Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of Ormosia Species

Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis

Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.

Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales

As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae)

Southwestern China, adjacent to the Qinghai-Tibetan Plateau (QTP), is known as a hotspot for plant diversity and endemism, and it is the origin and diversification center of Persicarieae. As one of the major lineages in Polygonaceae, Persicarieae represents a diverse adaptation to various habitats. As a result of morphological plasticity and poorly resolving molecular markers, phylogenetic relationships and infrageneric classification within Persicarieae have long been controversial. In addition, neither plastome phylogenomic studies nor divergence time estimates on a larger sample of Persicarieae species have been made thus far. We sequenced and assembled 74 complete plastomes, including all of the recognized genera within Persicarieae and their relatives. We conducted a comprehensive phylogenetic study of the major clades within Persicarieae and, based on the thus obtained robust phylogeny, also estimated divergence time and the evolution of diagnostic morphological traits. Major relationships found in previous phylogenetic studies were confirmed, including those of the backbone of the tree, which had been a major problem in previous phylogenies of the tribe. Phylogenetic analysis revealed strong support for Koenigia as sister to Bistorta, and together they were sister to the robustly supported Persicaria. Based on the phylogenetic and morphological evidence, we recognize five sections in Persicaria: Persicaria, Amphibia, Tovara, Echinocaulon, and Cephalophilon. It is estimated that the divergence of the Persicarieae began around the late Paleocene, with diversification concentrated in the Eocene and Miocene. In addition, it is suggested that the increasing westerly and monsoon winds in conjunction with the uplift of the QTP may be the driving force for origin and diversification of Persicarieae species. These results provide a valuable evolutionary framework for the study of adaptation in Polygonaceae and insights into plant diversification on the QTP and adjacent areas.

Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.

Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology

Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.

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.

Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources

Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.

Plastid Phylogenomic Data Offers Novel Insights Into the Taxonomic Status of the Trichosanthes kirilowii Complex (Cucurbitaceae) in South Korea

Trichosanthes is a genus in Cucurbitaceae comprising 90-100 species. Trichosanthes species are valuable as herbaceous medicinal ingredients. The fruits, seeds, and roots of species such as T. kirilowii and T. rosthornii are used in Korean traditional herbal medicines. T. rosthornii is only found in China, whereas in South Korea two varieties, T. kirilowii var. kirilowii and T. kirilowii var. japonica, are distributed. T. kirilowii var. kirilowii and T. kirilowii var. japonica have different fruit and leaf shapes but are recognized as belonging to the same species. Furthermore, although its members have herbal medicine applications, genomic information of the genus is still limited. The broad goals of this study were (i) to evaluate the taxonomy of Trichosanthes using plastid phylogenomic data and (ii) provide molecular markers specific for T. kirilowii var. kirilowii and T. kirilowii var. japonica, as these have differences in their pharmacological effectiveness and thus should not be confused and adulterated. Comparison of five Trichosanthes plastid genomes revealed locally divergent regions, mainly within intergenic spacer regions (trnT-UGU-trnL-UAA: marker name Tri, rrn4.5-rrn5: TRr, trnE-UUC-trnT-GGU: TRtt). Using these three markers as DNA-barcodes for important herbal medicine species in Trichosanthes, the identity of Trichosanthes material in commercial medicinal products in South Korea could be successfully determined. Phylogenetic analysis of the five Trichosanthes species revealed that the species are clustered within tribe Sicyoeae. T. kirilowii var. kirilowii and T. rosthornii formed a clade with T. kirilowii var. japonica as their sister group. As T. kirilowii in its current circumscription is paraphyletic and as the two varieties can be readily distinguished morphologically (e.g., in leaf shape), T. kirilowii var. japonica should be treated (again) as an independent species, T. japonica.

Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.

Chloroplast genome variation and phylogenetic relationships of Atractylodes species

Background

Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.

Results

The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT^(GGU), and trnT^(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus.

Conclusions

Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07394-8.

Comparative Chloroplast Genomics of Sophora Species: Evolution and Phylogenetic Relationships in the Early-Diverging Legume Subfamily Papilionoideae (Fabaceae)

The taxonomy and evolutionary history of Sophora L., a genus with high economic and medicinal value, remain uncertain due to the absence of genetic resource (especially in China) and low polymorphism of molecular markers. Our aim was to elucidate the molecular evolution and phylogenetic relationships in chloroplast genomes of Sophora species in the early-diverging legume subfamily Papilionoideae (Fabaceae). We reported nine Sophora chloroplast genome from China using Illumina sequencing. We performed a series of analyses with previously published genomes of Sophora species to investigate their genomic characteristics, identified simple sequence repeats, large repeat sequences, tandem repeats, and highly polymorphic loci. The genomes were 152,953-158,087 bp in length, and contained 111-113 unique genes, including 76-78 protein coding, 31 tRNA, and 4 rRNA. The expansion of inverted repeat boundary of Sophora resulted in rps12 entering into the LSC region and loss of trnT-CGU gene in some species. Also, we found an approximately 23 kb inversion between trnC-GCA and trnF-GAA within the genus. In addition, we identified seven highly polymorphic loci (pi (π) > 0.035) suitable for inferring the phylogeny of Sophora species. Among these, three regions also co-occurred with large repeat sequences and support use of repeats as a proxy for the identification of polymorphic loci. Based on whole chloroplast genome and protein-coding sequences data-set, a well-supported phylogenetic tree of Sophora and related taxa showed that this genus is monophyletic, but sect. Disamaea and sect. Sophora, are incongruent with traditional taxonomic classifications based on fruit morphology. Our finding provides significant genetic resources to support further investigation into the phylogenetic relationship and evolution of the genus Sophora.

Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae)

The genera Arnebia and Lithospermum (Lithospermeae-Boraginaceae) comprise 25-30 and 50-60 species, respectively. Some of them are economically valuable, as their roots frequently contain a purple-red dye used in the cosmetic industry. Furthermore, dried roots of Arnebia euchroma, A. guttata, and Lithospermum erythrorhizon, which have been designated Lithospermi Radix, are used as traditional Korean herbal medicine. This study is the first report on the floral micromorphology and complete chloroplast (cp) genome sequences of A. guttata (including A. tibetana), A. euchroma, and L. erythrorhizon. We reveal great diversity in floral epidermal cell patterns, gynoecium, and structure of trichomes. The cp genomes were 149,361-150,465 bp in length, with conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 tRNA genes, and four rRNA genes. Gene order, content, and orientation were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the four cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (atpH-atpI, petN-psbM, rbcL-psaI, ycf4-cemA, ndhF-rpl32, and ndhC-trnV-UAC). To facilitate species identification, we developed molecular markers psaA- ycf3 (PSY), trnI-CAU- ycf2 (TCY), and ndhC-trnV-UAC (NCTV) based on divergence hotspots. High-resolution phylogenetic analysis revealed clear clustering and a close relationship of Arnebia to its Lithospermum sister group, which was supported by strong bootstrap values and posterior probabilities. Overall, gynoecium characteristics and genetic distance of cp genomes suggest that A. tibetana, might be recognized as an independent species rather than a synonym of A. guttata. The present morphological and cp genomic results provide useful information for future studies, such as taxonomic, phylogenetic, and evolutionary analysis of Boraginaceae.

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.