Comprehensive Analysis of the Complete Mitochondrial Genome of Rehmannia chingii: An Autotrophic Species in the Orobanchaceae Family.

Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.

Atmospheric particulate matter retention capacity of bark and leaves of urban tree species.

Urban vegetation can effectively filter and adsorb particulate matter (PM). However, limited studies have been conducted on the PM retention capacity of tree barks. This study investigated the ability of five common urban tree species in the Yangtze River Delta region to retain PM through their barks and leaves by conducting a 14-day tree PM retention experiment on the five tree species during autumn and winter. The results showed that (1) the PM retention per unit area of bark was 6.9 times and 11.8 times higher than that of leaves during autumn and winter, respectively; (2) when considering total surface area, bark and leaves exhibited comparable PM retention capacities at the whole-plant scale; (3) the ability of bark to retain PM is species-specific, which can be attributed to different bark morphology among different tree species; and (4) bark and leaves exhibited distinct preferences for retaining PM of different particle sizes, even when exposed to similar environmental conditions. This study highlights the remarkable ability of tree bark to PM removal and provides valuable insights into the role of urban trees in mitigating PM pollution. Furthermore, these findings can provide valuable insights into studies on dry deposition modelling, urban planning, and green space management strategies.

Chlorinated paraffins in multimedia during residential interior finishing: Occurrences, behavior, and health risk.

Though with bioaccumulation and toxicity, chlorinated paraffins (CPs) are still high produced and widely utilized in various daily necessities for extender plasticization and flame retardation. CPs can be released during the reprocessing processes of finishing materials and distributed in multi-environmental media. Herein, concentrations and compositions of CPs in four representative media including interior finishing materials, PM10, total suspended particulate (TSP), and dust samples collected from eight interior finishing stages were studied. Unexpectedly, CP concentrations in ceramic tiles was found to be high with a mean value of 7.02 × 103 µg g-1, which could be attributed to the presence of CPs in the protective wax coated on ceramic tiles surfaces. Furthermore, the pollution characteristics of short-chain and medium-chain CPs (SCCPs and MCCPs) in those samples were inconsistent. According to the investigation regarding Kdust-TSP and [Formula: see text] , the occurrence and distribution of CPs in indoor atmospheric particles (PM10 and TSP) and dust were highly affected by reprocessing processes (cutting, hot melting, etc.) compared to that in the finishing materials. Moreover, dermal contact was the primary pathway of CP exposure for the occupational population (interior construction workers) for most interior finishing stages, and the interior finishing process is the prime CP exposure period for the occupational groups. As suggested by our assessment, though hardly posing an immediate health risk, CPs exposure still presents unneglected adverse health effects, which calls for adequate personal protections during interior finishing, especially in developing countries.

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.

Phylogenomics and phylogeography of Menispermum (Menispermaceae).

Introduction: Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. Menispermum L. (Menispermaceae) consists of three species, M. dauricum DC., M. canadense L., and M. mexicanum Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether M. mexicanum is a distinct species, a variety of M. dauricum, or simply a synonym of M. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses. Methods: In this study, we examined phylogenomics and phylogeography of Menispermum across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of Menispermum and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family. Results and discussion: Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that Menispermum clusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense + M. mexicanum). However, M. mexicanum is nested within M. canadense and, as a result, we support that M. mexicanum is a synonym of M. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK, ycf1), four introns (trnK intron, rpl16 intron, rps16 intron, ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA, ndhF-rpl32, trnK-rps16, and trnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.

Effects of green infrastructure on the dispersion of PM2.5 and human exposure on urban roads.

Urban green infrastructure (GI) has been widely demonstrated to effectively improve air quality in the built environment. However, due to the lack of comparative studies of the effects of different GI forms on PM2.5 dispersion, optimal GI designs suitable for different urban road types currently remain unclear. In this study, we adopted different roadside GI types in Hangzhou city as case studies and used the ENVI-met model to compare the effects of the different GI forms on PM2.5 dispersion and human exposure to PM2.5. The results indicated that 1) In open roads, the concave-shaped GI type could effectively reduce PM2.5 aggregation and human exposure on motorways, and the all-tree GI type performed the best in terms of sidewalk PM2.5 purification. 2) In street canyons, green roof and green screen were highly conducive to PM2.5 concentration reduction under commuter exposure compared with traditional green solutions. 3) There were trade-offs in the GI-PM2.5 interaction. GI types which can reduce pedestrian exposure tend to increase exposure in motorways. The same GI type deployed along the two different road types could yield completely opposite dispersion effects. Novel GI types had better environmental performance and relatively high economic cost. All decision-making should be based on the trade-offs between the advantages and disadvantages of GI. Our study also highlights the importance of comprehensive consideration of GI and road types and local wind conditions in future urban road planning and GI applications.

Plastome evolution and phylogenomics of Impatiens (Balsaminaceae).

MAIN CONCLUSION: This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538 bp to 152,917 bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.

Influence of exposure history on the particle retention capacity and physiological responses of Euonymus japonicus Thunb. var. aurea-marginatus Hort.

Green plants in urban environments experience cyclical particulate matter stress. And this history of exhaust exposure may generate stress memory in plants, which may alter their subsequent response. Studies combining urban pollution characteristics and stress memory are limited. Therefore, we selected E. japonicus var. aurea-marginatus, a common urban greening tree species in the Yangtze River Delta, and conducted an experiment in three periods: the initial pollution period (S1: 28 days), the recovery period (R: 14 days) and the secondary pollution period (S2: 28 days). The experimental design consisted of an elevated pollution treatment (173 µg•cm-3) and an ambient control (34 µg•cm-3) with three replicates. In S2, the net total particle retention and saturated particle retention decreased by 11.5% and 19.3%, respectively, while PM10 and PM2.5 did not change significantly. E. japonicus var. aurea-marginatus exhibited recovery of chlorophyll levels, slower degradation of carotenoid, faster accumulation of ASA, lower accumulation of MDA, reduced activity of SOD under the second pollution period, and the period had a significant effect on the physiological indicators. Collectively, the effect of autoexhaust exposure history on the particle retention capacity of selected plant varied across particle sizes, and stress memory may confer plant resistance to recurrent exhaust pollution via combined regulations of physiological responses. Fine particles which pose a great risk to human health arise predominantly from vehicular traffic and energy production. So, E. japonicus tends to play a stabilising role in particle retention in industrial, traffic and residential areas.

The neglected potential source of microplastics from daily necessities: A study on protective mobile phone cases.

Microplastics (MPs) pollution has become a serious global environment problem. It is therefore of practical significance to investigate the MP pollution caused by using plastic materials on a daily basis. In this study, different protective mobile phone cases (PMPCs) were selected as a representative plastic commodity that are in contact with the human body for long periods to explore the generation and transportation of MPs during 3 months of actual use. The average abundances were 1122 particles cm-2 on the PMPC and 314 particles cm-2 on the palm, respectively. There were four main kinds of MPs produced during the use of different PMPCs, which indicated that waste plastics may be recycled and used as raw materials, resulting in a complex PMPC composition. The median sizes of MPs on the surfaces of PMPCs and palms were 28 and 32 µm, respectively, which were smaller than the sizes reported in other studies. The combined effect of ultraviolet ageing and friction was the main reason for MP generation during daily PMPC use. Based on the results of a fitted regression equation and Monte Carlo simulation, the sharply generation of MPs may occur when PMPC was used for approximately 33 days.

The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications.

Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (Trebouxiophyceae sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30-35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and Trebouxiophyceae sp. DW1 is sister to the clade of Koliella longiseta and Pabia signiensis.

New insights into the phylogeny of the complex thalloid liverworts (Marchantiopsida) based on chloroplast genomes.

Marchantiopsida (complex thalloid liverworts) are one of the earliest lineages of embryophytes (land plants), and well-known for their air pores and chambers, pegged rhizoids, and absence of organellular RNA editing sites. Despite their importance to an understanding of early embryophyte evolution, many key nodes within this class remain poorly resolved, owing to the paucity of genetic loci previously available for phylogenetic analyses. Here, we sequenced 54 plastomes, representing 28 genera, nearly all families, and all orders of Marchantiopsida. Based on these plastomes, we present a hypothesis of deep relationships within the class, and make the first investigations of gene contents and synteny. Overall, the Marchantiopsida plastomes were well-conserved, with the exception of the genus Cyathodium that has plastomes with higher GC content, fewer single sequence repeats (SSRs), and more structural variations, implying that this genus might possess RNA editing sites. Abundant repetitive elements and six highly divergent regions were identified as suitable for future infrafamilial taxonomic studies. The phylogenetic topology of Sphaerocarpales, Neohodgsoniales and Blasiales within Marchantiopsida was essentially congruent with previous studies but generally we obtained higher support values. Based on molecular evidence and previous morphological studies, we include Lunulariales in Marchantiales and suggest the retention of narrowed delimitation of monotypic families. The phylogenetic relationships within Marchantiales were better resolved, and 13 monophyletic families were recovered. Our analyses confirmed that the loss of intron 2 of ycf3 is a synapomorphy of Marchantiidae. Finally, we propose a new genus, Asterellopsis (Aytoniaceae), and present an updated classification of Marchantiopsida. The highly supported phylogenetic backbone provided here establishes a framework for future comparative and evolutionary studies of the complex thalloid liverworts.

Effects of periodic drought with severe exhaust exposure on particle retention capacity and physiological responses of Photinia × fraseri Dress.

Urban plants are regarded as an effective agent to control particulate matter (PM) pollution by absorbing PM. Repeated PM and drought stress in urban areas often cause morphological and physiological damage to plants, resulting in lower ecological benefits. Nevertheless, knowledge in PM retention capability, morphology and physiology of plants under repeated stress and cross stress has been barely available. In order to investigate changes in these aspects under repeated stress, we applied periodic drought with severe exhaust exposure on Photinia × fraseri Dress (a common urban tree species with strong PM retention ability). The study was carried out in a six-period scenario, with a duration of 10 days for each period: initial value (R0), initial stress period (S1), initial recovery period (R1) second stress period (S2), second recovery period (R2) and final stress period (S3). The results are as follows: In terms of periodic factor, PM retention of tail gas stress group (P) and cross stress group (PD) in S2 decreased by 10.00 µg/cm2 and 12.60 µg/cm2 respectively compared with those during S1 (p > 0.05). During S3, the total amount of PM on leaf surface in both P and PD demonstrated a significant decrease (p < 0.05). The retention capacity of P. fraseri may be dramatically limited under multi-period stress. In this experiment, we attribute the decrease of PM retention to the morphological changes (shedding of mature leaves, smaller leaf area and thinner wax layer) and physiological responses (an increase in gas exchange) under multi-period stress. In terms of cross-stress factor, the total retained PM on leaf surface in PD was higher than that in P, especially during S3, and the interaction between drought and PM reached a significant level (p < 0.01, η2 = 0.808), which indicated that drought reduced the loss of dust under PM stress. Changes in morphology and gas exchange indicated that the mechanisms for the high dust retention rate on the leaf surface of PD group varied in the three stress periods. In addition, except the chlorophyll relative value, the alleviated accumulation of MDA and intense production of soluble sugar with PD showed favorable responses to disturbance compared with those in P under the repeated stress. Therefore, we infer that, under multi-period stress of drought and tail gas, P. fraseri may better maintain PM retention ability and resistance than under single stress.

Smilax weniae, a New Species of Smilacaceae from Limestone Areas Bordering Guizhou and Guangxi, China.

A new species, Smilax weniae (Smilacaceae), from Southwest China, is described and illustrated. The new species bears peltate leaves, which was previously a unique feature of S. luei. However, it differs from the latter by having a broad ovate leaf blade, longer peduncle, and sexual dimorphic flowers. Further phylogenetic analyses revealed that the new species were placed in a unique position in a subclade of Old World Smilax based on ptDNA and nrITS sequences. Combining detailed morphological comparisons and molecular evidence, we validated that S. weniae is an undescribed new species. Moreover, the plastome characteristics of S. weniae are reported.

Three-dimensional building morphology impacts on PM2.5 distribution in urban landscape settings in Zhejiang, China.

Three-dimensional (3D) urban landscape patterns and building morphology are crucial for urban planning and essential for urban landscape functions. In this study, fixed and mobile monitoring sites were used to determine the spatial distribution of PM2.5 concentrations in Hangzhou. Six 3D metrics were selected to analyze the response of PM2.5 pollution to landscape patterns and building morphology, while their two-dimensional (2D) counterparts' metrics were also analyzed to contrast the differences. A variance partitioning analysis (VPA) was performed to measure the combined and relative contribution of 3D and 2D metrics to the changes in PM2.5 concentrations. The results showed that: (1) on the 3D scale, forming a building pattern with a combination of different building heights can eliminate the accumulation of PM2.5; (2) on the 2D scale, fragmentation and decentralization of landscapes and building patches alleviate PM2.5 pollution; and (3) 3D building morphology indicators have the highest explanatory power (40.94%) for the changes of PM2.5 concentrations. It turns out that the explanatory power of 3D metrics for PM2.5 concentrations changes is much greater than that of 2D metrics. In addition, when compared to building morphology indicators from a single dimension, the combination of 2D and 3D metrics is better able to reflect urban PM2.5 pollution. The results of this study expand our understanding of how PM2.5 pollution responds to 2D and 3D metrics and provide useful information for urban planning.

Elsholtziazhongyangii (Lamiaceae), a new species from Sichuan, China.

Elsholtziazhongyangii (Lamiaceae), a new species from Sichuan Province, China, is described and illustrated. The new species is morphologically similar to E.feddeif.feddei, but it can be easily distinguished from E.feddeif.feddei by smaller corolla (3.2-3.5 mm vs. 4.5-5.3 mm), bract indumentum (glabrous, except margin ciliate vs. villous, especially on veins abaxially, glabrous adaxially) and bract stalked (ca. 1.2 mm vs. sessile). Phylogenetic analyses, based on two nuclear ribosomal (ETS, ITS) and five plastid (rbcL, matK, trnL-F, ycf1, ycf1-rps15) regions, confirmed that the new species formed a monophyletic clade with robust support. The new species is currently known from western Sichuan.

The complete plastome of Andreaea rupestris Hedw. (Andreaeaceae, Bryophyta).

Andreaea rupestris Hedw., one of the lantern mosses, is the lectotype of the genus Andreaea Hedw. (Andreaeaceae). Here we present its complete plastome. The plastome of A. rupestris is successfully assembled from raw reads sequenced by HiSeq X ten system. Its total length is 135,214 bp consisting of four regions: large single copy (LSC) region (92,780 bp), small single copy (SSC) region (21,102 bp), and two inverted repeat regions (IRs; 10,666 bp per each). It contains 134 genes (88 coding genes, 8 rRNAs, and 38 tRNAs). The overall GC content is 30.3% and in the LSC, SSC, and IR regions are 27.5%, 26.5%, and 46.2%, respectively. The present data will be an important sequence resource for further studies on the important early diverging lineage of mosses.

The complete plastome of Polytrichum commune Hedw. (Polytrichaceae, Bryophyta).

Polytrichum commune, one of hair-cap mosses, is the type species of the genus Polytrichum Hedw. (Polytrichaceae). Here we present its complete plastome. The plastome of P. commune is successfully assembled from raw reads sequenced by HiSeq X ten system. Its total length is 126,323 bp consisting of four regions: large single copy (LSC) region (88,070 bp), small single copy (SSC) region (16,717 bp), and inverted repeats (IRs; 9,680 bp per each). It contains 128 genes (84 coding genes, eight rRNAs, and 36 tRNAs); nine genes (four rRNAs and five tRNAs) are duplicated in IR regions. The overall GC content is 28.9% and in the LSC, SSC and IR regions is 26.1%, 25.1%, and 45.5%, respectively. This plastome is an important sequence resource for further studies on the class Polytrichopsida.

Design, synthesis and in vitro evaluation of amidoximes as histone deacetylase inhibitors for cancer therapy.

Amindoximes are geometric isomers of N-hydroxyamidines which are bioisosteres of hydroxamates. Since amindoxime group is capable of chelating transition metal ions including zinc ion, amindoximes should possess histone deacetylases (HDACs) inhibitory activity. In this work, we designed and synthesized a series of amindoximes, examined their inhibitory activities against HDACs, and investigated their cytotoxicity to human cancer cells. Preliminary results demonstrated that amindoximes possessed submicromolar HDACs inhibitory activity, with noteworthy enhancement compared with hydroxamates. Furthermore, the amindoximes arrested HCT116 and A549 cells in G2/M phase and showed good efficacy in inducing cells death. We provided a proof-of-concept that amindoximes could be used as HDACs inhibitors and hold great promise as epigenetic drugs.

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing.

Phylogenetic relationships among Chinese species of Morella (Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic relationships among Morella rubra, M. adenophora, M. nana and M. esculenta. Three methods for inferring phylogeny, maximum parsimony (MP), maximum likelihood (ML) and Bayesian concordance, were applied to data sets including as many as 4253 RAD loci with 8360 parsimony informative variable sites. All three methods significantly favored the topology of (((M. rubra, M. adenophora), M. nana), M. esculenta). Two species from North America (M. cerifera and M. pensylvanica) were placed as sister to the four Chinese species. According to BEAST analysis, we deduced speciation of M. rubra to be at about the Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence in M. rubra occurred in the late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and 23552 de novo contigs with an average length of 229, 234 and 234 bp for M. rubra, M. nana and M. esculenta respectively. The contigs were used to investigate functional classification of RAD tags in a BLASTX search. Additionally, we identified 3808 unlinked SNP sites across the four populations of M. rubra and discovered genes associated with fruit ripening and senescence, fruit quality and disease/defense metabolism based on KEGG database.

Understanding the formation of Mediterranean-African-Asian disjunctions: evidence for Miocene climate-driven vicariance and recent long-distance dispersal in the Tertiary relict Smilax aspera (Smilacaceae).

Tethyan plant disjunctions, including Mediterranean-African-Asian disjunctions, are thought to be vicariant, but their temporal origin and underlying causes remain largely unknown. To address this issue, we reconstructed the evolutionary history of Smilax aspera, a hypothesized component of the European Tertiary laurel forest flora. Thirty-eight populations and herbarium specimens representing 57 locations across the species range were sequenced at seven plastid regions and the nuclear ribosomal internal transcribed spacer region. Time-calibrated phylogenetic and phylogeographic inferences were used to trace ancestral areas and biogeographical events. The deep intraspecific split between Mediterranean and African-Asian lineages is attributable to range fragmentation of a southern Tethyan ancestor, as colder and more arid climates developed shortly after the mid-Miocene. In the Mediterranean, climate-induced vicariance has shaped regional population structure since the Late Miocene/Early Pliocene. At around the same time, East African and South Asian lineages split by vicariance, with one shared haplotype reflecting long-distance dispersal. Our results support the idea that geographic range formation and divergence of Tertiary relict species are more or less gradual (mostly vicariant) processes over long time spans, rather than point events in history. They also highlight the importance of the Mediterranean Basin as a centre of intraspecific divergence for Tertiary relict plants.