Characterisation of the complete chloroplast genome of Solanum tuberosum cv. White Lady.

Potato (Solanum tuberosum) is considered worldwide as one of the most important non-cereal food crops. As a result of its adaptability and worldwide production area, potato displays a vast phenotypical variability as well as genomic diversity. Chloroplast genomes have long been a core issue in plant molecular evolution and phylogenetic studies, and have an important role in revealing photosynthetic mechanisms, metabolic regulations and the adaptive evolution of plants. We sequenced the complete chloroplast genome of the Hungarian cultivar White Lady, which is 155 549 base pairs (bp) in length and is characterised by the typical quadripartite structure composed of a large- and small single-copy region (85 991 bp and 18 374 bp, respectively) interspersed by two identical inverted repeats (25 592 bp). The genome consists of 127 genes of which 82 are protein-coding, eight are ribosomal RNAs and 37 are transfer RNAs. The overall gene content and distribution of the genes on the White Lady chloroplast was the same as found in other potato chloroplasts. The alignment of S. tuberosum chloroplast genome sequences resulted in a highly resolved tree, with 10 out of the 13 nodes recovered having bootstrap values over 90%. By comparing the White Lady chloroplast genome with available S. tuberosum sequences we found that gene content and synteny are highly conserved. The new chloroplast sequence can support further studies of genetic diversity, resource conservation, evolution and applied agricultural research. The new sequence can support further potato genetic diversity and evolutionary studies, resource conservation, and also applied agricultural research.

Intergrative Taxonomic Study of the Frullania parvistipula Complex with a Modern Circumscription of the Section Trachycolea (Frullaniaceae, Marchantiphyta).

Frullania (subg. Trachycolea) sect. Trachycolea has been studied using integrative taxonomy methods and utilizing sampling from almost all areas of distribution of the species previously referred to this section. A phylogenetic analysis based on nuclear ribosomal ITS1-2 and chloroplast trnL-F sequence data and a morphological study reveal a wide range of morphological variability within specimens that has largely disguised the overall taxonomic diversity. Frullania parvistipula, previously regarded as a widespread species, has been found to represent a group of separate species within different sections of F. subg. Trachycolea: F. caucasica and F. conistipula in F. sect. Trachycolea, F. parvistipula in F. sect. Australes, and F. fukuzawana in F. sect. Integristipulae II. Illustrations of the type specimens of F. conistipula, F. fukuzawana, and F. parvistipula, as well as illustrations of the sequenced specimens belonging to two of the discussed species (F. conistipula and F. parvistipula), are provided. The morphological differences separating the highly similar F. caucasica, F. conistipula, F. fukuzawana, F. koponenii, and F. parvistipula are discussed. A dichotomous key is presented for accepted species. New combinations are provided for two taxa.

Organellar Genomes of Sargassum hemiphyllum var. chinense Provide Insight into the Characteristics of Phaeophyceae.

Sargassum hemiphyllum var. chinense, a prevalent seaweed along the Chinese coast, has economic and ecological significance. However, systematic positions within Sargassum and among the three orders of Phaeophyceae, Fucales, Ectocarpales, and Laminariales are in debate. Here, we reported the organellar genomes of S. hemiphyllum var. chinense (34,686-bp mitogenome with 65 genes and 124,323 bp plastome with 173 genes) and the investigation of comparative genomics and systematics of 37 mitogenomes and 22 plastomes of Fucales (including S. hemiphyllum var. chinense), Ectocarpales, and Laminariales in Phaeophyceae. Whole genome collinearity analysis showed gene number, type, and arrangement were consistent in organellar genomes of Sargassum with 360 SNP loci identified as S. hemiphyllum var. chinense and two genes (rps7 and cox2) identified as intrageneric classifications of Sargassum. Comparative genomics of the three orders of Phaeophyceae exhibited the same content and different types (petL was only found in plastomes of the order Fucales and Ectocarpales) and arrangements (most plastomes were rearranged, but trnA and trnD in the mitogenome represented different orders) in genes. We quantified the frequency of RNA-editing (canonical C-to-U) in both organellar genomes; the proportion of edited sites corresponded to 0.02% of the plastome and 0.23% of the mitogenome (in reference to the total genome) of S. hemiphyllum var. chinense. The repetition ratio of Fucales was relatively low, with scattered and tandem repeats (nine tandem repeats of 14-24 bp) dominating, while most protein-coding genes underwent negative selection (Ka/Ks < 1). Collectively, these findings provide valuable insights to guide future species identification and evolutionary status of three important Phaeophyceae order species.

Phylogenetic positions of Thai members of Gymnema, Gymnemopsis and Sarcolobus (Apocynaceae, Asclepiadoideae, Marsdenieae), and two new Sarcolobus species uncovered by morpho-molecular evidence.

The present study assesses the phylogenetic position of certain Thai members of Gymnema, Gymnemopsis, and Sarcolobus in relation to other known Marsdenieae species. Fifteen accessions newly sequenced from Thailand were added to the dataset of the homologous sequences of 125 accessions of Marsdenieae downloaded from GenBank. In our molecular phylogeny, almost all the delimited major clades and their relationships are largely congruent with those revealed in previous studies. The monophyly of Gymnema (including the former Jasminanthes species) and that of Sarcolobus, as presently circumscribed, are confirmed. The new accessions of these two genera from Thailand are well grouped with the members of their respective genera. Our analyses provide the first molecular evidence for recognition of Gymnemopsis, a small Asian genus that has never been included in the previous phylogenetic studies, as a distinct genus. All elements of Gymnemopsis are retrieved as a well-supported monophyletic group that is strongly supported as sister to Lygisma, another small Asian genus that most closely resembles it in growth habit, color of latex, indumentum on plant parts, corona structure and follicle traits. Combined molecular phylogenetic, morphological and ecological data also support recognition of two new Sarcolobus species from Thailand, Sarcolobus busbanianus sp. nov. and S. flavus sp. nov. Similarities and differences between these new species and their close relative, S. carinatus, are discussed. In addition, this study also reveals the first record for Thailand of Gymnema lacei. Keys to the species of Gymnemopsis (for all members of the genus), Gymnema and Sarcolobus (for Thai members of these genera) are provided.

Molecular phylogenetic reconstruction improves the taxonomic understanding of Indian Dipcadi (Asparagaceae) and reveals a new species from the bank of Hiranyakeshi River, Maharashtra, India.

Dipcadi (Scilloideae: Asparagaceae) is a genus of bulbous monocots with approximately 40 species, of which 13 occur in India. Species delimitation within the genus has been troublesome hindering a comprehensive phylogenetic analysis. The most recent phylogeny of the subfamily Ornithogaloideae included six species of Dipcadi only from Africa. Here, we reconstructed the phylogeny of Ornithogaloideae including 23 accessions comprising 13 recognized taxa (11 species and two varieties) of Indian Dipcadi. The phylogenetic analyses were based on nucleotide sequences of three plastid regions (rbcL, matK and trnL-F spacer) and one nuclear region (ITS). Pseudogaltonia clavata exhibited sister relationship to Dipcadi. Our combined nuclear + plastid dataset analyses revealed a monophyletic Dipcadi with five clades, Clade I-V. Clade I, II and III included mainly Indian species whereas Clade V included mostly African species. Clade IV comprised D. serotinum. Clade I included nine taxa including our newly described species, D. mukaianum. The new species was phylogenetically placed with D. erythraeum, D. saxorum and D. ursulae. Morphologically, the species resembled D. montanum and D. ursulae but differed in characters such as tepal cohesion, number of ovules per locule and foul-smelling flowers. Clade II and III included 11 and six taxa, respectively. D. erythraeum which has a native range from Egypt to western India was found in Clades I and V. The widespread Dipcadi species, viz. D. erythraeum and D. serotinum showed polyphyly however, the monophyly of Dipcadi is established. Our studies suggest that additional molecular markers (plastid as well as nuclear) should be tested for their taxonomy utility. Further work on the historical biogeography of Dipcadi on the subfamily Ornithogaloideae with more genetic data will yield insights how aridification of the landscape would have shaped the evolution of the geographical clades.

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance.

BACKGROUND: Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. RESULTS: We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. CONCLUSION: We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.

Phylogeographic Structure and Population Dynamics of Baoxing Osmanthus (Osmanthus serrulatus), an Endemic Species from the Southwest Sichuan Basin, China.

The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (FST = 0.812, p < 0.05) and a notable phylogeographic structure (NST = 0.698 > GST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region.

Extraction and analysis of high-quality chloroplast DNA with reduced nuclear DNA for medicinal plants.

BACKGROUND: Obtaining high-quality chloroplast genome sequences requires chloroplast DNA (cpDNA) samples that meet the sequencing requirements. The quality of extracted cpDNA directly impacts the efficiency and accuracy of sequencing analysis. Currently, there are no reported methods for extracting cpDNA from Erigeron breviscapus. Therefore, we developed a suitable method for extracting cpDNA from E. breviscapus and further verified its applicability to other medicinal plants. RESULTS: We conducted a comparative analysis of chloroplast isolation and cpDNA extraction using modified high-salt low-pH method, the high-salt method, and the NaOH low-salt method, respectively. Subsequently, the number of cpDNA copies relative to the nuclear DNA (nDNA ) was quantified via qPCR. As anticipated, chloroplasts isolated from E. breviscapus using the modified high-salt low-pH method exhibited intact structures with minimal cell debris. Moreover, the concentration, purity, and quality of E. breviscapus cpDNA extracted through this method surpassed those obtained from the other two methods. Furthermore, qPCR analysis confirmed that the modified high-salt low-pH method effectively minimized nDNA contamination in the extracted cpDNA. We then applied the developed modified high-salt low-pH method to other medicinal plant species, including Mentha haplocalyx, Taraxacum mongolicum, and Portulaca oleracea. The resultant effect on chloroplast isolation and cpDNA extraction further validated the generalizability and efficacy of this method across different plant species. CONCLUSIONS: The modified high-salt low-pH method represents a reliable approach for obtaining high-quality cpDNA from E. breviscapus. Its universal applicability establishes a solid foundation for chloroplast genome sequencing and analysis of this species. Moreover, it serves as a benchmark for developing similar methods to extract chloroplast genomes from other medicinal plants.

The complete chloroplast genome sequence of Psittacanthus schiedeanus (Cham. & Schltdl.) G.Don. (Santalales: Loranthaceae), the first plastome of a mistletoe species in the Psittacantheae tribe.

Psittacanthus schiedeanus (Cham. & Schltdl.) G.Don., 1834, is a mistletoe species in the Loranthaceae, characteristic of the canopy in cloud forest edges and widely distributed in northern Mesoamerica. Here, we report the complete chloroplast genome sequence of P. schiedeanus, the first for a species in the Psittacantheae tribe. The circularized quadripartite structure of the P. schiedeanus chloroplast genome was 122,586 bp in length and included a large single-copy region of 72,507 bp and two inverted repeats of 21,283 bp separated by a small single-copy region of 7,513 bp. The genome contained 112 genes, of which 96 are unique, including 65 protein-coding genes, 27 transfer RNA, and four ribosomal RNA. The overall GC content in the plastome of P. schiedeanus is 36.9%. Based on 43 published complete chloroplast genome sequences for species in the families Loranthaceae and Santalaceae (Santalales), the maximum-likelihood phylogenetic tree with high-support bootstrap values indicated that P. schiedeanus in the Psittacantheae tribe is sister to the tribe Lorantheae. The chloroplast genome provided in this study represents a valuable resource for genetic, phylogenetic and conservation studies of Psittacanthus species, and an important advance for unraveling the evolutionary history of these hemiparasitic plants.

A taxonomic revision of the genus Angelica (Apiaceae) in Taiwan with a new species A. aliensis.

BACKGROUND: Angelica L. sensu lato is a taxonomically complex genus, and many studies have utilized morphological and molecular features to resolve its classification issues. In Taiwan, there are six taxa within Angelica, and their taxonomic treatments have been a subject of controversy. In this study, we conducted a comprehensive analysis incorporating morphological and molecular (cpDNA and nrDNA) characteristics to revise the taxonomic treatments of Angelica in Taiwan. RESULTS: As a result of our research, we have revised the classification between A. dahurica var. formosana and A. pubescens and merged two varieties of A. morrisonicola into a single taxon. A new taxon, A. aliensis, has been identified and found to share a close relationship with A. tarokoensis. Based on the morphological and molecular characteristics data, it has been determined that the former three taxa should be grouped into the Eurasian Angelica clade, while the remaining four taxa should belong to the littoral Angelica clade. Furthermore, Angelica species in Taiwan distributed at higher altitudes displayed higher genetic diversity, implying that the central mountain range of Taiwan serves as a significant reservoir of plant biodiversity. Genetic drift, such as bottlenecks, has been identified as a potential factor leading to the fixation or reduction of genetic diversity of populations in most Angelica species. We provide key to taxa, synopsis, phenology, and distribution for each taxon of Taiwan. CONCLUSIONS: Our comprehensive analysis of morphological and molecular features has shed light on the taxonomic complexities within Angelica in Taiwan, resolving taxonomic issues and providing valuable insights into the phylogenetic relationships of Angelica in Taiwan.

A novel in-situ-process technique constructs whole circular cpDNA library.

BACKGROUND: The chloroplast genome (cp genome) is directly related to the study and analysis of molecular phylogeny and evolution of plants in the phylogenomics era. The cp genome, whereas, is highly plastic and exists as a heterogeneous mixture of sizes and physical conformations. It is advantageous to purify/enrich the circular chloroplast DNA (cpDNA) to reduce sequence complexity in cp genome research. Large-insert, ordered DNA libraries are more practical for genomics research than conventional, unordered ones. From this, a technique of constructing the ordered BAC library with the goal-insert cpDNA fragment is developed in this paper. RESULTS: This novel in-situ-process technique will efficiently extract circular cpDNA from crops and construct a high-quality cpDNA library. The protocol combines the in-situ chloroplast lysis for the high-purity circular cpDNA with the in-situ substitute/ligation for the high-quality cpDNA library. Individually, a series of original buffers/solutions and optimized procedures for chloroplast lysis in-situ is different than bacterial lysis in-situ; the in-situ substitute/ligation that reacts on the MCE membrane is suitable for constructing the goal-insert, ordered cpDNA library while preventing the large-insert cpDNA fragment breakage. The goal-insert, ordered cpDNA library is arrayed on the microtiter plate by three colonies with the definite cpDNA fragment that are homologous-corresponds to the whole circular cpDNA of the chloroplast. CONCLUSION: The novel in-situ-process technique amply furtherance of research in genome-wide functional analysis and characterization of chloroplasts, such as genome sequencing, bioinformatics analysis, cloning, physical mapping, molecular phylogeny and evolution.

Dispersal capacities of pollen, seeds and spores: insights from comparative analyses of spatial genetic structures in bryophytes and spermatophytes.

Introduction: The dramatic fluctuations of climate conditions since the late Tertiary era have resulted in major species range shifts. These movements were conditioned by geographic barriers and species dispersal capacities. In land plants, gene flow occurs through the movement of male gametes (sperm cells, pollen grains), which carry nDNA, and diaspores (spores, seeds), which carry both cpDNA and nDNA, making them an ideal model to compare the imprints of past climate change on the spatial genetic structures of different genomic compartments. Based on a meta-analysis of cpDNA and nDNA sequence data in western Europe, we test the hypotheses that nDNA genetic structures are similar in bryophytes and spermatophytes due to the similar size of spores and pollen grains, whereas genetic structures derived from the analysis of cpDNA are significantly stronger in spermatophytes than in bryophytes due to the substantially larger size of seeds as compared to spores. Methods: Sequence data at 1-4 loci were retrieved for 11 bryophyte and 17 spermatophyte species across their entire European range. Genetic structures between and within southern and northern populations were analyzed through F and N statistics and Mantel tests. Results and discussion: Gst and Nst between southern and northern Europe derived from cpDNA were significantly higher, and the proportion of significant tests was higher in spermatophytes than in bryophytes. This suggests that in the latter, migrations across mountain ranges were sufficient to maintain a homogenous allelic structure across Europe, evidencing the minor role played by mountain ranges in bryophyte migrations. With nDNA, patterns of genetic structure did not significantly differ between bryophytes and spermatophytes, in line with the hypothesis that spores and pollen grains exhibit similar dispersal capacities due to their size similarity. Stronger levels of genetic differentiation between southern and northern Europe, and within southern Europe, in spermatophytes than in bryophytes, caused by higher long-distance dispersal capacities of spores as compared to seeds, may account for the strikingly higher levels of endemism in spermatophytes than in bryophytes in the Mediterranean biodiversity hotspot.

Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection.

To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03785-8.

Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae.

Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.

Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations.

BACKGROUND: Climate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles. METHODS: In this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera. RESULTS: The genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding. CONCLUSION: Our study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.

Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments.

Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Genetic structure and genetic differentiation were explored using haplotype distribution maps and genetic distance matrices. A total of 15 haplotypes were identified in the 32 populations of P. polyphylla var. yunnanensis. Five unique haplotypes were identified from the fourteen haplotypes of the cultivated populations, while only one unique haplotype was identified from the ten haplotypes of the wild populations. The haplotype richness and genetic diversity of the cultivated populations were higher than those of the wild populations (HT = 0.900 vs. 0.861). In addition, there were no statistically significant correlations between geographic distance and genetic distance in the cultivated populations (r = 0.16, p > 0.05), whereas there was a significant correlation between geographical distance and genetic structure in the wild populations (r = 0.32, p > 0.05), indicating that there was a geographical and genetic connection between the wild populations. There was only 2.5% genetic variation between the wild populations and cultivated populations, indicating no obvious genetic differentiation between the wild and cultivated populations. Overall, the genetic background of the cultivated populations was complex, and it was hypothesized that the unique haplotypes and higher diversity of the cultivated populations were caused by the mixed provenance of the cultivated populations.

No wonder, it is a hybrid. Natural hybridization between Jacobaea vulgaris and J. erucifolia revealed by molecular marker systems and its potential ecological impact.

Progressive changes in the environment are related to modifications of the habitat. Introducing exotic species, and interbreeding between species can lead to processes that in the case of rare species or small populations threatens their integrity. Given the declining trends of many populations due to increased hybridization, early recognition of hybrids becomes important in conservation management. Natural hybridization is prevalent in Jacobaea. There are many naturally occurring interspecific hybrids in this genus, including those between Jacobaea vulgaris and its relatives. Although Jacobaea erucifolia and J. vulgaris often co-occur and are considered closely related, apart from the few reports of German botanists on the existence of such hybrids, there is no information on research confirming hybridization between them. Morphologically intermediate individuals, found in the sympatric distributions of J. vulgaris and J. erucifolia, were hypothesized to be their hybrids. Two molecular marker systems (nuclear and chloroplast DNA markers) were employed to test this hypothesis and characterize putative hybrids. Nuclear and chloroplast DNA sequencing results and taxon-specific amplified fragment length polymorphism (AFLP) fragment distribution analysis confirmed the hybrid nature of all 25 putative hybrids. The AFLP patterns of most hybrids demonstrated a closer relationship to J. erucifolia, suggesting frequent backcrossing. Moreover, they showed that several individuals previously described as pure were probably also of hybrid origin, backcrosses to J. erucifolia and J. vulgaris. This study provides the first molecular confirmation that natural hybrids between J. vulgaris and J. erucifolia occur in Poland. Hybridization appeared to be bidirectional but asymmetrical with J. vulgaris as the usual maternal parent.

The complete chloroplast genome sequence and phylogenetic analysis of Heritiera fomes Buch.-Ham. (Malvales: Sterculiaceae).

Heritiera fomes Buch.-Ham. (1800) is a species of mangrove in the family Malvaceae, widely distributed in the Indo-Pacific and listed as 'endangered' (EN) on the International Union for Conservation of Nature's (IUCN) red list. We reported the complete chloroplast genome sequence of H. fomes. The genome was 168,521 bp in length and included two inverted repeats (IRs) of 34,496 bp, separated by a large single-copy (LSC) region of 88,604 bp and a small single-copy (SSC) region of 10,925 bp, respectively. The genome contained 87 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The maximum-likelihood (ML) phylogenetic tree suggested that H. fomes is closely related to Heritiera angustata and Heritiera parvifolia with relatively high support bootstrap values of 86% and 100% with other species (Heritiera littoralis and Heritiera javanica), suggesting a relatively close genetic relationship between the five Heritiera plants. The chloroplast genome sequence provided a useful resource for conservation genetics studies of H. fomes and for phylogenetic studies of Heritiera.

Chimeric deletion mutation of rpoC2 underlies the leaf-patterning of Clivia miniata var. variegata.

KEY MESSAGE: The deletion mutated rpoC2 leads to yellow stripes of Clivia miniata var. variegata by down regulating the transcription of 28 chloroplast genes and disturbing chloroplast biogenesis and thylakoid membrane development. Clivia miniata var. variegata (Cmvv) is a common mutant of Clivia miniata but its genetic basis is unclear. Here, we found that a 425 bp deletion mutation of chloroplast rpoC2 underlies the yellow stripes (YSs) of Cmvv. Both RNA polymerase PEP and NEP coexist in seed-plant chloroplasts and the ß″ subunit of PEP is encoded by rpoC2. The rpoC2 mutation changed the discontinuous cleft domain required to form the PEP central cleft for DNA binding from 1103 to 59 aa. RNA-Seq revealed that 28 chloroplast genes (cpDEGs) were all down-regulated in YSs, of which, four involved in chloroplast protein translation and 21 of photosynthesis system (PS)I, PSII, cytochrome b6/f complex and ATP synthase are crucial for chloroplast biogenesis/development. The accuracy and reliability of RNA-Seq was verified by qRT-PCR. Moreover, the chlorophyll (Chl) a/b content, ratio of Chla/Chlb and photosynthetic rate (Pn) of YS decreased significantly. Meanwhile, chloroplasts of the YS mesophyll cells were smaller, irregular in shape, contain almost no thylakoid membrane, and even proplastid was found in YS. These findings indicate that the rpoC2 mutation down-regulated expression of the 28 cpDEGs, which disturb chloroplast biogenesis and its thylakoid membrane development. Thus, there are not enough PSI and II components to bind Chl, so that the corresponding areas of the leaf are yellow and show a low Pn. In this study, the molecular mechanism of three phenotypes of F1 (Cmvv ♀ × C. miniata ♂) was revealed, which lays a foundation for the breeding of variegated plants.

The molecular phylogenetic position of Harpagocarpus (Polygonaceae) sheds new light on the infrageneric classification of Fagopyrum.

In the context of the molecular phylogeny of Polygonaceae, the phylogenetic positions of most genera and their relationships have been resolved. However, the monotypic genus Harpagocarpus has never been included in any published molecular phylogenetic studies. In the present study, we adopt a two-step approach to confirm the phylogenetic placement of Harpagocarpus using two datasets: (1) a concatenated dataset of three chloroplast DNA (cpDNA) regions (matK, rbcL and trnL-F) for Polygonaceae and (2) a combined cpDNA dataset of five sequences (accD, matK, psbA-trnH, rbcL and trnL-F) for Fagopyrum. Our analyses confirm the previous hypothesis based on morphological, anatomical and palynological investigations that Harpagocarpus is congeneric with Fagopyrum and further reveal that H.snowdenii (≡ F.snowdenii) is sister to the woody buckwheat F.tibeticum. Within Fagopyrum, three highly supported clades were discovered and the first sectional classification was proposed to accommodate them: sect. Fagopyrum comprises the two domesticated common buckwheat (F.esculentum and F.tataricum) and their wild relatives (F.esculentumsubsp.ancestrale, F.homotropicum and F.dibotrys) which are characterised by having large corymbose inflorescences and achenes greatly exceeding the perianth; sect. Tibeticum, including F.snowdenii and F.tibeticum, is characterised by the achene having appurtenances along the ribs, greatly exceeding the perianth and the perianth accrescent in fruit; sect. Urophyllum contains all other species of which the achenes were completely enclosed in the perianth. This study is very helpful to understand the phylogeny of the Fagopyrum and sheds light on the future study of taxonomy, biogeography, diversification and character evolution of the genus.