Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.

Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation.

Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B. alternifolia, the first within the family Scrophulariaceae. Whole-genome re-sequencing data from 48 populations plus morphological and petal colour reflectance data covering its full distribution range were collected. Three distinct genetic lineages of B. alternifolia were uncovered, corresponding to Himalayan, HDM and LP populations, with the last also differentiated morphologically and phenologically, indicating occurrence of allopatric speciation likely to be facilitated by geographic isolation and divergent adaptation to distinct ecological niches. Moreover, speciation with gene flow between populations from either side of a mountain barrier could be under way within LP. The current disjunctions within B. alternifolia might result from vicariance of a once widespread distribution, followed by several past contraction and expansion events, possibly linked to climate fluctuations promoted by the Kunlun-Yellow river tectonic movement. Several adaptive genes are likely to be either uniformly or diversely selected among regions, providing a footprint of local adaptations. These findings provide new insights into plant biogeography, adaptation and different processes of allopatric speciation.

Natural hybridization and asymmetric introgression at the distribution margin of two Buddleja species with a large overlap.

BACKGROUND: Natural hybridization in plants is universal and plays an important role in evolution. Based on morphology it has been presumed that hybridization occurred in the genus Buddleja, though genetic studies confirming this assumption have not been conducted to date. The two species B. crispa and B. officinalis overlap in their distributions over a wide range in South-West China, and we aimed to provide genetic evidence for ongoing hybridization in this study. RESULTS: We investigated the occurrence of hybrids between the two species at the southern-most edge of the distribution of B. crispa using five nuclear loci and pollination experiments. The genetic data suggest substantial differentiation between the two species as species-specific alleles are separated by at least 7-28 mutations. The natural hybrids found were nearly all F1s (21 of 23), but backcrosses were detected, and some individuals, morphologically indistinguishable from the parental species, showed introgression. Pollen viability test shows that the percentage of viable pollen grains was 50 ± 4% for B. crispa, and 81 ± 2% for B. officinalis. This difference is highly significant (t = 7.382, p < 0.0001). Hand cross-pollination experiments showed that B. crispa is not successful as pollen-parent, but B. officinalis is able to pollinate B. crispa to produce viable hybrid seed. Inter-specific seed-set is low (8 seeds per fruit, as opposed to about 65 for intra-specific pollinations), suggesting post-zygotic reproductive barriers. In addition, one of the reference populations also suggests a history of introgression at other localities. CONCLUSIONS: The occurrence of morphologically intermediate individuals between B. crispa and B. officinalis at Xishan Mountain is unequivocally linked to hybridization and almost all examined individuals of the putative hybrids were likely F1s. Despite pollination experiments indicating higher chances for introgression into B. officinalis (hybrids only produced viable seed when crossed with B. officinalis), observed introgression was asymmetrical into B. crispa. This could be due to seeds produced by hybrids not contributing to seedlings, or other factors favoring the establishment of backcrosses towards B. crispa. However, further research will be needed to confirm these observations, as the small number of plants used for the pollination experiments could have introduced an artifact, for example if used individuals were more or less compatible than the species average, and also the small number of loci used could convey a picture of introgression that is not representative for the whole genome.

Investigation of Compton profiles of molecular methane and ethane.

The Compton profiles of methane and ethane molecules have been determined at an incident photon energy of 20 keV based on the third generation synchrotron radiation, and the statistical accuracy of 0.2% is achieved near pz = 0. The density functional theory with aug-cc-pVTZ basis set was used to calculate the Compton profiles of methane and ethane. The present experimental Compton profiles are in better agreement with the theoretical calculations in the whole pz region than the previous experimental results, which indicates that the present experimental Compton profiles are accurate enough to serve as the benchmark data for methane and ethane molecules.

Effect of sulfide on the nitrogen removal performance and microbial community of low-substrate Anammox process.

Anammox is one of the most innovative nitrogen removal technologies, while its functional bacteria-anaerobic ammonia-oxidizing bacteria (AAOB) is sensitive to the impurities in the wastewater. In this study, the long-term effects of sulfide at different concentrations (0, 5, 10, 20, 30, 50, 25 mg L-1) on low substrate Anammox process were studied. The results showed that when the sulfide was 25-30 mg L-1, AAOB was well coupled with sulfide-denitrifying bacteria and the total nitrogen removal efficiency (TNRE) reached a maximum of 91.0%. The hydroxylamine oxidoreductase activity and Heme-c reached 1.678 EU g-1 SS and 0.0023 mmol g-1 SS, respectively, with the hzo and nosZ gene concentrations as 2.52 × 108 and 4.45 × 107 copies mL-1. 50 mg L-1 sulfide inhibited the nitrogen removal by AAOB, resulting in the TNRE decreasing to 81.7%. The experimental results provide a reference for the practical application of Anammox in treating sulfur-containing wastewater.

Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub.

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

Does the critically endangered Rhododendron amesiae deserve top priority for conservation?

1.If a threatened plant has the problem of inaccurate species delimitation, its conservation programs that have previously been implemented might be debated.2.We made a comprehensive comparison of the critically endangered R. amesiae and its close relative R. concinnum, employing both morphological and population genomic data (ddRAD-seq).3.We suggest that the critically endangered R. amesiae can be merged into R. concinnum. Hence, the threatened status of R. amesiae is needed to be reevaluated.

Fruiting character variability in wild individuals of Malania oleifera, a highly valued endemic species.

Malania oleifera (Olacaceae), a tree species endemic to Southwest China, has seed oils enriched with nervonic acid and is therefore good source of this chemical. Because of this, there are promising industrial perspective in the artificial cultivation and use of this species. Understanding the variability in the fruit characters among individuals forms the basis or resource prospection. In the current investigation, fifty-three mature fruiting trees were sampled from two locations with divergent climates (Guangnan and Funing). Morphological characterization of fruits (fruit and stone weight, fruit transverse and longitudinal diameter, stone transverse and longitudinal diameter) was conducted, and the concentration of seed oil and its fatty acid composition were also analyzed in all individuals. Differences in all the morphological characters studied were more significant among individual trees than between different geographic localities, even though these had different climates. Eleven fatty acids were identified contributing between 91.39 and 96.34% of the lipids, and the major components were nervonic acid (38.93-47.24%), octadecenoic acid (26.79-32.08%), docosenoic acid (10.94-17.24%). The seed oil content (proportion of oil in seed kernel) and the proportion of nervonic acid were both higher in Funing, which has a higher average climatic temperature than Guangnan. The concentrations of nervonic acid and octadecenoic acid with the low coefficients of variation in the seed oil of M. oleifera were relatively stable in contrast to the other fatty acids. There were significant positive correlations between fruit morphological characters, but the amount of seed oil and the concentrations of its components were not correlated with any morphological character. This study provides an understanding of morphological variation in wild M. oleifera individuals. Wild individuals with excellent fruit traits could be selected and would make promising candidates for commercial cultivation.

Rhododendron kuomeianum (Ericaceae), a new species from northeastern Yunnan (China), based on morphological and genomic data.

Rhododendron kuomeianum Y.H. Chang, J. Nielsen & Y.P. Ma, a new species of Rhododendron (Ericaceae) within subsect. Maddenia in sect. Rhododendron from Yiliang County, NE Yunnan, China, is described and illustrated. The new species is similar to R. valentinianum, but it can be easily distinguished by its sparse scales on the abaxial surface of the leaf blade, fewer flowers per inflorescence and white corolla with pale red margins. There are also differences in the widths of calyx lobes, leaf blade shape and indumentum characteristics of the petiole between the new species and Rhododendron linearilobum. We confirmed that R. kuomeianum is a new species closely related to R. valentinianum and R. changii with phylogenomic studies of 10 species within this subsection based on restriction site-associated DNA sequencing (RAD-seq) data. These phylogenomic analyses also clarified additional taxonomic problems in this subsection previously raised by morphological analysis. Our findings make a strong case for using next-generation sequencing to explore phylogenetic relationships and identify new species, especially in plants groups with complicated taxonomic problems.

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations.

Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H E  = 0.0742 ± 0.002). Both F ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

Occurrence and Prevention of Delayed Autonomous Selfing in Salvia umbratica (Lamiaceae).

Delayed autonomous selfing (DAS) provides reproductive assurance under conditions of pollinator and/or pollen-limitation. Few plant species have been investigated to determine if DAS is terminated when a flower is sufficiently pollinated by a pollen vector, thereby saving plant resources for other purposes. We examined this possibility in bumblebee-pollinated Salvia umbratica. We first showed that DAS resulting in high fruit set (100%) and seed set (>80%) per flower occurred in the absence of insect pollinators by means of style recurvature and was completed in 94% of flowers 72 h after they opened. In contrast, in flowers pollinated immediately after opening, DAS was prevented by corollas dropping away before styles recurve toward the upper thecae. We next showed that hand-pollination of flowers immediately after they opened resulted in high fruit set (100%) and seed set (>80%) when 5-10 pollen grains or more were deposited on their stigmas, whereas fruit set and seed set were reduced to 45.00 and 22.50%, respectively, when pollen loads were reduced to 1-3 pollen grains. Finally, we showed that on average single pollinator visits deposited 26 pollen grains on stigmas of flowers that had just opened, which is more than enough to ensure high fruit and seed set. Our results indicate that flower longevity is highly correlated with the pollinator environment and female fitness of S. umbratica, with extended flower longevity allowing DAS to occur being advantageous when pollinators are absent, while reduced floral longevity and prevention of DAS being favored when flowers are pollinated by pollinators. Thus, flower longevity in S. umbratica varies so as to optimize reproductive output and resource efforts, and is dependent on the availability and effectiveness of pollinators to pollinate flowers.

Repellent, larvicidal and adulticidal activities of essential oil from Dai medicinal plant Zingiber cassumunar against Aedes albopictus.

Zingiber cassumunar is an important plant used in traditional medicine and as a natural mosquito repellent. However, the compounds responsible for the repellent activity of the plant are still unknown. The aim of the study is to identify the components of Z. cassumunar essential oil that show repellent activity against Aedes albopictus. We also evaluated the larvicidal and adulticidal activities of Z. cassumunar essential oil against Ae. albopictus. In-cage mosquito repellent experiments showed that Z. cassumunar essential oil possessed moderate repellent activity with a minimum effective dose (MED) of 0.16 ± 0.01 mg/cm2, compared to reference standard N,N-diethyl-3-methylbenzamide (DEET, 0.03 ± 0.01 mg/cm2). Bioassay-guided fractionation identified the major active compound of Z. cassumunar essential oil as (-)-terpinen-4-ol (1) (MED: 0.19 ± 0 mg/cm2). We also found that Z. cassumunar essential oil showed moderate larvicidal activity against first instar larvae of Ae. albopictus with a LC50 (50% lethal concentration) of 44.9 µg/L after 24 h. Fumigation bioassays showed that Z. cassumunar essential oil exhibits moderate adulticidal activity against Ae. albopictus with a LC50 of 5.44%, while (-)-terpinen-4-ol showed significant adulticidal activity with a LC50 of 2.10% after 24 h. This study verifies that the Z. cassumunar essential oil has mosquito repellent activity, and that (-)-terpinen-4-ol is mainly responsible for this activity. Furthermore, this study provides scientific support for the folk usage of Z. cassumunar essential oil as mosquito repellent and indicates that Z. cassumunar essential oil and (-)-terpinen-4-ol can be used as plant-derived repellents and insecticides for mosquito control.

Natural hybridization between Rhododendron delavayi and R. cyanocarpum (Ericaceae), from morphological, molecular and reproductive evidence.

The natural hybridization that occurs between two sympatric species of Rhododendron subgenus Hymenanthes in Yunnan, China, was investigated. In field observations, it was noted that the putative hybrids between R. delavayi Franch. and R. cyanocarpum (Franch.) Franch. ex W.W. Sm. had intermediate morphologies. On the basis of morphology, chloroplast DNA (trnL-rpl32) and nuclear DNA (waxy), hybrids and parental species were identified. Hybridization occurred in both directions, but was asymmetrical, with R. delavayi as the major maternal parent. Reciprocal hand pollination treatments showed that either species, as pollen donor or pollen receiver, could produce fruits. It was noted that fruit set varied among treatments. The same pollinators (bumblebees) were shared in both parental species. From these results, we conclude that individuals with intermediate morphologies are indeed of hybrid origin from natural hybridization between R. cyanocarpum and R. delavayi. Furthermore, we presume the hybridization at the study site could have been initiated by habitat disturbance in the 1950s, and we may hence witness the early stages of hybrid swarm formation.

[Plant diversity monitoring: A review]. / æ¤ç‰©å¤šæ ·æ€§ç›‘æµ‹ç ”ç©¶è¿›å±•.

Plant diversity monitoring is an essential basis for plant conservation and policy making, and is critical to the sustainable use and protection of biological resources. We reviewed the research progress on plant diversity monitoring, and proposed further research direction. Plant diversity monitoring is developing rapidly at a new situation, and enters a new era referring to intelligent, integration of macroscopic and microscopic, networked monitoring, big data, large-scale, multidisciplinary, all-dimensional, from species level to family level, community level or ecosystem level, and even the global level. The construction of biodiversity monitoring network promotes the uniform of essential biodiversity variables and networked monitoring. Internet information and database had become a main data source of plant diversity. There are many new challenges in plant diversity monitoring, including standardization, effective utilization and sharing of the monitoring data, as well as the monitoring for genetic diversity and individuals. Ecological monitoring would be large-scale, automated and standardized. Many things should be addressed in further research, including to improve the monitoring networks, to find innovative ways and build new models, to carry out monitoring at hotspots and give priority to important species as well as community or even larger scale, to pay more attention to the background investigation of plant resource.

A new species of Rhododendron (Ericaceae) from Guizhou, China.

A new species of the Rhododendron (Ericaceae) in subgen. Tsutsusisect.Tsutsusi from Puding county of Guizhou, China, is described and illustrated. The new species, R.pudingense X.Y. Dai, C.H. Yang & Y.P. Ma, is similar to R.myrsinifolium Ching ex Fang et M. Y. He and R.minutiflorum Hu, but it can be easily distinguished by its length and being pubescent on inner surface of corolla tube, sparse hairs below the middle of filament and the glabrous style.

How a New Conservation Action Concept Has Accelerated Plant Conservation in China.

Since 2005, a new conservation action concept has been implemented to address the most threatened plant species requiring priority conservation in China. The concept is now widely recognized at different levels of governmental departments and by the general public, and is leading to great achievements for plant conservation in China.

New Sweet-Tasting C21 Pregnane Glycosides from the Roots of Myriopteron extensum.

To investigate the sweet-tasting components in the roots of Myriopteron extensum, the phytochemical study of its roots was conducted, which led to the discovery of 12 new C21 pregnane glycosides (extensumside M-X, 1-12) and two known ones (extensumside C and extensumside E, 13-14). Their chemical structure elucidation was accomplished by means of spectroscopic methods: IR, UV, ESI-MS, and NMR (1H NMR, 13C NMR, HSQC, 1H-1H COSY, HMBC, HSQC-TOCSY, and ROESY), as well as the chemical evidence. Sensory analysis of these compounds revealed that nine of them (1, 3, 4, 5, 6, 7, 8, 13, and 14) are highly sweet-tasting compounds. Their sweetness intensities are 25 to 400 times greater than that of sucrose. Analysis of the structure-activity relationship (SAR) indicated that the sweet intensities of the isolated compounds are closely related to the aglycone 3ß,16α-dihydroxy-pregn-5-en-20-one, the number and type of the monosaccharide in the sugar chain linked to C-3 and C-16 and the position of the mBe group.