Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

BACKGROUND

Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced.

RESULTS

The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported.

CONCLUSIONS

The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

Phylogeny and Flow Cytometry of the Genus Kalidium Moq. (Amaranthaceae s.l.) in Kazakhstan

The article presents data on phylogeny, genome size, and ploidy of species of the genus Kalidium Moq. in the flora of Kazakhstan. Genus Kalidium belongs to the tribe Salicornieae of the subfamily Salicornioideae of the family Chenopodiaceae and unites eight species, the main range of which covers the Iranian-Turanian and Central Asian deserts. There are four species in the flora of Kazakhstan: K. foliatum, K. caspicum, K. schrenkianum, and the recently described K. juniperinum. Populations of species of the genus Kalidium in the saline deserts of Kazakhstan occupy large areas, often forming monodominant communities. Sometimes there is a joint growth of two and very rarely three species of the genus. During the period of fieldwork (2021-2022), populations were identified in which these species grew together with a predominance, in most cases, of K. caspicum. Samples of representatives from 15 populations were collected for research. Selected plant samples were studied by flow cytometry to determine plant ploidy. Sequencing of nrITS and two chloroplast fragments were used to build a phylogenetic tree, including sequences from the NCBI database., A phylogenetic tree of species of the genus Kalidium was compiled, which takes previously published data into consideration. In the valley of the middle reaches of the Syrdarya River, tetraploid populations of K. caspicum were found. A hybrid between K. foliatum and K. caspicum was found in the Ili River valley (Almaty region, Uigur district). To identify phylogenetic processes at the intraspecific level, the SCoT (Start codon targeted) fingerprinting method was used.

Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients

Identifying plant, fungal, and animal ingredients in a specific mixture remains challenging during the limitation of PCR amplification and low specificity of traditional methods. Genomic DNA was extracted from mock and pharmaceutical samples. Four type of DNA barcodes were generated from shotgun sequencing dataset with the help of a local bioinformatic pipeline. Taxa of each barcode was assigned by blast to TCM-BOL, BOLD, and GenBank. Traditional methods including microscopy, thin layer chromatography (TLC), and high-performance liquid chromatography (HPLC) were carried out according to Chinese pharmacopoeia. On average, 6.8 Gb shotgun reads were sequenced from genomic DNA of each sample. Then, 97, 11, 10, 14, and one operational taxonomic unit (OTU) were generated for ITS2, psbA-trnH, rbcL, matK, and COI, respectively. All the labeled ingredients including eight plant, one fungal, and one animal species were successfully detected in both the mock and pharmaceutical samples, in which Chebulae Fructus, Poria, and Fritilariae Thunbergia Bulbus were identified via mapping reads to organelle genomes. In addition, four unlabeled plant species were detected from pharmaceutical samples, while 30 genera of fungi, such as Schwanniomyces, Diaporthe, Fusarium were detected from mock and pharmaceutical samples. Furthermore, the microscopic, TLC, and HPLC analysis were all in accordance with the standards stipulated by Chinese Pharmacopoeia. This study indicated that shotgun metabarcoding could simultaneously identified plant, fungal, and animal ingredients in herbal products, which has the ability to serve as a valuable complement to traditional methods.

Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution

Diospyros (Ebenaceae) is a widely distributed genus of trees and shrubs from pantropical to temperate regions, with numerous species valued for their fruits (persimmons), timber, and medicinal values. However, information regarding their plastomes and chloroplast evolution is scarce. The present study performed comparative genomic and evolutionary analyses on plastomes of 45 accepted Diospyros species, including three newly sequenced ones. Our study showed a highly conserved genomic structure across the Diospyros species, with 135-136 encoding genes, including 89 protein-coding genes, 1-2 pseudogenes (Ψycf1 for all, Ψrps19 for a few), 37 tRNA genes and 8 rRNA genes. Comparative analysis of Diospyros identified three intergenic regions (ccsA-ndhD, rps16-psbK and petA-psbJ) and five genes (rpl33, rpl22, petL, psaC and rps15) as the mutational hotspots in these species. Phylogenomic analysis identified the phylogenetic position of three newly sequenced ones and well supported a monophylogenetic (sub)temperate taxa and four clades in the pantropical taxa. The analysis codon usage identified 30 codons with relative synonymous codon usage (RSCU) values >1 and 29 codons ending with A and U bases. A total of three codons (UUA, GCU, and AGA) with highest RSCU values were identified as the optimal codons. Effective number of codons (ENC)-plot indicated the significant role of mutational pressure in shaping codon usage, while most protein-coding genes in Diospyros experienced relaxed purifying selection (d N/d S < 1). Additionally, the psbH gene showed positive selection (d N/d S > 1) in the (sub)temperate species. Thus, the results provide a meaningful foundation for further elaborating Diospyros's genetic architecture and taxonomy, enriching genetic diversity and conserving genetic resources.

Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos

Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.

Genome-Wide Association Study of Phenolic Content and Antioxidant Properties in Eggplant Germplasm

The phenolic compounds in eggplant offer potential natural antioxidants for improved health. A large number of samples were examined in order to find eggplant germplasm with a high potential for health promotion. A genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNPs) associated with variations in total phenolic content (TPC) and antioxidant activity in eggplants, including ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) scavenging activity and ferric reducing antioxidant power (FRAP). TPC values varied from 14.19 to 842.90 mg gallic acid equivalent (GAE)/100 g of dry weight of eggplant fruit powder. TPC showed a strong positive correlation with both FRAP and ABTS (r = 0.89 *** and 0.77 ***, respectively). The GWAS identified 20 SNPs that were significantly associated out of 29,183 SNPs. Out of the 20 significant SNPs, 11 showed associations with TPC, 4 with ABTS activity, and 5 with FRAP. Among the SNPs associated with TPC, one SNP was found on each of Chromosomes 3, 4, 7, and 12. In contrast, Chromosome 5 comprised two SNPs associated to TPC. Furthermore, the gene encoding IRX12 laccase-4 on Chromosome 10 was found to contain five SNPs associated with TPC. Four significantly linked SNPs on Chromosomes 1 (1 SNP), 4 (2 SNPs), and 10 (1 SNP) were found to be related to ABTS activity. The identified SNPs will be further examined as markers for selecting desirable eggplant varieties and exploring the links between candidate genes, phenolic content, and antioxidant activity. The findings of this study could assist in further study and the development of eggplants with improved health advantages through targeted breeding.

The complete chloroplast genome sequence of Chrysojasminum subhumile and its phylogenetic position within Oleaceae

We assembled and characterized the complete chloroplast genome sequence of Chrysojasminum subhumile (W.W.Sm.) Banfi & Galasso 2014, a valuable horticultural and medicinal plant species. The total genome size was 159,918 bp in length and the GC content was 37.4%. It displayed a circular structure and could be divided into a large single-copy region, a small single-copy region, and a pair of inverted repeat regions. The genome encoded a total of 131 unique genes, including 82 protein-coding genes, 41 tRNA genes, and eight rRNA genes. Among these genes, 17 contained a single intron, and two genes had two introns. Phylogenetic analysis results showed that C. subhumile was closely related to Jasminum.

Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference

Dioscorea sect. Stenophora (Dioscoreaceae) comprises about 30 species that are distributed in the temperate and subtropical regions of the Northern Hemisphere. Despite being evolutionarily "primitive" and medically valuable, genomic resources and molecular studies of this section are still scarce. Here, we conducted low-coverage whole genome sequencing of 11 Stenophora species/subspecies to retrieve their plastome information (whole plastome characteristics, plastome-divergent hotspots, plastome-derived SSRs, etc.) and polymorphic nuclear SSRs, as well as performed comparative plastome and phylogenetic analyses within this section. The plastomes of Stenophora species/subspecies ranged from 153,691 bp (D. zingiberensis) to 154,149 bp (D. biformifolia) in length, and they all contained the same 114 unique genes. All these plastomes were highly conserved in gene structure, gene order and GC content, although variations at the IR/SC borders contributed to the whole length differences among them. The number of plastome-derived SSRs among Stenophora species/subspecies varied from 74 (D. futschauensis) to 93 (D. zingiberensis), with A/T found to be the most frequent one. Seven highly variable regions and 12 polymorphic nuclear SSRs were identified in this section, thereby providing important information for further taxonomical, phylogenetic and population genetic studies. Phylogenomic analyses based on whole plastome sequences and 80 common protein coding genes strongly supported D. biformifolia and D. banzhuana constituted the successive sister species to the remaining sampled species, which could be furtherly divided into three clades. Overall, this study provided a new perspective for plastome evolution of Stenophora, and proved the role of plastome phylogenomic in improving the phylogenetic resolution in this section. These results also provided an important reference for the protection and utilization of this economically important section.

A complete chloroplast genome of a traditional Chinese medicine herb, Rubia podantha, and phylogenomics of Rubiaceae

Rubia podantha Diels is endemic to southwestern China and belongs to the family Rubiaceae. It is used in traditional Chinese medicines. To enrich the genetic data and resolve Rubiaceae's phylogeny, we assembled a complete chloroplast (cp) genome of R. podantha using Illumina HiSeq reads. The whole length of the cp genome was 154,866 bp. Annotation using PGA software found 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy region was 84,717 bp, the inverted repeat B (IRa) region was 26,516 bp, the small single copy was 17,117 bp, and the inverted repeats B (IRb) region was 26,516 bp. Moreover, 64 SSRs were identified. Phylogenomic analysis using cp genomes of 109 Rubiaceae species found that R. podantha is closely related to R. cordifola. Rubiaceae was separated into three subfamilies: Ixoroideae, Cinchonoideae, and Rubiodeae. The genus Saprosma was not imbedded within the Spermacoceae alliance as reported in previous studies. Instead, it was imbedded within the Psychotrieae alliance. Divergence time estimation indicated that R. podantha split from its relative R. cordifolia around 1.25 million years ago. The assembled chloroplast genome in this study provided useful molecular information about the evolution of R. podantha and was a basis for phylogenetic analyses of Rubiaceae.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01302-y.

Phylogenetic relationships and biogeography of Asia Callicarpa (Lamiaceae), with consideration of a long-distance dispersal across the Pacific Ocean -insights into divergence modes of pantropical flora

There are about 140 species of Callicarpa L. 1753 (Lamiaceae), with more species richness in tropical to subtropical Asia and the New World. The genus might provide an insight into the amphi-Pacific disjunction pattern of tropical and subtropical vegetation. This study has greatly improved the phylogenetic underpinning for Callicarpa, derived from more inclusive taxonomic samplings, and employing data on both two-nuclear and eight-chloroplast regions. To address time and patterns of diversification in Callicarpa, we conducted divergence time and biogeographic analyses, and inferred shifts in the distribution areas across the phylogenetic clades. Our phylogenetic results show that Callicarpa is monophyletic with respect to the groups considered, and eight well-supported primary clades were discerned in the combined analyses. Our estimates indicated that the crown group of Callicarpa originates around the Late-Eocene (ca. 36.23 Ma) and diversification within most clades is concentrated in the Miocene and continued to the Pleistocene. In addition, our biogeographic analyses suggested that the probable ancestor of the Callicarpa crown clade originated in East Asia and Southeast Asia. Multiple dispersal and vicariance events contributed to the current distribution of the taxa. Furthermore, this genus expanded eastward out of East and Southeast Asia to the New World by long-distance dispersal, which inspired us to better understand the amphi-Pacific disjunct distribution.

Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China

Introduction

Begonia L., one of the 10 largest plant genera, contains over 2,100 species, most of which have a very limited distribution range. Understanding the spatial genetic structure and distribution dynamics of a widespread species in this genus will contribute to clarifying the mechanism responsible for Begonia speciation.

Methods

In this study, we used three chloroplast DNA markers (ndhF-rpl32, atpI-atpH, and ndhA intron), coupled with species distribution modeling (SDM), to investigate the population genetic structure and distribution dynamics of Begonia grandis Dryand., the species of Begonia with the widest distribution in China.

Results

Thirty-five haplotypes from 44 populations clustered into two groups, and haplotype divergence began in the Pleistocene (1.75 Mya). High genetic diversity (H _d = 0.894, H _T = 0.910), strong genetic differentiation (F _ST = 0.835), and significant phylogeographical structure (G _ST/N _ST = 0.848/0.917, P < 0.05) were observed. The distribution range of B. grandis migrated northwards after the last glacial maximum, but its core distribution area remained stable.

Discussion

Combined, the observed spatial genetic patterns and SDM results identified the Yunnan-Guizhou Plateau, the Three Gorges region, and the Daba Mountains as potential refugia of B. grandis. BEAST-derived chronogram and haplotype network analysis do not support the Flora Reipublicae Popularis Sinicae and Flora of China for subspecies classification based on morphological characteristics. Our results support the hypothesis that population-level allopatric differentiation may be an important speciation process for the Begonia genus and a key contributor to its rich diversity.

Meeting in Liguria: hybridisation between Apennine endemic Euphorbia barrelieri and western Mediterranean E. nicaeensis led to the allopolyploid origin of E. ligustica

The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity.

The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

BACKGROUND

Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated.

RESULTS

In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya.

CONCLUSIONS

The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.

The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment

PREMISE

The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula.

METHODS

We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses.

RESULTS

The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance.

CONCLUSIONS

The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.

Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae)

The papilionoid legume genus Sophora (Fabaceae) exhibits a worldwide distribution, but a phylogenetic framework to understand the evolution of this group is lacking to date. Previous studies have demonstrated that Sophora is not monophyletic and might include Ammodendron, Ammothamnus, and Echinosophora, but the relationships among these four genera (defined as Sophora s.l.) are unclear. Here we used a nuclear DNA dataset (ETS, ITS, SQD1) and a plastid DNA dataset (matK, rbcL, rpl32-trnL, trnL-F) of 654 accession sequences to reconstruct the phylogenetic relationships, estimate the divergence times and ancestral range of Sophora s.l., and infer the evolution of chromosome number and morphological characteristics. Our major aim was to reconstruct phylogenetic relationships to test monophyly and elucidate relationships within the genus. Our results indicated that Ammodendron, Ammothamnus, and Echinosophora are embedded within Sophora s.s. and that nine well-supported clades can be recognized within comprise Sophora s.l. Ancestral character state estimation revealed that the most recent common ancestor of Sophora s.l. was a deciduous shrub that lacks rhizome spines and has unwinged legumes. Divergence times estimation and ancestral area reconstruction showed that Sophora s.l. originated in Central Asia and/or adjacent Southeast China in the early Oligocene (ca. 31 Mya) and dispersed from these regions into East and South Asia's adjacent areas and North America via the Bering land bridge. The analyses also supported a South American origin for S. sect. Edwardsia, which experienced rapid radiation with its major lineages diversifying over a relatively narrow timescale (8 Mya).

Phylogeography of Eriotheca species complex: insights into the origin and range expansion of apomictic and polyploid trees in Neotropical Savannas

Polyploidy and whole genome duplication are major evolutionary drivers in plants. Climate variations during the Pleistocene have influenced distribution and range expansion worldwide. Similar trends have been reported for Cerrado plants, but no attempt has been made to link phylogeography with ploidy and breeding changes. Thus, we aimed to (i) assess ploidy and genome size of Eriotheca estevesiae Carv.-Sobr., and compare it with E. pubescens (Mart.) Schott & Endl. (Both included into the Eriotheca Stellate Trichome Species Complex - ESTSC). (ii) Subsequently, we investigated their phylogeography to see whether genetic structure and range expansion trends were similar to those previously described for the Cerrado biome. Finally (iii), we discuss whether ESTSC phylogeographic patterns could be associated with geographic parthenogenesis processes. Common cytogenetic techniques and flow cytometry were used to confirm chromosome number and genome size of E. estevesiae. We used three cpDNA regions to analyse 14 ESTSC Cerrado populations, for which we also obtained ploidy level and breeding information. We investigated haplotype diversity, population structure and tested neutrality, aiming to reconstruct phylogeographic scenarios. We found three ploidy levels and eight cpDNA haplotypes in ESTSC, one shared by most populations. Haplotype and ploidy distribution corroborated that E. pubescens, the widely distributed polyploid and apomictic species, may have originated from northern diploid and probably sexual E. estevesiae. Matrilinear cpDNA links support the idea that apomixis and polyploidy in ESTSC may have allowed range expansion during the Pleistocene, in a process analogous to the geographic parthenogenesis described elsewhere.

Callicarpa stoloniformis (Lamiaceae), a new species from Southeast China based on morphological characters and phylogenetic evidence

Callicarpa stoloniformis sp. nov. (Lamiaceae) is described as a new species from Fujian Province of China on the basis of both morphological and molecular data. The new species is morphologically most close to C. hainanensis. However, it can be distinguished from the latter by its unique procumbent life form, adventitious roots at nodes, papery leaves, cup‐shaped or campanulate calyx, truncate or shallow fissure calyx lobes, and smaller fruits. In addition, the new species is also similar with C. basitruncata, a species only known from the original description and the photograph of holotype, but it can differ from the latter by its procumbent shrub, purple terete branchlets with apparent linear lenticels, adventitious roots at nodes, and papery larger leaves with prominently cordate leaf base. Original photographs, illustration, distribution map, and a comparative morphological table, as well as an identification key of the related taxa are provided.

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

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

Homoploid hybrids are common but evolutionary dead ends, whereas polyploidy is not linked to hybridization in a group of Pyrenean saxifrages

Hybridization and polyploidy are major forces in plant evolution. Homoploid hybridization can generate new species via hybrid speciation, or modify extant evolutionary lineages through introgression. Polyploidy enables instantaneous reproductive isolation from the parental lineage(s) and is often coupled with evolutionary innovations, especially when linked to hybridization. While allopolyploidy is a well-known and common mechanism of plant speciation, the evolutionary role of autopolyploidy might have been underestimated. Here, we studied the saxifrages of Saxifraga subsection Saxifraga in the Pyrenees, which easily hybridise and include polyploid populations of uncertain origin, as a model to unravel evolutionary consequences and origin of hybridization and polyploidy. Additionally, we investigate the phylogenetic relationship between the two subspecies of the endemic S. pubescens to ascertain whether they should rather be treated as different species. For these purposes, we combined ploidy-informed restriction associated DNA analyses, plastid DNA sequences and morphological data on a comprehensive population sample of seven species. Our results unravel multiple homoploid hybridization events at the diploid level between different species pairs, but with limited evolutionary impact. The ploidy-informed analyses reveal that all tetraploid populations detected in the present study belong to the widespread alpine species S. moschata. Although of autopolyploid origin, they are to some extent morphologically differentiated and underwent a different evolutionary pathway than their diploid parent. However, the high plastid DNA diversity and the internal structure within eastern and western population groups suggest multiple origins of the polyploids. Finally, our phylogenetic analyses show that S. pubescens and S. iratiana are clearly not sister lineages, and should consequently be considered as independent species.

New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes

The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, and a small part of continental Africa (Tanzania). Because these bamboos rarely flower, field identification is challenging, and inferring the evolutionary history of Hickeliinae from herbarium specimens is even more so. Molecular phylogenetic work is critical to understanding this group of bamboos. Here, comparative analysis of 22 newly sequenced plastid genomes showed that members of all genera of Hickeliinae share evolutionarily conserved plastome structures. We also determined that Hickeliinae plastome sequences are informative for phylogenetic reconstructions. Phylogenetic analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which is paraphyletic and forms two distant clades. The type species of Nastus (Clade II) is endemic to Reunion Island and is not closely related to other sampled species of Nastus endemic to Madagascar (Clade VI). Clade VI (Malagasy Nastus) is sister to the Sokinochloa + Hitchcockella clade (Clade V), and both clades have a clumping habit with short-necked pachymorph rhizomes. The monotypic Decaryochloa is remarkable in having the longest floret in Bambuseae and forms a distinct Clade IV. Clade III, which has the highest generic diversity, consists of Cathariostachys, Perrierbambus, Sirochloa, and Valiha, which are also morphologically diverse. This work provides significant resources for further genetic and phylogenomic studies of Hickeliinae, an understudied subtribe of bamboo.

From everywhere all at once: Several colonization routes available to Svalbard in the early Holocene

For many arctic species, the spatial (re-)colonization patterns after the last Pleistocene glaciation have been described. However, the temporal aspects of their colonization are largely missing. Did one route prevail early, while another was more important later? The high Arctic archipelago Svalbard represents a good model system to address timeframe of postglacial plant colonization. Svalbard was almost fully glaciated during last glacial maximum and (re-)colonization of vascular plants began in early Holocene. Early Holocene climatic optimum (HCO) supported an expanded establishment of a partly thermophilic vegetation. Today, we find remnants of this vegetation in sheltered regions referred to as "Arctic biodiversity hotspots". The oldest record of postglacial plant colonization to Svalbard is found in Ringhorndalen-Flatøyrdalen. Even though thermophilic species could establish also later in Holocene, only HCO was favorable for vast colonization, and only hotspots offered stable conditions for thermophilic populations throughout Holocene. Thus, these relic populations may reflect colonization patterns of HCO. We investigate whether the colonization direction of thermophilic plants (Arnica angustifolia, Campanula uniflora, Pinguicula alpina, Tofieldia pusilla, and Vaccinium uliginosum ssp. microphyllum) in Ringhorndalen-Flatøyrdalen was uniform and different from later colonization events in other localities and non-thermophilic plants (Arenaria humifusa, Bistorta vivipara, Juncus biglumis, Oxyria digyna, and Silene acaulis). We analyzed plastid haplotypes of the 10 taxa from Ringhorndalen-Flatøyrdalen, from later-colonized localities in Svalbard, and from putative source regions outside Svalbard. Only rare and thermophilic taxa Campanula uniflora and Vaccinium uliginosum ssp. microphyllum provided results suggesting at least two colonization events from different source regions. Tofieldia pusilla and all the non-thermophilic plants showed no clear phylogeographically differentiation within Svalbard. Two of the thermophilic species showed no sequence variation. Based on the results, a uniform colonization direction to Svalbard in early Holocene is not probable; several source areas and dispersal directions were contemporarily involved.

Living on the edge: morphological, karyological and genetic diversity studies of the Hungarian Plantago maxima populations and established ex situ collection

BACKGROUND

The analysis of genetic diversity of protected plant species can greatly support conservation efforts. Plantago maxima Juss. ex Jacq. is a perennial species distributed along the Eurasian steppe. The westernmost range edge of the species' distribution is located in the Pannonian basin, in Hungary where it is represented by a few, fragmented and highly endangered populations. We studied population diversity of all Hungarian range edge, natural populations, and one established ex situ population. One population from the centre of distribution (Kazakhstan) was implemented in the cpDNA haplotype study to compare the peripheral vs. central populations. We performed morphometric trait-based analysis, chromosome studies (morphometric analyses and FISH) and genetic diversity evaluations using inter simple sequence repeats (ISSR) and cpDNA trnL-trnF to evaluate differences between the in situ and ex situ populations as well as central vs. peripheral populations.

RESULTS

Our results showed no obvious morphological differences among the in situ and ex situ populations in the period between 2018 and 2020. One ex situ subpopulation develops flowers three years in a row from 2019, which is a favourable indicator of the introduction success. Hungarian populations are exclusively diploids (2n = 2x = 12). The karyogram consists of 5 metacentric and 1 acrocentric chromosome pair. Plantago maxima has one 35S and two 5S rDNA loci, located on the acrocentric chromosome pair. Eight variable ISSR primers yielded 100 fragments, of which 74.6% were polymorphic (mean H_e = 0.220). A high level of genetic variation within population was observed (92%) while the genetic differentiation among the populations was only 8%. STRUCTURE analysis revealed that the largest Kunpeszér population separated from the rest of the Hungarian populations, indicating a high rate of admixture among the other ones. Based on the trnL-trnF sequence analysis the Hungarian populations represent a single haplotype, which can indicate a reduced diversity due to isolation and recent population decline. By contrast, Kazakh population represents a distinct haplotype compared to the Hungarian samples.

CONCLUSIONS

The present study draws the attention to the high conservation value of the Plantago maxima populations from the westernmost range edge of the species' distribution.

Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China

Background

Bupleuri Radix (Chaihu) is a famous traditional Chinese medicine derived from Bupleurum, Apiaceae. The origin of cultivated Chaihu germplasm in China is unclear, which has led to unstable Chaihu quality. In this study, we reconstructed the phylogeny of the main Chaihu germplasm species in China and identified potential molecular markers to authenticate its origin.

Methods

Three Bupleurum species (eight individuals), B. bicaule, B. chinense, and B. scorzonerifolium, were selected for genome skimming. Published genomes from B. falcatum and B. marginatum var. stenophyllum were used for comparative analysis.

Results

Sequences of the complete plastid genomes were conserved with 113 identical genes ranging from 155,540 to 155,866 bp in length. Phylogenetic reconstruction based on complete plastid genomes resolved intrageneric relationships of the five Bupleurum species with high support. Conflicts between the plastid and nuclear phylogenies were observed, which were mainly ascribed to introgressive hybridization. Comparative analysis showed that noncoding regions of the plastomes had most of the variable sequences. Eight regions (atpF-atpH, petN-psbM, rps16-psbK, petA-psbJ, ndhC-trnV/UAC and ycf1) had high divergence values in Bupleurum species and could be promising DNA barcodes for Chaihu authentication. A total of seven polymorphic cpSSRs and 438 polymorphic nSSRs were detected across the five Chaihu germplasms. Three photosynthesis-related genes were under positive selection, of which accD reflected the adaptation fingerprint of B. chinense to different ecological habitats. Our study provides valuable genetic information for phylogenetic investigation, germplasm authentication, and molecular breeding of Chaihu species.

Why is the beautyberry so colourful? Evolution, biogeography, and diversification of fruit colours in Callicarpa (Lamiaceae)

Fruit colour is essential to seed dispersal, speciation, and biological diversity in global ecosystems. The relationship between fruit-colour variation and species diversification has long been of interest in evolutionary biology, but remains poorly understood at the genus level. Here, we used Callicarpa, a typical representative of pantropical angiosperm, to analyse whether fruit colours are correlated with biogeographic distribution, dispersal events, and diversification rate. We estimated a time-calibrated phylogeny for Callicarpa and reconstructed ancestral fruit colour. Utilizing phylogenetic methods, we estimated the major dispersal events across the phylogenetic tree and the most likely fruit colours related to each dispersal event, and tested whether the dispersal frequencies and distances of the four fruit colours between major biogeographical areas were equal. We then tested whether fruit colours are correlated with latitude, elevation, and diversification rate. Biogeographical reconstructions showed that Callicarpa originated in the East Asia and Southeast Asia during the Eocene (∼35.53 Ma) and diverse species diverged mainly in the Miocene and lasted into the Pleistocene. Large-scale dispersal events were significantly associated with violet-fruited lineages. Furthermore, different fruit colours were markedly correlated with different latitudes and elevations (e.g., violet fruits were correlated with higher latitudes and elevations; red fruits and black fruits with lower latitudes; white fruits with higher elevations). Notably, violet fruits were statistically associated with highest diversification rates, driving fruit colour variation among different regions globally. Our results contribute to further understanding why fruit colour is so variable at the genus level of angiosperms in different areas around the world.

Biogeography of Rhaponticoides, an Irano-Turanian element in the Mediterranean flora

Floristic relationships between the Irano-Turanian and Mediterranean regions have been known from old. However, only a few biogeographical analyses based on molecular data have evaluated the history of steppe plants within the Mediterranean basin. Our study aims to contribute to a better understanding of the migratory and diversification processes by reconstructing the biogeography of Rhaponticoides (Cardueae), distributed in the Mediterranean and Irano-Turanian regions. We generated nuclear and plastid sequences that were analyzed by Bayesian inference. We used the resulting phylogeny for dating the diversification of the genus and examining the dispersal pathways. Two clades were recovered, an Irano-Turanian clade and a Mediterranean clade. The origin of the genus was placed in the Anatolian plateau in the Middle Miocene. The genus experienced several diversifications and expansions correlated to the Messinian salinity crisis and the environmental changes in the Pliocene and the Quaternary. Rhaponticoides migrated following two routes reflecting the two souls of the genus: Irano-Turanian taxa colonized the steppes of Eurasia whilst Mediterranean species migrated via eastern and central Mediterranean and North Africa, leaving a trail of species; both pathways ended in the Iberian Peninsula. Our study also confirms that more work is needed to unravel phylogenetic relationships in Rhaponticoides.

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.

Allium sulaimanicum: A new Allium species and section from Pakistan

A new species, Allium sulaimanicum, is described from northern Balochistan and southern Khyber Pakhtunkhwa in Pakistan based on morphological, molecular, and cytological studies. The new species is characterised by long runner-like cylindrical rhizomes of adult plants, cylindrical bulbs, linear leaves with minute soft hairs along veins, campanulate perigonium, and white to creamy white, ovate to elliptical, 4.5-5-mm-long acute tepals, with brownish to purplish nerves, stamens as long as to slightly longer than tepals, yellow to brick red anthers, hexagonal ovary, and white and papillate/warty along angles. The presence of long herbaceous rhizomes indicated serious isolation of the new species; hence, a new section Sulaimanicum is proposed to accommodate the new species. The new species is diploid with a chromosome number of 2n = 16. Detailed morphological description, illustrations, phylogenetic analyses based on sequences of plastid spacers (rpl32-trnL (UAG) and trnQ-rps16) and nuclear ITS, karyotype features, and a distribution map of the new species are provided.

Comparative plastomes and phylogenetic analysis of seven Korean endemic Saussurea (Asteraceae)

BACKGROUND

Saussurea is one of the most species-rich genera in the Cardueae, Asteraceae. There are approximately 40 Saussurea species distributed in Korea, with nearly 40% of them endemics. Infrageneric relationships remain uncertain due to insufficient resolutions and low statistical support. In this study, we sequenced the plastid genomes of five Korean endemic Saussurea (S. albifolia, S. calcicola, S. diamantica, S. grandicapitula, and S. seoulensis), and comparative analyses including two other endemics (S. chabyoungsanica and S. polylepis) were conducted.

RESULTS

The plastomes of Korean endemics were highly conserved in gene content, order, and numbers. Exceptionally, S. diamantica had mitochondrial DNA sequences including two tRNAs in SSC region. There were no significant differences of the type and numbers of SSRs among the seven Korean endemics except in S. seoulensis. Nine mutation hotspots with high nucleotide diversity value (Pi > 0.0033) were identified, and phylogenetic analysis suggested that those Korean endemic species most likely evolved several times from diverse lineages within the genus. Moreover, molecular dating estimated that the Korean endemic species diverged since the late Miocene.

CONCLUSIONS

This study provides insight into understanding the plastome evolution and evolutionary relationships of highly complex species of Saussurea in Korean peninsula.

A new synonym of Enkianthusperulatus (Ericaceae) in East Asia, based on morphological and molecular evidence

Enkianthuscalophyllus was once treated as a synonym of E.serrulatus. However, field observations indicate that E.calophyllus is distinct from E.serrulatus but resembles E.perulatus in flowers, leaves, fruits and seeds. Hence, a taxonomic revision of these species was conducted based on morphological comparisons of flowers, leaves, fruits and seeds, as well as molecular analyses of nuclear ribosomal internal transcribed spacer (nrITS) and six plastid DNA markers (psbA-trnH, rpl32-trnL, trnL-trnF, rps16-trnQ, psbJ-petA and matK). The morphological and molecular results reject the synonymization of E.calophyllus with E.serrulatus, and instead show it to be placed in a clade with E.perulatus. Based on molecular evidence and a reassessment of the morphology we synonymize E.calophyllus with the older name E.perulatus.

Characterization of the Evolutionary Pressure on Anisodus tanguticus Maxim. with Complete Chloroplast Genome Sequence

Anisodus tanguticus Maxim. (Solanaceae), a traditional endangered Tibetan herb, is endemic to the Qinghai-Tibet Plateau. Here, we report the de novo assembled chloroplast (cp) genome sequences of A. tanguticus (155,765 bp). The cp contains a pair of inverted repeated (IRa and IRb) regions of 25,881 bp that are separated by a large single copy (LSC) region (86,516 bp) and a small single copy SSC (17,487 bp) region. A total of 132 functional genes were annotated in the cp genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Moreover, 199 simple sequence repeats (SSR) and 65 repeat structures were detected. Comparative plastome analyses revealed a conserved gene order and high similarity of protein-coding sequences. The A. tanguticus cp genome exhibits contraction and expansion, which differs from Przewalskia tangutica and other related Solanaceae species. We identified 30 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which may be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Anisodus and family Solanaceae. Analysis of the Ka/Ks ratios of the Hyoscyameae tribe revealed significant positive selection exerted on the cemA, rpoC2, and clpP genes, which suggests that protein metabolism may be an important strategy for A. tanguticus and other species in Hyoscyameae in adapting to the adverse environment on the Qinghai-Tibetan Plateau. Phylogenetic analysis revealed that A. tanguticus clustered closer with Hyoscyamus niger than P. tangutica. Our results provide reliable genetic information for future exploration of the taxonomy and phylogenetic evolution of the Hyoscyameae tribe and related species.

Genotyping-by-sequencing reveals range expansion of Adonis vernalis (Ranunculaceae) from Southeastern Europe into the zonal Euro-Siberian steppe

The Euro-Siberian steppe flora consists of warm- and cold-adapted species, which may have responded differently to Pleistocene glacials and interglacials. Genotyping-by-sequencing individuals from across the distribution range of the pheasant's eye (Adonis vernalis), we aimed to gain insight into steppe florogenesis based on the species' evolutionary history. Although the primary area of origin of the species group comprising A. vernalis, A. villosa and A. volgensis is in Asia, our results indicate that recent populations of A. vernalis are not of Asian origin but evolved in the southern part of Europe during the Pleistocene, with Spanish populations clearly genetically distinct from the Southeastern European populations. We inferred that A. vernalis migrated eastwards from the sub-Mediterranean forest-steppes of Southeastern Europe into the continental forest-steppe zone. Eastern European populations had the highest private allelic richness, indicating long-term large population sizes in this region. As a thermophilic species, A. vernalis seems unlikely to have survived in the cold deserts of the Last Glacial Maximum in Western Siberia, so this region was likely (re)colonized postglacially. Overall, our results reinforce the importance of identifying the area of origin and the corresponding ecological requirements of steppe plants in order to understand the composition of today's steppe flora.

Complete chloroplast genomes of Sorbus sensu stricto (Rosaceae): comparative analyses and phylogenetic relationships

BACKGROUND

Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections.

RESULTS

The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny.

CONCLUSION

Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.

Phylogeography of Himalrandia lichiangensis from the dry-hot valleys in Southwest China

Both changing tectonics and climate may shape the phylogeographic patterns of plant species. The dry-hot valleys in southwestern China harbor a high number of endemic plants. In this study, we investigated the evolutionary history and potential distribution of an endemic shrub Himalrandia lichiangensis (Rubiaceae), to evaluate the effects of tectonic and climatic processes on this thermophilic plant species from the dry-hot valleys. By sequencing DNA from four plastid non-coding regions (psbM-trnD, trnD-trnT, atpB-rbcL and accD-psaI) and the CAMX1F-CAMX2R region and ITS for 423 individuals from 23 populations, we investigated the genetic diversity, phylogeographical pattern and population dynamics of H. lichiangensis. We found a high degree of differentiation in H. lichiangensis during the middle Miocene (15-13 Myr), possibly triggered by the rapid tectonic uplift event in this period area. accompanied by frequent orogeneses in this period. This hypothesis is also supported by the association between genetic differentiation and altitudinal gradients among populations. The middle reach of the Jinsha River, which harbors the greatest genetic diversity, is most likely to have been a refugia for H. lichiangensis during Quaternary. We also detected a strong barrier effect between the Nanpan River and Jinsha River, suggesting the river system may play a role in geographical isolation between clades on both sides of the barrier. The Maximum Entropy Model (MaxEnt) results showed that future climate warming will lead to the niche expansion in some areas for H. lichiangensis but will also cause a scattered and fragmented distribution. Given the high among-population differentiation and no recent expansion detected in H. lichiangensis, its current phylogeographical pattern is possibly due to a long-term geographical barrier caused by uplifting mountains since the Miocene, as well as Quaternary climate refugia isolated also by high mountains. This study illustrated tectonic and climatic processes may have a continuous effect on plant phylogeography and offers insights into the origin of biodiversity and endemism in the dry-hot valleys of southwestern China.

Complete chloroplast genome sequencing and comparative analysis of threatened dragon trees Dracaena serrulata and Dracaena cinnabari

Dracaena (Asparagaceae family) tree is famous for producing "dragon blood"—a bioactive red-colored resin. Despite its long history of use in traditional medicine, little knowledge exists on the genomic architecture, phylogenetic position, or evolution. Hence, in this study, we sequenced the whole chloroplast (cp) genomes of D. serrulata and D. cinnabari and performed comparative genomics of nine genomes of the genus Dracaena. The results showed that the genome sizes range from 155,055 (D. elliptica) to 155,449 (D. cochinchinensis). The cp genomes of D. serrulata and D. cinnabari encode 131 genes, each including 85 and 84 protein-coding genes, respectively. However, the D. hokouensis had the highest number of genes (133), with 85 protein coding genes. Similarly, about 80 and 82 repeats were identified in the cp genomes of D. serrulata and D. cinnabari, respectively, while the highest repeats (103) were detected in the cp genome of D. terniflora. The number of simple sequence repeats (SSRs) was 176 and 159 in D. serrulata and D. cinnabari cp genomes, respectively. Furthermore, the comparative analysis of complete cp genomes revealed high sequence similarity. However, some sequence divergences were observed in accD, matK, rpl16, rpoC2, and ycf1 genes and some intergenic spacers. The phylogenomic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, sister to the remaining Dracaena species sampled in this study, with high bootstrap values. In conclusion, this study provides valuable genetic information for studying the evolutionary relationships and population genetics of Dracaena, which is threatened in its conservation status.

A phylogenetic analysis of Bromus (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on Bromus sect. Bromus

To investigate phylogenetic relationships among and within major lineages of Bromus, with focus on Bromus sect. Bromus, we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid (rpl32-trnL_UAG , matK) regions. We sampled 103 ingroup accessions representing 26 taxa of B. section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B. sect. Boissiera and B. sect. Nevskiella, respectively. These species are sister groups and are closely related to B. densus (B. sect. Mexibromus) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis, Ceratochloa, Neobromus, and Genea plus B. rechingeri of B. sect. Bromus form a clade, in which B. tomentellus is sister to a B. sect. Genea-B. rechingeri clade. In the plastid trees, by contrast, B. sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B. sect. Bromus and B. sect. Genea species. Affinities of B. gedrosianus, B. pulchellus, and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii, are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B. sect. Bromus and B. sect. Genea. Within B. sect. Bromus, B. alopecuros subsp. caroli-henrici, a clade comprising B. hordeaceus and B. interruptus, and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B. sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B. sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus.

Complete chloroplast genome structure of four Ulmus species and Hemiptelea davidii and comparative analysis within Ulmaceae species

In this study, the chloroplast (cp) genomes of Hemiptelea davidii, Ulmus parvifolia, Ulmus lamellosa, Ulmus castaneifolia, and Ulmus pumila ‘zhonghuajinye’ were spliced, assembled and annotated using the Illumina HiSeq PE150 sequencing platform, and then compared to the cp genomes of other Ulmus and Ulmaceae species. The results indicated that the cp genomes of the five sequenced species showed a typical tetrad structure with full lengths ranging from 159,113 to 160,388 bp. The large single copy (LSC), inverted repeat (IR), and small single copy (SSC) lengths were in the range of 87,736–88,466 bp, 26,317–26,622 bp and 18,485–19,024 bp, respectively. A total of 130–131 genes were annotated, including 85–86 protein-coding genes, 37 tRNA genes and eight rRNA genes. The GC contents of the five species were similar, ranging from 35.30 to 35.62%. Besides, the GC content was different in different region and the GC content in IR region was the highest. A total of 64-133 single sequence repeat (SSR) loci were identified among all 21 Ulmaceae species. The (A)_n and (T)_n types of mononucleotide were highest in number, and the lengths were primarily distributed in 10–12 bp, with a clear AT preference. A branch-site model and a Bayes Empirical Bayes analysis indicated that the rps15 and rbcL had the positive selection sites. Besides, the analysis of mVISTA and sliding windows got a lot of hotspots such as trnH/psbA, rps16/trnQ, trnS/trnG, trnG/trnR and rpl32/trnL, which could be utilized as potential markers for the species identification and phylogeny reconstruction within Ulmus in the further studies. Moreover, the evolutionary tree of Ulmaceae species based on common protein genes, whole cp genome sequences and common genes in IR region of the 23 Ulmaceae species were constructed using the ML method. The results showed that these Ulmaceae species were divided into two branches, one that included Ulmus, Zelkova and Hemiptelea, among which Hemiptelea was the first to differentiate and one that included Celtis, Trema, Pteroceltis, Gironniera and Aphananthe. Besides, these variations found in this study could be used for the classification, identification and phylogenetic study of Ulmus species. Our study provided important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Ulmus and Ulmaceae species.

Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species (Iris Series Chinenses, Iridaceae)

The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.

BIOMORPHOLOGY AND TAXONOMIC STATUS OF <i>ADENOCAULON ADHAERESCENS</i> MAXIM. (ASTERACEAE), AN INVASIVE SPECIES IN THE MOSCOW REGION

The results of the study of the only species, which "escaped" from the Main Botanical Garden (MBG RAS, Moscow) and invaded the anthropogenically disturbed territories of the Moscow Region, Adenocaulon adhaerescens Maxim, were summarized. The history of intentional introduction of the species and stages of formation of spontaneous invasive population were described. The characteristic of the plant communities and habitats of the species was given. Data on the population size, seed productivity in the native and the secondary ranges and on vegetative propagation of plants were given. The morphological characters at different stages of plant ontogenesis were described. A comparative analysis of morphometric characters of seeds, leaves, and inflorescences in the native and secondary ranges of the species has been performed. Molecular genetic analysis of A. adhaerescens samples from the natural and secondary ranges and closely related species of the genus Adenocaulon was performed. The analysis has confirmed the validity of A. adhaerescens recognition as a separate species. Diagnostic characters of A. adhaerescens were described. The results of management invasive population in MBG RAS were presented and recommendations on control measures of A. adhaerescens dispersal were given.

The Volatile Profiles and DNA Barcodes of Lauraceae Species from the Ocotea Complex with Occurrence in the Brazilian Amazon

The Ocotea complex accommodates most of the taxonomic diversity of Neotropical Lauraceae with economic importance and biological potential attributed to their essential oils (EOs) and extracts. However, the botanical taxonomy has had limitations due to the difficulty of identifying and delimiting species and genera. The chemical and molecular markers of Ocotea complex species in Pará state, Brazil, were assessed according to their EO compositions and DNA sequences of matK, trnL-trnF, and ITS regions. The multivariate analysis of EOs constituents has classified them into two main clusters characterized by oils rich in (I) terpenoids and phenylpropanoids and (II) sesquiterpenes. We conducted a phylogenetic analysis of species based on DNA barcode sequences on the Bayesian Inference (PP: 0.70-1,0) and Maximum Likelihood (BS: 72-100 %). The comparison between the volatile profiles and phylogenetic data indicates two main groups for these species collected from the Ocotea complex.

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 evolutionary history of two closely related desert plant, Convolvulus tragacanthoide and Convolvulus gortschakovii (Convolvulaceae) from northwest China

Desert ecosystems are one of the most fragile ecosystems on Earth. The study of the effects of paleoclimatic and geological changes on genetic diversity, genetic structure, and species differentiation of desert plants is not only helpful in understanding the strategies of adaptation of plants to arid habitats, but can also provide reference for the protection and restoration of vegetation in desert ecosystem. Northwest China is an important part of arid regions in the northern hemisphere. Convolvulus tragacanthoides and Convolvulus gortschakovii are closely related and have similar morphology. Through our field investigation, we found that the annual precipitation of the two species distribution areas is significantly different. Thus, C. tragacanthoides and C. gortschakovii provide an ideal comparative template to investigate the evolutionary processes of closely related species, which have adapted to different niches in response to changes in paleogeography and paleoclimate in northwest China. In this study, we employed phylogeographical approaches (two cpDNA spacers: rpl14-rpl36 and trnT-trnY) and species distribution models to trace the demographic history of C. tragacanthoides and C. gortschakovii, two common subshrubs and small shrubs in northwest China. The results showed the following: (1) Populations of C. tragacanthoides in northwest China were divided into three groups: Tianshan Mountains-Ili Valley, west Yin Mountains-Helan Mountains-Qinglian Mountains, and Qinling Mountains-east Yin Mountains. There was a strong correlation between the distribution of haplotypes and the floristic subkingdom. The three groups corresponded to the Eurasian forest subkingdom, Asian desert flora subkingdom, and Sino-Japanese floristic regions, respectively. Thus, environmental differences among different flora may lead to the genetic differentiation of C. tragacanthoides in China. (2) The west Yin Mountains-Helan Mountains-Qinglian Mountains, and Qinling Mountains-east Yin Mountains were thought to form the ancestral distribution range of C. tragacanthoides. (3) C. tragacanthoides and C. gortschakovii adopted different strategies to cope with the Pleistocene glacial cycle. Convolvulus tragacanthoides contracted to the south during the glacial period and expanded to the north during the interglacial period; and there was no obvious north-south expansion or contraction of C. gortschakovii during the glacial cycle. (4) The interspecific variation of C. tragacanthoides and C. gortschakovii was related to the orogeny in northwest China caused by the uplift of the Tibetan Plateau during Miocene. (5) The 200 mm precipitation line formed the dividing line between the niches occupied by C. tragacanthoides and C. gortschakovii, respectively. In this study, from the perspective of precipitation, the impact of the formation of the summer monsoon limit line on species divergence and speciation is reported, which provides a new perspective for studying the response mechanism of species to the formation of the summer monsoon line, and also provides a clue for predicting how desert plants respond to future environmental changes.

Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae

BACKGROUND

Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems.

RESULTS

In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA. We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs.

CONCLUSIONS

The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.

Boliviadendron, a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the interior Andean valleys of Bolivia

Phylogenetic analyses of DNA sequence data sampling all species of Leucochloron alongside representatives of genera of the Inga and Albizia clades of the larger ingoid clade of mimosoid legumes (sensu Koenen et al. 2020) confirm the non-monophyly of the genus Leucochloron. We show that Leucochloronbolivianum is placed in the Albizia clade, while the remaining four species of Leucochloron are placed in the Inga clade, in line with previous results. To rectify this non-monophyly, L.bolivianum is segregated as the new genus, Boliviadendron, with a single species, Boliviadendronbolivianum, narrowly endemic to the interior Andean valleys of Bolivia. We illustrate this new segregate genus, present a map of its distribution and discuss the striking lack of morphological distinctions between Boliviadendron and Leucochloron, as well as the phylogenetic and morphological affinities of Boliviadendron to the genera Enterolobium and Albizia.

Phylogeny and classification of the Australasian and Indomalayan mimosoid legumes Archidendron and Archidendropsis (Leguminosae, subfamily Caesalpinioideae, mimosoid clade)

The morphologically variable genus Archidendron is the second largest mimosoid legume genus from the Indomalayan-Australasian region, yet it has not been well represented in phylogenetic studies. Phylogenies that have included multiple representatives of Archidendron suggest it may not be monophyletic, and the same applies to Archidendropsis, another understudied genus of the Archidendron clade. The most comprehensive phylogeny of Archidendron and Archidendropsis to date is presented, based on four nuclear markers (ITS, ETS, SHMT and RBPCO). Exemplars from all genera of the wider Archidendron clade are sampled, including representatives of all series within Archidendron and the two subgenera of Archidendropsis. Our results confirm that Archidendron and Archidendropsis are not monophyletic. Within Archidendron, only one series (ser. Ptenopae) is resolved as monophyletic and species of Archidendron are divided into two primarily geographic lineages. One clade is distributed in western Malesia and mainland Asia and includes most representatives of series Clypeariae, while the other is mostly restricted to eastern Malesia and Australia and includes representatives of the seven other series plus two samples of series Clypeariae. No taxonomic changes are made for Archidendron due to the high level of topological uncertainty and the lack of discrete macromorphological characters separating these two lineages. Each of the two subgenera of Archidendropsis is monophyletic but they are not closely related. A new genus endemic to Queensland (Australia), Heliodendron Gill.K. Br. & Bayly, gen. nov., is described for the former Archidendropsissubg.Basaltica, and combinations for its three species are proposed: Heliodendronbasalticum (F. Muell.) Gill.K. Br. & Bayly, comb. nov., Heliodendronthozetianum (F. Muell.) Gill.K. Br. & Bayly, comb. nov., and Heliodendronxanthoxylon (C.T. White & W.D. Francis) Gill.K. Br. & Bayly, comb. nov.

Relationships within Mcneillia Indicate a Complex Evolutionary History and Reveal a New Species of Minuartiella (Caryophyllaceae, Alsinoideae)

The genus Mcneillia has been recently segregated from Minuartia L. based on molecular results, also supported by morphology. However, to date, a comprehensive study on the phylogenetic relationships within this genus is lacking. In this paper, we provide a multigene phylogeny of all the species and subspecies of Mcneillia employing two nuclear and six chloroplast markers. We documented extensive gene flow between taxa, sometimes separated at specific rank. In addition, Mcneillia as currently circumscribed, is not monophyletic. In fact, Mcneillia graminifolia subsp. brachypetala, strictly endemic to Greece, truly belongs to Minuartiella, a genus otherwise limited to South-West Asia. Moreover, even after removal of this taxon, our results do not support the monophyly of the taxa included in M. graminifolia s.l., the most variable and widespread species of the genus. Further controversial subspecies of Mcneillia graminifolia, i.e., subsp. hungarica and subsp. rosanoi, are shown to deserve taxonomic recognition as separate species, whereas Mc. moraldoi is not distinct at specific rank. In addition, Mc. saxifraga subsp. tmolea is here regarded as a further distinct species. A consistent taxonomic treatment is therefore proposed with six new combinations and nomenclatural notes, providing the necessary typifications.

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.