for distinguishing among Alpinia species, we report the complete chloroplast (CP) genomes of Alpinia galanga and Alpinia kwangsiensis species, obtained via high-throughput Illumina sequencing. The CP genomes of A. galanga and A. kwangsiensis exhibited a typical circular tetramerous structure, including a large single-copy region (87,565 and 87,732 bp, respectively), a small single-copy region (17,909 and 15,181 bp, respectively), and a pair of inverted repeats (27,313 and 29,705 bp, respectively). The guanine-cytosine content of the CP genomes is 36.26 and 36.15%, respectively. Furthermore, each CP genome contained 133 genes, including 87 protein-coding genes, 38 distinct tRNA genes, and 8 distinct rRNA genes. We identified 110 and 125 simple sequence repeats in the CP genomes of A. galanga and A. kwangsiensis, respectively. We then combined these data with publicly available CP genome data from four other Alpinia species (A. hainanensis, A. oxyphylla, A. pumila, and A. zerumbet) and analyzed their sequence characteristics. Nucleotide diversity was analyzed based on the alignment of the complete CP genome sequences, and five candidate highly variable site markers (trnS-trnG, trnC-petN, rpl32-trnL, psaC-ndhE, and ndhC-trnV) were found. Twenty-eight complete CP genome sequences belonging to Alpinieae species were used to construct phylogenetic trees. The results fully demonstrated the phylogenetic relationship among the genera of the Alpinieae, and further proved that Alpinia is a non-monophyletic group. The complete CP genomes of the two medicinal Alpinia species provides lays the foundation for the use of CP genomes in species identification and phylogenetic analyses of Alpinia species.

Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.

Differentiation of Hedyotis diffusa and Common Adulterants Based on Chloroplast Genome Sequencing and DNA Barcoding Markers

Chinese herbal tea, also known as Liang Cha or cooling beverage, is popular in South China. It is regarded as a quick-fix remedy to relieve minor health problems. Hedyotis diffusa Willd. (colloquially Baihuasheshecao) is a common ingredient of cooling beverages. H. diffusa is also used to treat cancer and bacterial infections. Owing to the high demand for H. diffusa, two common adulterants, Hedyotis brachypoda (DC.) Sivar and Biju (colloquially Nidingjingcao) and Hedyotis corymbosa (L.) Lam. (colloquially Shuixiancao), are commonly encountered in the market. Owing to the close similarity of their morphological characteristics, it is difficult to differentiate them. Here, we sequenced the complete chloroplast genomes of the three species of Hedyotis using next-generation sequencing (NGS). By comparing the complete chloroplast genomes, we found that they are closely related in the subfamily Rubioideae. We also discovered that there are significant differences in the number and repeating motifs of microsatellites and complex repeats and revealed three divergent hotspots, rps16-trnQ intergenic spacer, ndhD and ycf1. By using these species-specific sequences, we propose new DNA barcoding markers for the authentication of H. diffusa and its two common adulterants.

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

BACKGROUND

The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted.

RESULTS

Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value.

CONCLUSION

The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae

Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.

Lineage-specific evolution of mangrove plastid genomes

Mangroves is an umbrella term for plants located across the tropics and sub-tropics that live in the coastal region, between the sea and the land. All mangroves evolved from terrestrial plants, providing the opportunity to assess convergence, as well as the lineage-specific features, at the genetic level. In this study, we compared chloroplast genomes from 21 mangrove species, covering main phylogenetic clades. We demonstrate that chloroplast gene order, content, and genome size is largely conserved in mangroves. The exceptions are loss of the photosystem I gene psaZ in Acanthus ilicifolius and inversion of the ribosomal protein gene rpl23 in Avicennia germinans. The repeat content of mangrove chloroplast varied between species, but was conserved within species of the same order. Sequence diversity analysis revealed that the IR (invert repeat) region was highly conserved compared to the SC (single-copy) region in most phylogenetic clades, except clade core leptosporangiates (ferns). The ribosomal protein gene rps7 was under positive selection in Kandelia obovato, Rhizophora stylosa, Bruguiera sexangular and Rhizophora mangle, a monophyletic branch of clade fabids, while no evidence of positive selection was found in other mangrove lineages. Taken together, our data suggests that convergent evolutionary dynamics leaves no significant signal on the plastid genome of mangroves. The complete chloroplast genomes provided in this study shed light on the evolution of these important plastids and provides a valuable resource for further research efforts.

Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae)

Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.

Complete Chloroplast Genome Sequence of Hibiscus cannabinus and Comparative Analysis of the Malvaceae Family

Kenaf (Hibiscus cannabinus) is one of the most fast-growing bast in the world and belongs to the family Malvaceae. However, the systematic classification and chloroplast (cp) genome of kenaf has not been reported to date. In this study, we sequenced the cp genome of kenaf and conducted phylogenetic and comparative analyses in the family of Malvaceae. The sizes of H. cannabinus cp genomes were 162,903 bp in length, containing 113 unique genes (79 protein-coding genes, four rRNA genes, and 30 tRNA genes). Phylogenetic analysis indicated that the cp genome sequence of H. cannabinus has closer relationships with Talipariti hamabo and Abelmoschus esculentus than with Hibiscus syriacus, which disagrees with the taxonomical relationship. Further analysis obtained a new version of the cp genome annotation of H. syriacus and found that the orientation variation of small single copy (SSC) region exists widely in the family of Malvaceae. The highly variable ycf1 and the highly conserved gene rrn32 were identified among the family of Malvaceae. In particular, the explanation for two different SSC orientations in the cp genomes associated with phylogenetic analysis is discussed. These results provide insights into the systematic classification of the Hibiscus genus in the Malvaceae family.

Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at J_LB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera.

Complete chloroplast genomes of two Siraitia Merrill species: Comparative analysis, positive selection and novel molecular marker development

Siraitia grosvenorii fruit, known as Luo-Han-Guo, has been used as a traditional Chinese medicine for many years, and mogrosides are its primary active ingredients. Unfortunately, Siraitia siamensis, its wild relative, might be misused due to its indistinguishable appearance, not only threatening the reliability of the medication but also partly exacerbating wild resource scarcity. Therefore, high-resolution genetic markers must be developed to discriminate between these species. Here, the complete chloroplast genomes of S. grosvenorii and S. siamensis were assembled and analyzed for the first time; they were 158,757 and 159,190 bp in length, respectively, and possessed conserved quadripartite circular structures. Both contained 134 annotated genes, including 8 rRNA, 37 tRNA and 89 protein-coding genes. Twenty divergences (Pi > 0.03) were found in the intergenic regions. Nine protein-coding genes, accD, atpA, atpE, atpF, clpP, ndhF, psbH, rbcL, and rpoC2, underwent selection within Cucurbitaceae. Phylogenetic relationship analysis indicated that these two species originated from the same ancestor. Finally, four pairs of molecular markers were developed to distinguish the two species. The results of this study will be beneficial for taxonomic research, identification and conservation of Siraitia Merrill wild resources in the future.

Species Identification of Dracaena Using the Complete Chloroplast Genome as a Super-Barcode

The taxonomy and nomenclature of Dracaena plants are much disputed, particularly for several Dracaena species in Asia. However, neither morphological features nor common DNA regions are ideal for identification of Dracaena spp. Meanwhile, although multiple Dracaena spp. are sources of the rare traditional medicine dragon's blood, the Pharmacopoeia of the People's Republic of China has defined Dracaena cochinchinensis as the only source plant. The inaccurate identification of Dracaena spp. will inevitably affect the clinical efficacy of dragon's blood. It is therefore important to find a better method to distinguish these species. Here, we report the complete chloroplast (CP) genomes of six Dracaena spp., D. cochinchinensis, D. cambodiana, D. angustifolia, D. terniflora, D. hokouensis, and D. elliptica, obtained through high-throughput Illumina sequencing. These CP genomes exhibited typical circular tetramerous structure, and their sizes ranged from 155,055 (D. elliptica) to 155,449 bp (D. cochinchinensis). The GC content of each CP genome was 37.5%. Furthermore, each CP genome contained 130 genes, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. There were no potential coding or non-coding regions to distinguish these six species, but the maximum likelihood tree of the six Dracaena spp. and other related species revealed that the whole CP genome can be used as a super-barcode to identify these Dracaena spp. This study provides not only invaluable data for species identification and safe medical application of Dracaena but also an important reference and foundation for species identification and phylogeny of Liliaceae plants.

Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae

Artemisia L. is a complex genus of medicinal importance. Publicly available chloroplast genomes of few Artemisia species are insufficient to resolve taxonomic discrepancies at species level. We report chloroplast genome sequences of two further Artemisia species: A. maritima (151,061 bp) and A. absinthium (151,193 bp). Both genomes possess typical quadripartite structure comprising of a large single copy, a small single copy and a pair of long inverted repeats. The two genomes exhibited high similarities in genome sizes, gene synteny, GC content, synonymous and non-synonymous substitutions, codon usage, amino acids frequencies, RNA editing sites, microsatellites, and oligonucleotide repeats. Transition to transversion ratio was <1. Maximum likelihood tree showed Artemisia a monophyletic genus, sister to genus Chrysanthemum. We also identified 20 highly polymorphic regions including rpoC2-rps2, trnR-UCU-trnG-UCC, rps18-rpl20, and trnL-UAG-rpl32 that could be used to develop authentic and cost-effective markers to resolve taxonomic discrepancies and infer phylogenetic relationships among Artemisia species.

Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales

BACKGROUND

Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species.

RESULTS

We reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049 bp to 160,769 bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211-332 simple sequence repeats (SSRs) in six categories and 7-27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales.

CONCLUSIONS

The study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.

The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

Background

Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history.

Methods

Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data.

Results

Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia.

Discussions

This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

The Complete Chloroplast Genomes of Echinacanthus Species (Acanthaceae): Phylogenetic Relationships, Adaptive Evolution, and Screening of Molecular Markers

Among the four species of Echinacanthus (Acanthaceae), one distributed in the West Himalayan region and three restricted to the Sino-Vietnamese karst region. Because of its ecological significance, molecular markers are necessary for proper assessment of its genetic diversity and phylogenetic relationships. Herein, the complete chloroplast genomes of four Echinacanthus species were determined for the first time. The results indicated that all the chloroplast genomes were mapped as a circular structure and each genomes included 113 unique genes, of which 80 were protein-coding, 29 were tRNAs, and 4 were rRNAs. However, the four cp genomes ranged from 151,333 to 152,672 bp in length. Comparison of the four cp genomes showed that the divergence level was greater between geographic groups. We also analyzed IR expansion or contraction in the four cp genomes and the fifth type of the large single copy/inverted repeat region in Lamiales was suggested. Furthermore, based on the analyses of comparison and nucleotide variability, six most divergent sequences (rrn16, ycf1, ndhA, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, and psaA-ycf3) were identified. A total of 37-45 simple sequence repeats were discovered in the four species and 22 SSRs were identified as candidate effective molecular markers for detecting interspecies polymorphisms. These SSRs and hotspot regions could be used as potential molecular markers for future study. Phylogenetic analysis based on Bayesian and parsimony methods did not support the monophyly of Echinacanthus. The phylogenetic relationships among the four species were clearly resolved and the results supported the recognition of the Sino-Vietnamese Echinacanthus species as a new genus. Based on the protein sequence evolution analysis, 12 genes (rpl14, rpl16, rps4, rps15, rps18, rps19, psbK, psbN, ndhC, ndhJ, rpoB, and infA) were detected under positive selection in branch of Sino-Vietnamese Echinacanthus species. These genes will lead to understanding the adaptation of Echinacanthus species to karst environment. The study will help to resolve the phylogenetic relationship and understand the adaptive evolution of Echinacanthus. It will also provide genomic resources and potential markers suitable for future species identification and speciation studies of the genus.

Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae)

Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum. We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD, or within petB). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum. The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.

Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.

Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species

Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of Q. aquifolioides with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four Quercus cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the Q. aquifolioides repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the atpF gene of Q. aquifolioides compared to two deciduous oak species, and that there had been significant purifying selection on the atpF gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined Q. aquifolioides as belonging to sect. Heterobalanus and being closely related to Q. rubra and Q. aliena. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus Quercus.

Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences

Byrsonima is the third largest genus (about 200 species) in the Malpighiaceae family, and one of the most common in Brazilian savannas. However, there is no molecular phylogeny available for the genus and taxonomic uncertainties at the generic and family level still remain. Herein, we sequenced the complete chloroplast genome of B. coccolobifolia and B. crassifolia, the first ones described for Malpighiaceae, and performed comparative analyses with sequences previously published for other families in the order Malpighiales. The chloroplast genomes assembled had a similar structure, gene content and organization, even when compared with species from other families. Chloroplast genomes ranged between 160,212 bp in B. crassifolia and 160,329 bp in B. coccolobifolia, both containing 115 genes (four ribosomal RNA genes, 28 tRNA genes and 83 protein-coding genes). We also identified sequences with high divergence that might be informative for phylogenetic inferences in the Malpighiales order, Malpighiaceae family and within the genus Byrsonima. The phylogenetic reconstruction of Malpighiales with these regions highlighted their utility for phylogenetic studies. The comparative analyses among species in Malpighiales provided insights into the chloroplast genome evolution in this order, including the presence/absence of three genes (infA, rpl32 and rps16) and two pseudogenes (ycf1 and rps19).

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58-62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae)

Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae). The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp) region, and a small single-copy (SSC; 17,811 bp) region interspersed between inverted repeat (IRa/b; 25,717 bp) regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8%) and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%), and 54 simple sequence repeats (SSRs) with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species.