Plant species with extremely small populations conservation program: achieving Kunming-Montreal global biodiversity targets.

Conservation programs for plant species with extremely small populations (PSESP) have been successfully implemented for several decades in China. Here we highlight how their inclusion in several national conservation policies helps meet targets of the Kunming-Montreal Global Biodiversity Framework (KMGBF) and show how lessons from these programs can be applied more widely.

Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus.

Cotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538.4 Mb). We predicted 35,856 protein-coding genes, 1,401 miRNAs, 655 tRNAs, 425 rRNAs, and 795 snRNAs. The functions of 34,967 genes (97.52%) were predicted. The availability of this chromosome-level genome will provide valuable resources for molecular studies of this species, facilitating future research on speciation, functional genomics, and comparative genomics within the Rosaceae family.

Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark.

As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.

The key role of unsaturated olefin content on polysulfides prepared via inverse vulcanization of waste plant oils for mercury removal from wastewater.

Three waste plant oils (olive oil, coconut oil, and soybean oil) were utilized as monomer crosslinking agents to synthesize polysulfides by inverse vulcanization with elemental sulfur, for mercury removal from wastewater. NMR analysis showed that 92.1% of the olefins participated in the inverse vulcanization reaction, indicating that the quantity of unsaturated olefins in plant oil mainly affects the ring-opening ratio of sulfur for the formation of sulfur-based polymers. The experimental results showed that olive oil polysulfide (S-r-olive) achieved 100% Hg2+ removal within 2 h at a pH of 6. The S-r-olive, S-r-soybean, and S-r-coconut exhibited adsorption capacities of 130.23, 42.72, and 28.08 mg/g, respectively. The kinetic and adsorption isotherm illustrated that the Hg2+ adsorption by polysulfides conformed to the pseudo-second-order and Freundlich models, showing that the reaction rate constant of S-r-olive is approximately 14 times and 4.6 times greater than that of S-r-soybean and S-r-coconut, respectively. The adsorption mechanism is concluded that Hg2+ first enters the suspended S-r-olive by physical adsorption, then combined with sulfur to form HgS by chemical action and fixed in the S-r-olive adsorbent. This study demonstrates that utilizing waste plant oils as monomer crosslinking agents to synthesize adsorbents for Hg2+ removal is feasible and effective.

The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP).

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.

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 chromosomal-level genome assembly of Buzhaye (Microcos paniculata).

Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.

Seed Germination and Seedling Growth Influenced by Genetic Features and Drought Tolerance in a Critically Endangered Maple.

Understanding the adaptation of plant species will help us develop effective breeding programs, guide the collection of germplasm, and improve the success of population restoration projects for threatened species. Genetic features correlate with species adaptation. Acer yangbiense is a critically endangered plant species with extremely small populations (PSESP). However, no information was available on its seed germination and seedling growth in populations with different genetic characteristics. In this study, we investigated seed germination and compared the performance of 566 seedlings in 10 maternal half-sib families cultivated in Kunming Botanical Garden. The results showed that A. yangbiense seeds required an average of 44 days to start germinating, with a 50% germination rate estimated to take about 47-76 days, indicating slow and irregular germination. There is a trade-off between the growth and survival in A. yangbiense seedlings, with fast growth coming at the cost of low survival. Groups that were able to recover from a recent bottleneck consistently had higher relative growth rates. High genetic diversity and low levels of inbreeding are likely to be responsible for their improved survival during drought conditions and rapid growth under optimal environmental conditions. Our results suggest that maternal genetic traits might be used as indicators for conservation and population restoration. These findings provide us with new information that could be applied to support ex situ conservation and reintroduction of threatened species.

A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data.

Rhododendron vialii (subgen. Azaleastrum) is an evergreen shrub with high ornamental value. This species has been listed as a plant species with extremely small populations (PSESP) for urgent protection by China's Yunnan provincial government in 2021, due to anthropogenic habitat fragmentation. However, limited genomic resources hinder scientifically understanding of genetic threats that the species is currently facing. In this study, we assembled a high-quality haplotype-resolved genome of R. vialii based on PacBio HiFi long reads and Hi-C reads. The assembly contains two haploid genomes with sizes 532.73 Mb and 521.98 Mb, with contig N50 length of 35.67 Mb and 34.70 Mb, respectively. About 99.92% of the assembled sequences could be anchored to 26 pseudochromosomes, and 14 gapless assembled chromosomes were included in this assembly. Additionally, 60,926 protein-coding genes were identified, of which 93.82% were functionally annotated. This is the first reported genome of R. vialii, and hopefully it will lay the foundations for further research into the conservation genomics and horticultural domestication of this ornamentally important species.

The chromosome-level genome assembly and genes involved in biosynthesis of nervonic acid of Malania oleifera.

Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.

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.

Evolutionary history of two evergreen Rhododendron species as revealed by chromosome-level genome assembly.

Background: The genus Rhododendron (Ericaceae), a species-rich and widely distributed genus of woody plants, is distinguished for the beautiful and diverse flowers. Rhododendron delavayi Franch. and Rhododendron irroratum Franch., are highly attractive species widely distributed in south-west China and abundant new varieties have been selected from their genetic resources. Methods: We constructed chromosome-scale genome assemblies for Rhododendron delavayi and Rhododendron irroratum. Phylogenetic and whole-genome duplication analyses were performed to elucidate the evolutionary history of Rhododendron. Further, different types of gene duplications were identified and their contributions to gene family expansion were investigated. Finally, comprehensive characterization and evolutionary analysis of R2R3-MYB and NBS-encoding genes were conducted to explore their evolutionary patterns. Results: The phylogenetic analysis classified Rhododendron species into two sister clades, 'rhododendrons' and 'azaleas'. Whole-genome duplication (WGD) analysis unveiled only one WGD event that occurred in Rhododendron after the ancestral γ triplication. Gene duplication and gene family expansion analyses suggested that the younger tandem and proximal duplications contributed greatly to the expansion of gene families involved in secondary metabolite biosynthesis and stress response. The candidate R2R3-MYB genes likely regulating anthocyanin biosynthesis and stress tolerance in Rhododendron will facilitate the breeding for ornamental use. NBS-encoding genes had undergone significant expansion and experienced species-specific gain and loss events in Rhododendron plants. Conclusions: The reference genomes presented here will provide important genetic resources for molecular breeding and genetic improvement of plants in this economically important Rhododendron genus.

Impacts of exogenous quorum sensing signal molecule-acylated homoserine lactones (AHLs) with different addition modes on Anammox process.

Anammox was proved having the quorum sensing ability, and several acylated homoserine lactones (AHLs) signal molecules were detected in the system. In this study, the impact of exogenous N-dodecanoyl homoserine lactone (C12-HSL) with different addition modes on the nitrogen removal, key enzymes' activity, and microbial revolution were investigated in Anammox system. Results showed that once-addition of C12-HSL had no obvious impact on Anammox. Daily-addition with 40 nM slightly improved the TN removal from 71.1 % to 74.5 %, while 80 and 200 nM significantly decreased it to 62.7 % and 61.8 %, respectively. The enzyme activity of ammonia monooxygenase increased from 0.015 to 0.068, nitrite reductase increased from 0.25 to 1.23, and nitrate reductase increased from 0.05 to 0.11 µg NO2--N mg-1 Protein min-1. Arenimonas abundance showed positive correlation with TN removal while Candidatus Kuenenia was continuously suppressed. C12-HSL was beneficial for partial nitrification, and it could be adopted for regulating the nitrite production.

Regulating performance of CANON process via adding external quorum sensing signal molecules in membrane bioreactor.

In this study, the regulation effect of the external quorum sensing signals, N-dodecanoyl homoserine lactone (C12-HSL) on CANON process were investigated in a membrane bioreactor. C12-HSL significantly enhanced the aerobic ammonia-oxidizing bacteria and improved the ammonia monooxygenase activity to 0.134 from 0.076 µg NO2--N mg-1 protein min-1, while suppressed anaerobic ammonia-oxidizing bacteria and limited the TN removal to 0.07 from 0.22 kg m-3 d-1. Key enzymes synthesis were enhanced during the operation without C12-HSL addition, enabling the resistance of CANON system to high C12-HSL. As a result, the hydroxylamine oxidoreductase and nitrite reductase activity reached 35.9 EU g-1 SS and 1.28 µg NO2--N mg-1 protein min-1, respectively; Nitrosomonas and Candidatus Kuenenia, with the abundance as 12.5 % and 22.9 %, cooperatively contributed to the TN removal, which maintained at 0.19 kg m-3 d-1. C12-HSL was profitable for aerobic ammonia oxidation, which could be adopted for regulating the nitrite production rate.

Mercury removal from flue gas by a MoS2/H2O heterogeneous system based on its absorption kinetics.

An enhanced MoS2/C10TAB/H2O system was built and investigated for Hg0 removal based on strengthening the Hg0 gas-liquid mass transfer. The results showed that adding 7 mg/L C10TAB can improve the Hg0 removal efficiency from 76.5 to 88.7% as decrease of the solution surface tension. Keeping 2000 rpm of stirring rate accelerated the renewal rate of gas-liquid interface, thereby enhancing Hg0 removal. SO2 slightly promoted the Hg0 removal efficiency to 91% because of the absorption of SO2 causing a decrease in the solution pH from 6.9 to 4.3. NO participated in Hg0 removal reactions but not removed in this system which visibly enhanced the Hg0 removal efficiency to 94%. The Hg mass transfer kinetics were analyzed to determine how C10TAB promoted Hg0 removal. The Hg-TPD, Hg fate, and species results revealed that Hg0 was first oxidized to Hg2+, then bonded with S to generate HgS and enrich on the MoS2. Therefore, improving the Hg0 gas-liquid mass transfer can enhance Hg0 removal in MoS2/H2O system, which can provide reference for purification of other insoluble pollutants in absorption system.

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.

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.

Unusual patterns of hybridization involving two alpine Salvia species: Absence of both F1 and backcrossed hybrids.

Natural hybridization plays an important role in speciation; however, we still know little about the mechanisms underlying the early stages of hybrid speciation. Hybrid zones are commonly dominated by F1s, or backcrosses, which impedes further speciation. In the present study, morphological traits and double digest restriction-site associated DNA sequencing (ddRAD-seq) data have been used to confirm natural hybridization between Salvia flava and S. castanea, the first case of identification of natural hybridization using combined phenotypic and molecular evidence in the East Asian clade of Salvia. We further examined several reproductive barriers in both pre-zygotic and post-zygotic reproductive stages to clarify the causes and consequences of the hybridization pattern. Our results revealed that reproductive isolation between the two species was strong despite the occurrence of hybridization. Interestingly, we found that most of the hybrids were likely to be F2s. This is a very unusual pattern of hybridization, and has rarely been reported before. The prevalence of geitonogamy within these self-compatible hybrids due to short distance foraging by pollinators might explain the origin of this unusual pattern. F2s can self-breed and develop further, therefore, we might be witnessing the early stages of hybrid speciation. Our study provides a new case for understanding the diversification of plants on the Qinghai-Tibet Plateau.