A high-quality chromosome-level genome assembly of Ficus hirta.

Ficus species (Moraceae) play pivotal roles in tropical and subtropical ecosystems. Thriving across diverse habitats, from rainforests to deserts, they harbor a multitude of mutualistic and antagonistic interactions with insects, nematodes, and pathogens. Despite their ecological significance, knowledge about the genomic background of Ficus remains limited. In this study, we report a chromosome-level reference genome of F. hirta, with a total size of 297.27 Mb, containing 28,625 protein-coding genes and 44.67% repeat sequences. These findings illuminate the genetic basis of Ficus responses to environmental challenges, offering valuable genomic resources for understanding genome size, adaptive evolution, and co-evolution with natural enemies and mutualists within the genus.

Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies.

Fig wasps (Agaonidae; Hymenoptera) are the only pollinating insects of fig trees (Ficus; Moraceae), forming the most closely and highly specific mutualism with the host. We used transcriptome sequences of 25 fig wasps from six genera to explore the evolution of key molecular components of fig wasp chemosensory genes: odorant-binding proteins (OBPs) and chemosensory proteins (CSPs). We identified a total 321 OBPs and 240 CSPs, with each species recording from 6 to 27 OBP genes and 6-19 CSP genes. 318 OBP genes are clustered into 17 orthologous groups and can be divided into two groups: PBP sensitive to pheromone and GOBP sensitive to general odor molecules, such as alcohols, esters, acids, ketones, and terpenoids. 240 CSP genes are clustered into 12 orthologous groups, which can be divided into three major groups and have functions, such as olfactory, tissue formation and/or regeneration, developmental, and some specific and unknown function. The gene sequences of most orthologous groups vary greatly among species and are consistent with the phylogenetic relationships between fig wasps. Strong purifying selection of both OBP and CSP genes was detected, as shown by low ω values. A positive selection was detected in one locus in CSP1. In conclusion, the evolution of chemosensory proteins OBPs and CSPs in fig wasps is relatively conservative, and they play an indispensable role in the life activities of fig wasps. Our results provide a starting point for understanding the molecular basis of the chemosensory systems of fig wasps.

Evolution of Wolbachia reproductive and nutritional mutualism: insights from the genomes of two novel strains that double infect the pollinator of dioecious Ficus hirta.

Wolbachia is a genus of maternally inherited endosymbionts that can affect reproduction of their hosts and influence metabolic processes. The pollinator, Valisia javana, is common in the male syconium of the dioecious fig Ficus hirta. Based on a high-quality chromosome-level V. javana genome with PacBio long-read and Illumina short-read sequencing, we discovered a sizeable proportion of Wolbachia sequences and used these to assemble two novel Wolbachia strains belonging to supergroup A. We explored its phylogenetic relationship with described Wolbachia strains based on MLST sequences and the possibility of induction of CI (cytoplasmic incompatibility) in this strain by examining the presence of cif genes known to be responsible for CI in other insects. We also identified mobile genetic elements including prophages and insertion sequences, genes related to biotin synthesis and metabolism. A total of two prophages and 256 insertion sequences were found. The prophage WOjav1 is cryptic (structure incomplete) and WOjav2 is relatively intact. IS5 is the dominant transposon family. At least three pairs of type I cif genes with three copies were found which may cause strong CI although this needs experimental verification; we also considered possible nutritional effects of the Wolbachia by identifying genes related to biotin production, absorption and metabolism. This study provides a resource for further studies of Wolbachia-pollinator-host plant interactions.

Multi-omics analysis the differences of VOCs terpenoid synthesis pathway in maintaining obligate mutualism between Ficus hirta Vahl and its pollinators.

Inroduction: Volatile organic compounds (VOCs) emitted by the receptive syconia of Ficus species is a key trait to attract their obligate pollinating fig wasps. Ficus hirta Vahl is a dioecious shrub, which is pollinated by a highly specialized symbiotic pollinator in southern China. Terpenoids are the main components of VOCs in F. hirta and play ecological roles in pollinator attraction, allelopathy, and plant defense. However, it remains unclear that what molecular mechanism difference in terpenoid synthesis pathways between pre-receptive stage (A-phase) and receptive stage (B-phase) of F. hirta syconia. Methods: Transcriptome, proteome and Gas Chromatography-Mass Spectrometer (GC-MS) were applied here to analyze these difference. Results and discussion: Compared to A-phase syconia, the genes (ACAT2, HMGR3, GGPS2, HDR, GPS2, TPS2, TPS4, TPS10-4, TPS14) related to the terpenoid synthesis pathway had higher expression level in receptive syconia (B-phase) according to transcriptome sequencing. Seven differentially expressed transcription factors were screened, namely bHLH7, MYB1R1, PRE6, AIL1, RF2b, ANT, VRN1. Specifically, bHLH7 was only specifically expressed in B-phase. 235 differentially expressed proteins (DEPs) were mainly located in the cytoplasm and chloroplasts. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEPs were mainly enriched in the metabolic process. A total of 9 terpenoid synthesis proteins were identified in the proteome. Among them, 4 proteins in methylerythritol phosphate (MEP) pathway were all down-regulated. Results suggested the synthesis of terpenoids precursors in B-phase bracts were mainly accomplished through the mevalonic acid (MVA) pathway in cytoplasm. Correlation analysis between the transcriptome and proteome, we detected a total of 1082 transcripts/proteins, three of which are related to stress. From the VOCs analysis, the average percent of monoterpenoids emitted by A-phase and B-phase syconia were 8.29% and 37.08%, while those of sesquiterpenes were 88.43% and 55.02% respectively. Monoterpenes (camphene, myrcene, camphor, menthol) were only detected in VOCs of B-phase syconia. To attract pollinators, B-phase syconia of F. hirta need more monoterpenoids and less sesquiterpenes. We speculate that transcription factor bHLH7 may regulate the terpenoid synthesis pathway between A- and B-phase syconia. Our research provided the first global analysis of mechanism differences of terpenoid synthesis pathways between A and B phases in F. hirta syconia.

Global biogeography of warning coloration in the butterfly Danaus chrysippus.

Warning coloration provides a textbook example of natural selection, but the frequent observation of polymorphism in aposematic species presents an evolutionary puzzle. We investigated biogeography and polymorphism of warning patterns in the widespread butterfly Danaus chrysippus using records from citizen science (n = 5467), museums (n = 8864) and fieldwork (n = 2586). We find that polymorphism in three traits controlled by known mendelian loci is extensive. Broad allele frequency clines, hundreds of kilometres wide, suggest a balance between long-range dispersal and predation of unfamiliar morphs. Mismatched clines for the white hindwing and forewing tip in East Africa are consistent with a previous finding that the black wingtip allele has spread recently in the region through hitchhiking with a heritable endosymbiont. Light/dark background coloration shows more extensive polymorphism. The darker genotype is more common in cooler regions, possibly reflecting a trade-off between thermoregulation and predator warning. Overall, our findings show how studying local adaptation at the global scale provides a more complete picture of the evolutionary forces involved.

Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China.

The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.

Effects of exogenous silicon on maize seed germination and seedling growth.

As the global population continues to increase, global food production needs to double by 2050 to meet the demand. Given the current status of the not expansion of cultivated land area, agronomic seedlings are complete, well-formed and strong, which is the basis of high crop yields. The aim of this experiment was to study the effects of seed germination and seedling growth in response to silicon (from water-soluble Si fertilizer). The effects of Si on the maize germination, seedling growth, chlorophyll contents, osmoprotectant contents, antioxidant enzyme activities, non-enzymatic antioxidant contents and stomatal characteristics were studied by soaking Xianyu 335 in solutions of different concentrations of Si (0, 5, 10, 15, 20, and 25 g·L-1). In this study, Si treatments significantly increased the seed germination and per-plant dry weight of seedlings (P < 0.05), and the optimal concentration was 15 g·L-1. As a result of the Si treatment of the seeds, the chlorophyll content, osmotic material accumulation and antioxidant defence system activity increased, reducing membrane system damage, reactive oxygen species contents, and stomatal aperture. The results suggested that 15 g·L-1 Si significantly stimulated seed germination and promoted the growth of maize seedlings, laying a solid foundation for subsequent maize growth.

The complete chloroplast genome of Philadelphus pekinensis Rupr. (Hydrangeaceae).

Philadelphus pekinensis Rupr. is a common perennial deciduous shrub distributed in temperate China. Here, we report the complete chloroplast genome of P. pekinensis. The cp genome is totally 157,308 bp in length, including large single-copy (LSC) region of 86,457 bp, small single-copy (SSC) region of 18,735 bp, and two separated inverted regions (IRs) of 26,058 bp, respectively. It contains 134 genes, including 85 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The overall GC content is 43.1%. The phylogenetic analysis reveals the monophyly of P. pekinensis and P. calvescens, which is more related with Carpenteria californica than other species in the Hydrangeaceae family.

Enhanced Adsorption of Carbon Dioxide from Simulated Biogas on PEI/MEA-Functionalized Silica.

A series of efficient adsorbents were prepared by a wet-impregnation method for CO2 separation from simulated biogas. A type of commercially available silica, named as FNG-II silica (FS), was selected as supports. FS was modified with a mixture of polyethyleneimine (PEI) and ethanolamine (MEA) to improve the initial CO2 adsorption capacity and thermal stability of the adsorbents. The influence of different adsorbents on CO2 adsorption performance was investigated by breakthrough experiments. Scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FTIR), and N2 adsorption-desorption isotherm were used to characterize the silica before and after impregnating amine. Additionally, the thermal stability of adsorbents was measured by differential thermal analysis (TDA). Silica impregnated with mixtures of MEA and PEI showed increased CO2 adsorption performance and high thermal stability compared with those obtained from silica impregnated solely with MEA or PEI. With a simulated biogas flow rate of 100 mL/min at 0.2 MPa and 25 °C, FS-10%MEA-10%PEI exhibited a CO2 adsorption capacity of ca. 64.68 mg/g which increased by 81 % in comparison to FS-20%PEI. The thermal stability of FS-10%MEA-10%PEI was evidently higher than that of FS-20%MEA, and a further improvement of thermal stability was achieved with the increasing value of PEI/MEA weight ratio. It was showed that MEA was able to impose a synergistic effect on the dispersion of PEI in the support, reduce the CO2 diffusion resistance and thus increase CO2 adsorption performance. Additionally, if the total percentage of amine was the same, FS impregnated by different ratios of PEI to MEA did not exhibit an obvious difference in CO2 adsorption performance. FS-15%PEI-5%MEA could be regenerated under mild conditions without obvious loss of CO2 adsorption activity.

Identification and characterization of microsatellites in Aconitum reclinatum (Ranunculaceae), a rare species endemic to North America.

PREMISE OF THE STUDY: Aconitum reclinatum is the only representative species of Aconitum subg. Lycoctonum in North America, with restricted ranges and endangered populations. Polymorphic microsatellite markers were developed for A. reclinatum for further investigation of genetic diversity and population structure. METHODS AND RESULTS: Using Illumina HiSeq technology, we sequenced a genomic library for identification of simple sequence repeat markers. A total of 12 polymorphic primer pairs were developed and tested on 66 individuals from four populations in North America. The number of alleles ranged from one to seven per locus with an average of 3.48. Levels of observed and expected heterozygosity varied from 0 to 1.000 and 0 to 0.736, respectively, at population level. Three primer pairs were successfully amplified in three of four closely related species. CONCLUSIONS: The microsatellites isolated in this study will be useful in further research on the genetic diversity and conservation genetics of A. reclinatum populations in North America.

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae.

The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus.

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58-62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

A protease-insensitive feruloyl esterase from China Holstein cow rumen metagenomic library: expression, characterization, and utilization in ferulic acid release from wheat straw.

A metagenomic library of China Holstein cow rumen microbes was constructed and screened for novel gene cluster. A novel feruloyl esterase (FAE) gene was identified with a length of 789 bp and encoded a protein displaying 56% identity to known esterase sequences. The gene was functionally expressed in Escherichia coli BL21 (DE3), and the total molecular weight of the recombined protein was 32.4 kDa. The purified enzyme showed a broad specificity against the four methyl esters of hydroxycinnamic acids and high activity (259.5 U/mg) to methyl ferulate at optimum conditions (pH 8.0, 40 °C). High thermal and pH stability were also observed. Moreover, the enzyme showed broad resistance to proteases. FAE-SH1 can enhance the release of ferulic acid from wheat straw with cellulase, ß-1,4-endoxylanase, ß-1,3-glucanase, and pectase. These features suggest FAE-SH1 as a good candidate to enhance biomass degradation and improve the health effects of food and forage.