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Background Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences. Results We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata . Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL , and matK ) from 91 species, revealed that Baolia and Corispermoideae ( Agriophyllum , Anthochlamys , and Corispermum ) form a well-supported clade and sister to Acroglochin . According to our molecular dating results, a major divergence event between Acroglochin , Baolia , and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat. Conclusions Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum , Anthochlamys , and Corispermum ), as well as two new monotypic tribes, Acroglochineae ( Acroglochin ) and Baolieae ( Baolia ).

• Background and Aims Fine-scale, spatial heterogeneity in soil nutrient availability can increase the growth of individual plants, the productivity of plant communities and interspecific competition. If this is due to the ability of plants to concentrate their roots where nutrient levels are high, then nutrient heterogeneity should have little effect on intraspecific competition, especially when there are no genotypic differences between individuals in root plasticity. We tested this hypothesis in a widespread, clonal species in which individual plants are known to respond to nutrient heterogeneity. • Methods Plants derived from a single clone of Alternanthera philoxeroides were grown in the greenhouse at or high density (four or 16 plants per 27·5 × 27·5-cm container) with homogeneous or heterogeneous availability of soil nutrients, keeping total nutrient availability per container constant. After 9 weeks, measurements of size, dry mass and morphology were taken. • Key Results Plants grew more in the heterogeneous than in the homogeneous treatment, showing that heterogeneity promoted performance; they grew less in the high-than in the low-density treatment, showing that plants competed. There was no interactive effect of nutrient heterogeneity and plant density, supporting the hypothesis that heterogeneity does not affect intraspecific competition in the absence of genotypic differences in plasticity. Treatments did not affect morphological characteristics such as specific leaf area or root/shoot ratio. • Conclusions Results indicate that fine-scale, spatial heterogeneity in the availability of soil nutrients does not increase competition when plants are genetically identical, consistent with the suggestion that effects of heterogeneity on competition depend upon differences in plasticity between individuals. Heterogeneity is only likely to increase the spread of monoclonal, invasive populations such as that of A. philoxeroides in China.

Amphibious plants escape submergence by plastically accelerating shoot growth, yet the mechanism underlying this convergent strategy remains unclear. Here, we demonstrate that PHYTOCHROME A (PHYA), a light photoreceptor, acts as a central regulator of the contrasting submergence escape capacities between amphibious Alternanthera philoxeroides and its terrestrial congener A. pungens . PHYA is distinctively regulated upon submergence in two congeners and negatively regulates submergence-induced elongation. Crucially, we find a cis -regulatory element (CRE) variant in the PHYA promoter between two congeners, which governs EIN3-dependent transcriptional repression and drives species-specific PHYA expression. Expanded investigation unveils phyletic retention of this CRE in other amphibious species, providing preliminary evidence for convergent evolution in the submergence escape capacity through independent co-option of the same CREs. Our findings demonstrate a role of PHYA in mediating submergence responses, deepen the understanding of the molecular basis for plant secondary aquatic adaptation, and inform flood-resilient crops engineering via cis -regulatory manipulation. How did amphibious plants evolve the convergent strategy to escape submergence by fast shoot elongation? Yang et al. reveal the pivotal role of a cis -regulatory element in the PHYA promoter in promoting submergence-induced plastic growth of amphibious plants.

Quantifying the variation and coordination patterns of plant functional traits across different organs under environmental changes is crucial for understanding plant invasion and adaptation mechanisms. This study employed a space-for-time substitution experiment to compare the differential responses of root and leaf functional traits and their coordination in the invasive plant Alternanthera philoxeroides and the native plant Ludwigia peploides to nitrogen addition during different invasion degree. The results showed that: (1) nitrogen addition promoted the growth of both species, with A. philoxeroides exhibited greater biomass sensitivity. Compared to the positive effects of nitrogen fertilization, nitrogen addition facilitated A. philoxeroides in displacing L. peploides in communities with 50% (2 A. philoxeroides seedlings) and 75% (3 A. philoxeroides seedlings) invasion degree. (2) invasion degree, nitrogen addition, and their interaction significantly influenced most root and leaf traits of both species. But the two species differed markedly in their response of root and leaf traits to environmental factors. (3) The correlations between root traits, leaf traits, and total biomass were stronger in A. philoxeroides than in L. peploides , as were the linkages between root and leaf traits. Under environmental changes, the two species exhibited distinct adaptive strategies in root and leaf traits, with A. philoxeroides ’s trait advantages likely contributing to its invasion success. In conclusion, our study demonstrates that nitrogen deposition facilitates alien plant invasion, particularly in mixed communities experiencing moderate to severe invasion.

Soil biota community structure can change with latitude, but the effects of changes on native plants, invasive plants, and their herbivores remain unclear. Here, we examined latitudinal variation in the soil biota community associated with the invasive plant Alternanthera philoxeroides and its native congener A. sessilis , and the effects of soil biota community variation on these plants and the beetle Agasicles hygrophila . We characterized the soil bacterial and fungal communities and root-knot nematodes of plant rhizospheres collected from 22 °N to 36.6 °N in China. Soil biota community structure changed with latitude as a function of climate and soil properties. Root-knot nematode abundance and potential soil fungal pathogen diversity (classified with FUNGuild) decreased with latitude, apparently due to higher soil pH and lower temperatures. A greenhouse experiment and lab bioassay showed native plant mass, seed production, and mass of beetles fed native foliage increased with soil collection latitude. However, there were no latitudinal patterns for the invasive plant. These results suggest that invasive and native plants and, consequently, their herbivores have different responses to latitudinal changes in soil-borne enemies, potentially creating spatial variation in enemy release or biotic resistance. This highlights the importance of linking above- and below-ground multitrophic interactions to explore the role of soil biota in non-native plant invasions with a biogeographic approach.

C4 photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C4 evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO2 levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C4 lineages in eudicots. The oldest chenopod C4 lineage dates back to the Eocene/Oligocene boundary, representing one of the first origins of C4 in plants, but still corresponding with the Oligocene decline of atmospheric CO2. In contrast to grasses, the rate of transitions from C3 to C4 is highest in ancestrally drought resistant (salt-tolerant and succulent) lineages, implying that adaptation to dry or saline habitats promoted the evolution of C4; and possible reversions from C4 to C3 are apparent. We conclude that the paradigm established in grasses must be regarded as just one aspect of a more complex system of C4 evolution in plants in general.

Key message Cd induces photosynthetic inhibition and oxidative stress damage in H. citrina , which mobilizes the antioxidant system and regulates the expression of corresponding genes to adapt to Cd and Pb stress. Cd and Pb are heavy metals that cause severe pollution and are highly hazardous to organisms. Physiological measurements and transcriptomic analysis were combined to investigate the effect of 5 mM Cd or Pb on Hemerocallis citrina Baroni. Cd significantly inhibited H. citrina growth, while Pb had a minimal impact. Both Cd and Pb suppressed the expression levels of key chlorophyll synthesis genes, resulting in decreased chlorophyll content. At the same time, Cd accelerated chlorophyll degradation. It reduced the maximum photochemical efficiency of photosystem (PS) II, damaging the oxygen-evolving complex and leading to thylakoid dissociation. In contrast, no such phenomena were observed under Pb stress. Cd also inhibited the Calvin cycle by down-regulating the expression of Rubisco and SBPase genes, ultimately disrupting the photosynthetic process. Cd impacted the light reaction processes by damaging the antenna proteins, PS II and PS I activities, and electron transfer rate, while the impact of Pb was weaker. Cd significantly increased reactive oxygen species and malondialdehyde accumulation, and inhibited the activities of antioxidant enzymes and the expression levels of the corresponding genes. However, H. citrina adapted to Pb stress by the recruitment of antioxidant enzymes and the up-regulation of their corresponding genes. In summary, Cd and Pb inhibited chlorophyll synthesis and hindered the light capture and electron transfer processes, with Cd exerting great toxicity than Pb. These results elucidate the physiological and molecular mechanisms by which H. citrina responds to Cd and Pb stress and provide a solid basis for the potential utilization of H. citrina in the greening of heavy metal-polluted lands.

Aims Planting halophytes is a widely used method of phytoremediation for saline soils. The succulent halophytes Halogeton glomeratus and Suaeda glauca are widely used for remediation of saline soil in the arid region of Northwestern China. However, whether intercropping of H. glomeratus and S. glauca can increase the improvement effect for saline soil is yet to be proved. Materials and methods Therefore, this study analyzed three phytoremediation planting modes: monocropping of H. glomeratus (Hg), monocropping of S. glauca (Sg), and H. glomeratus and S. glauca intercropping (Hg||Sg). These were applied in field experiments, with biomass and soil physicochemical properties measured for each treatment, and the mechanism was analyzed using macrogenomics. Results After harvesting the halophytes after one season, the Hg treatment had the highest dry biomass and soil total dissolved salt content was reduced; correspondingly, soil pH were decreased and soil organic matter content were increased. The results showed that Actinobacteria, Acidobacteria and Proteobacteria were the dominant phylum under the four treatments. This suggests that Hg treatment was more capable of producing microorganisms favorable to saline soil remediation. Conclusions Thus, H. glomeratus monocropping is a more effective phytoremediation strategy for saline soil in the dry zone of Northwestern China. Graphical Abstract

This study aims to validate a new cosmetic ingredient from Salicornia ramosissima S J. Woods through in vitro and ex vivo assays. The halophyte extracts were obtained by subcritical water extraction (SWE) at different temperatures (110, 120, 140, 160 and 180 °C). The antioxidant/radical scavenging activities and the phenolic profile were screened for all extracts. The optimal extract was assessed in keratinocytes and fibroblasts, while permeation assays were performed in Franz cells. The inhibitory activity of hyaluronidase and elastase was also evaluated. The sample extracted at 180 °C presented the highest phenolic content (1739.28 mg/100 g of dry weight (dw)). Despite not being efficient in the sequestration of ABTS[sup.•+], this extract scavenged the DPPH[sup.•] (IC[sub.50] = 824.57 µg/mL). The scavenging capacity of superoxide (O[sub.2] [sup.•−]) and hypochlorous acid (HOCl) was also considerable (respectively, IC[sub.50] = 158.87 µg/mL and IC[sub.50] = 5.80 µg/mL). The cell viability assays confirmed the absence of negative effects on keratinocytes, while the fibroblasts’ viability slightly decreased. The ex vivo permeation of rutin, quercetin and syringic acid after 24 h was, respectively, 11, 20 and 11%. Additionally, the extract showed a good elastase and hyaluronidase inhibitory activity. The results obtained support the S. ramosissima bioactivity as a cosmetic ingredient.

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. thatwas previously supported bymorphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.