Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.

The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression. Binding of p300 and RNAPII are key features of these constituents. We determine two key parameters of enhancer activity in single cells: their penetrance in a population and their contribution to expression in these cells. Through combinatorial interrogation, we find that simultaneous repression of multiple weak constituents can alter super-enhancer activity in a manner greatly exceeding repression of individual constituents.

A single factor elicits multilineage reprogramming of astrocytes in the adult mouse striatum.

SignificanceOutside the neurogenic niches, the adult brain lacks multipotent progenitor cells. In this study, we performed a series of in vivo screens and reveal that a single factor can induce resident brain astrocytes to become induced neural progenitor cells (iNPCs), which then generate neurons, astrocytes, and oligodendrocytes. Such a conclusion is supported by single-cell RNA sequencing and multiple lineage-tracing experiments. Our discovery of iNPCs is fundamentally important for regenerative medicine since neural injuries or degeneration often lead to loss/dysfunction of all three neural lineages. Our findings also provide insights into cell plasticity in the adult mammalian brain, which has largely lost the regenerative capacity.

Whole genome resequencing reveal patterns of genetic variation within Colletotrichum acutatum species complex from rubber trees in China.

The Colletotrichum acutatum species complex possesses a diverse number of important traits, such as a wide host range and host preference, different modes of reproduction, and different strategies of host infection. Research using comparative genomics has attempted to find correlations between these traits. Here, we used multi-locus techniques and gene genealogical concordance analysis to investigate the phylogenetic relationships and taxonomic status of the Colletotrichum acutatum species complex using field isolates obtained from rubber trees. The results revealed that the dominant species was C. australisinense, followed by C. bannaense, while strain YNJH17109 was identified as C. laticiphilum. The taxonomic status of strains YNLC510 and YNLC511 was undetermined. Using whole-genome single nucleotide polymorphism data to analyze population structure, 18 strains of C. australisinense were subsequently divided into four populations, one of which was derived from an admixture of two populations. In addition, the strains LD1687, GD1628, and YNLC516, did not belong to any populations, and were considered to be admixtures of two or more populations. A split decomposition network analysis also provided evidence for genetic recombination within Colletotrichum acutatum species complex from rubber trees in China. Overall, a weak phylogeographic sub-structure was observed. Analysis also revealed significant differences in morphological characters and levels of virulence between populations.

A tunable perfect absorber based on a black phosphorus/bowtie shaped cavity hybrid metasurface.

The practical application of black phosphorus (BP) is limited by its low absorption characteristics. In this work, we propose a perfect absorber based on a BP and bowtie shaped cavity, which has high tunability and excellent optical performance. This absorber effectively increases the light-matter interaction and achieves perfect absorption by using a monolayer BP and a reflector to form a Fabry-Perot cavity. We study the influence of structural parameters on the absorption spectrum and realize the adjustment of frequency and absorption in a certain range. Applying an external electric field on the surface of BP by electrostatic gating, we can change its carrier concentration to control its optical properties. In addition, we can flexibly tune the absorption and Q-factor by varying the polarization direction of incident light. This absorber has promising applications in optical switches, sensing, and slow light, which provides a new perspective for the practical application of BP and a foundation for future research, offering possibilities for more applications.

Isolation and Identification of Secondary Metabolites Produced by Phytopathogenic Fungus Corynespora cassiicola from Hevea brasiliensis.

The secondary metabolites of the phytopathogenic fungus Corynespora cassiicola CC01 from Hevea brasiliensis were investigated. As a result, two new compounds, 5-acetyl-7-hydroxy-6- methoxybenzofuran-2(3H)-one (1) and (S)-2-(2,3-dihydrofuro [3,2-c]pyridin-2-yl)propan-2-ol (2), together with seven known compounds, 4,6,8-trihydroxy-3,4-dihydronaphthalen-1(2H)-one (3), 3,6,8-trihydroxy-3,4-dihydronaphthalen-1(2H)-one (4), curvulin acid (5), 2-methyl-5-carboxymethyl- 7-hydroxychromone (6), tyrosol (7), p-hydroxybenzoic acid (8) and cerevisterol (9), were isolated from the fermentation extract by comprehensive silica gel, reverse phase silica gel, Sephadex-LH20 column chromatography and high-performance liquid chromatography (HPLC). The structures of these compounds were identified by using high-resolution electrospray mass spectrometry (HRESIMS), nuclear magnetic resonance spectroscopy (NMR), optical rotation, ultraviolet and infrared spectroscopy techniques and a comparison of NMR data with those reported in the literature. Compounds 1 and 2 were new compounds, and compounds 3-9 were discovered from this phytopathogenic fungus for the first time. Compounds 1-9 were tested for phytotoxicity against the fresh tender leaf of Hevea brasiliensis, and the results show that none of them were phytotoxic. Additionally, these compounds were subjected to an antimicrobial assay against three bacteria (E. coli, methicillin-resistant Staphylococcus aureus and Micrococcus luteus), but they showed no activity.

First Report on Neopestalotiopsis aotearoa of Rubber Tree in China.

Natural rubber is an important industrial raw material and an economically important perennial in China. In recent years, A new leaf fall disease, caused by Neopestalotiopsis aotearoa Maharachch., K.D. Hyde & Crous, has occurred in Indonesia, Malaysia, Thailand, Sri Lanka, and other major rubber planting countries. In May and July of 2020, this disease was first found on 2-year-old rubber seedlings in two plantations located in Ledong and Baisha counties in Hainan Province, China. In the two plantations of approximately 32 ha, 15% of the rubber seedlings had the disease and the defoliation was more than 20%. The infected leaves turned yellow and watery, and dark brown and nearly round lesions of 1-2 mm in diameter were formed on the leaves. When the humidity was high, the center of the lesion was grey-white, and the lesions had many small black dots, black margins and surrounded by yellow halos. When the disease was severe, leaves fell off. To identify the pathogen, leaf tissues were collected from lesion margins after leaf samples were surface-sterilized in 75% ethanol, rinsed with sterile water for three times, and air dried. The leaf tissues were plated on potato dextrose agar (PDA) and incubated at 28°C for seven days. Fungal cultures with similar morphology were isolated from 90% of tested samples and two isolates (HNPeHNLD2001 and HNPeHNLD2002) were used in pathogenicity and molecular tests. Rubber leaves (clone PR107) were inoculated with conidial suspension (106 conidia/ml), and inoculated with PDA were used as the control, Each treatment had 3 leaves, and each leaf was inoculated with 3 spots and incubated at 28oC under high moisture conditions. Five days later, leaves inoculated with conidial suspension showed black leaf spots resembling the disease in the field, whereas the control leaves remained symptomless. The fungal cultures isolated from the inoculated tissues, had identical morphology compared with the initial isolates. Colonies on PDA were 55-60 mm in diameter after seven days at 28°C, with undulate edges, pale brown, thick mycelia on the surface with black, gregarious conidiomata; and the reverse side was similar in color. Black conidia were produced after eight days of culture on PDA. Conidia were fusoid, ellipsoid, straight to slightly curved, 4-septate, ranged from 18.35 to 27.12 µm (mean 22.34 µm) × 4.11 to 7.03 µm (mean 5.41 µm). The basal cells were conic with a truncate base, hyaline, rugose and thin-walled, 4.35 to 6.33 µm long (mean 4.72 µm). Three median cells were doliform, 12.53 to 18.97 µm long (mean 15.26 µm), hyaline, cylindrical to subcylindrical, thin- and smooth-walled, with 2-3 tubular apical appendages, arising from the apical crest, unbranched, filiform, 14.7 to 25.3 µm long (mean 19.94 µm). The basal appendages were singlar, tubular, unbranched, centric, 3.13 to 7.13 µm long (mean 5.48 µm). Morphological characteristics of the isolates were similar to the descriptions of N. aotearoa (Maharachchikumbura et al. 2014). The rDNA internal transcribed spacer (ITS) region, translation elongation factor 1-αgenes (TEF), and beta-tubulin (TUB2) gene were amplified using the primer pairs ITS1/ITS4, EF1-728F/EF1-986R and T1/Bt-2b (Pornsuriya et al. 2020), respectively. The sequences of these genes were deposited in GenBank (ITS Accession Nos.: MT764947 and MT764948; TUB2: MT796262 and MT796263; TEF: MT800516 and MT800517). According to the latest classification of Neoprostalotiopsis spp. (Maharachchikumbura et al. 2014) and multilocus phylogeny, isolates HNPeHNLD2001 and HNPeHNLD2002 were clustered in the same branch with N. aotearoa. Thus, the pathogen was identified as N. aotearoa, which is different from N. cubana and N. formicarum reported in Thailand (Pornsuriya et al. 2020; Thaochan et al. 2020). The Neopestalotiopsis leaf spotdisease of rubber tree (H. brasiliensis) was one of the most serious and destructive leaf diseases in major rubber planting countries in Asia. ( Tajuddin et al. 2020) The present study of leaf fall disease on rubber tree caused byN. aotearoa is the first report in China. The finding provides the basic pathogen information for further monitoring the disease and its control.

Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae.

BACKGROUND: Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of S. brachiariae and compared it with the genome of S. oryzae to identify differences between a Sarocladium plant pathogen and an endophyte. RESULTS: In this study, we reported a gapless genome sequence of a newly identified endophytic fungus Sarocladium brachiariae isolated from Brachiaria brizantha. The genome of S. brachiariae is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of S. brachiariae and its closest species was identified as S. oryzae. Comparative genomics analysis revealed that S. brachiaria has 14.9% more plant cell wall degradation related CAZymes to S. oryzae, and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of S. brachiaria. Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in S. oryzae. However, S. brachiaria had seven fewer terpene gene clusters, including helvolic acid BGC, compared with S. oryzae and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the S. brachiariae could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity. CONCLUSIONS: The data provided a better understanding of the Sarocladium brachiariae genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.

Facile synthesis of Fe3O4@Au core-shell nanocomposite as a recyclable magnetic surface enhanced Raman scattering substrate for thiram detection.

The Fe3O4@Au core-shell nanocomposites, as the multifunctional magnetic surface enhanced Raman scattering (SERS) substrates, were fabricated successfully by the seeds growth method based on the Fe3O4-Au core-satellite nanocomposites. The SERS properties of the Fe3O4-Au core-satellite nanocomposites and the Fe3O4@Au core-shell nanocomposites were compared using 4-aminothiophenol (4-ATP) as the probe molecule. It was found that Fe3O4@Au core-shell nanocomposites showed better SERS performance than Fe3O4-Au core-satellite nanocomposites. The Au shell provided an effectively large surface area for forming sufficient plasmonic hot spots and capturing target molecules. The integration of magnetic core and plasmonic Au nanocrystals endowed the Fe3O4@Au core-shell nanocomposites with highly efficient magnetic separation and enrichment ability and abundant interparticle hot spots. The Fe3O4@Au core-shell nanocomposites could be easily recycled because of the intrinsic magnetism of the Fe3O4 cores and had good reproducibility of the SERS signals. For practical application, the Fe3O4@Au core-shell nanocomposites were also used to detect thiram. There was a good linear relationship between the SERS signal intensity and the concentration of thiram from 1 × 10-3 to 1 × 10-8 M and the limit of detection was 7.69 × 10-9 M. Moreover, residual thiram on apple peel was extracted and detected with a recovery rate range of 99.3%. The resulting substrate with high SERS activity, stability and strong magnetic responsivity makes the Fe3O4@Au core-shell nanocomposites a perfect choice for practical SERS detection applications.

The WRKY Transcription Factor WRKY71/EXB1 Controls Shoot Branching by Transcriptionally Regulating RAX Genes in Arabidopsis.

Plant shoot branching is pivotal for developmental plasticity and crop yield. The formation of branch meristems is regulated by several key transcription factors including REGULATOR OF AXILLARY MERISTEMS1 (RAX1), RAX2, and RAX3. However, the regulatory network of shoot branching is still largely unknown. Here, we report the identification of EXCESSIVE BRANCHES1 (EXB1), which affects axillary meristem (AM) initiation and bud activity. Overexpression of EXB1 in the gain-of-function mutant exb1-D leads to severe bushy and dwarf phenotypes, which result from excessive AM initiation and elevated bud activities. EXB1 encodes the WRKY transcription factor WRKY71, which has demonstrated transactivation activities. Disruption of WRKY71/EXB1 by chimeric repressor silencing technology leads to fewer branches, indicating that EXB1 plays important roles in the control of shoot branching. We demonstrate that EXB1 controls AM initiation by positively regulating the transcription of RAX1, RAX2, and RAX3. Disruption of the RAX genes partially rescues the branching phenotype caused by EXB1 overexpression. We further show that EXB1 also regulates auxin homeostasis in control of shoot branching. Our data demonstrate that EXB1 plays pivotal roles in shoot branching by regulating both transcription of RAX genes and auxin pathways.

Theoretical analysis of ultrahigh figure of merit sensing in plasmonic waveguides with a multimode stub.

We propose an expanded coupled mode theory to analyze sensing performance in a plasmonic slot waveguide side-coupled with a multimode stub resonator. It is confirmed by the finite-difference time-domain simulations. Through adjusting the parameters, we can realize figure of merit (FOM) of ∼59,010, and the sensitivity S can reach to 75.7. Compared with the plasmonic waveguide systems in recent Letters, our proposed structure has the advantages of easy fabrication, compactness, sensitivity, and high FOM. The proposed theory model and findings provide guidance for fundamental research of the integrated plasmonic nanosensor applications.

Theoretical analysis and applications in inverse T-shape structure.

An inverse T-shape structure, consisting of a bus waveguide coupled with two perpendicular rectangular cavities, has been investigated numerically and theoretically. The position of the transparency window can be manipulated by adjusting the lateral displacement between the two perpendicular cavities. The effects of changing different structural parameters on the transmission features are investigated in detail. The results indicate that the length of two cavities play important roles in optimizing optical response. Finally, two simple applications based on the inverse T-shape structure are briefly discussed. The findings demonstrate that the first- and second-order modes can be separated without interference, and the sensitivity of the inverse T-shape is as high as 1750 nm per refractive index unit (RIU); the corresponding figure of merit (FOM) reaches up to 77.1 RIU-1, which is higher than in previous reports. The plasmonic configuration possesses the advantages of easy fabrication, compactness, and higher sensitivity as well as higher FOM, which will greatly benefit the compact plasmonic filter and high-sensitivity nanosensor in highly integrated optical devices.

Sensing analysis based on plasmon induced transparency in nanocavity-coupled waveguide.

We report the sensing characteristic based on plasmon induced transparency in nanocavity-coupled metal-dielectric-metal waveguide analytically and numerically. A simple model for the sensing nature is first presented by the coupled mode theory. We show that the coupling strength and the resonance detuning play important roles in optimizing the sensing performance and the detection limit of sensor, and an interesting double-peak sensing is also obtained in such plasmonic sensor. In addition, the specific refractive index width of the dielectric environment is discovered in slow-light sensing and the relevant sensitivity can be enhanced. The proposed model and findings provide guidance for fundamental research of the integrated plasmonic nanosensor applications and designs.

Plasmon-induced transparency in a single multimode stub resonator.

We investigate electromagnetically induced transparency (EIT)-like effect in a metal-dielectric-metal (MDM) waveguide coupled to a single multimode stub resonator. Adjusting the geometrical parameters of the stub resonator, we can realize single or double plasmon-induced transparency (PIT) windows in the plasmonic structure. Moreover, the consistency between analytical results and finite difference time domain (FDTD) simulations reveals that the PIT results from the destructive interference between resonance modes in the stub resonator. Compared with previous EIT-like scheme based on MDM waveguide, the plasmonic system takes the advantages of easy fabrication and compactness. The results may open up avenues for the control of light in highly integrated optical circuits.

Integrated photonic reservoir computing based on hierarchical time-multiplexing structure.

An integrated photonic reservoir computing (RC) based on hierarchical time-multiplexing structure is proposed by numerical simulations. A micro-ring array (MRA) is employed as a typical time delay implementation of RC. At the output port of the MRA, a secondary time-multiplexing is achieved by multi-mode interference (MMI) splitter and delay line array. This hierarchical time-multiplexing structure can ensure a large reservoir size with fast processing speed. Simulation results indicate that the proposed RC system yields better performance than previously reported ones. The achieved normalized mean square error between the system output and target sequence are 0.5% and 2.7% for signal classification and chaotic time series prediction, respectively, while the sample rate is as high as 1.3 Gbps.

Combined theoretical analysis for plasmon-induced transparency in waveguide systems.

We propose a novel combination of a radiation field model and the transfer matrix method (TMM) to demonstrate plasmon-induced transparency (PIT) in bright-dark mode waveguide structures. This radiation field model is more effective and convenient for describing direct coupling in bright-dark mode resonators, and is promoted to describe transmission spectra and scattering parameters quantitatively in infinite element structures by combining it with the TMM. We verify the correctness of this novel combined method through numerical simulation of the metal-dielectric-metal (MDM) waveguide side-coupled with typical bright-dark mode, H-shaped resonators; the large group index can be achieved in these periodic H-shaped resonators. These results may provide a guideline for the control of light in highly integrated optical circuits.

Theoretical analysis and applications on nano-block loaded rectangular ring.

We propose compact and switchable optical filters based on nano-block loaded rectangular rings, and investigate the selection property numerically and theoretically. A simple and convenient phase model is established for the theoretical analysis. The dependent factors, such as the number, size, and positions of the loaded blocks, are discussed in detail. It is found that a longer wavelength can be obtained without increasing the device dimension, and the selected wave is more sensitive to the length of the loaded blocks. The loading positions play key roles in the realization of separating the second-order modes. Finally, applications of this proposed structure are discussed simply. We find that the loaded filter device provides a more compact size than the unloaded one for the same properties, and a tunable plasmon induced transparency based switch effect is also achieved. These findings suggest potential applications in compact filters, tunable slow light devices, and sensor fields.

Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm.

Comprehensive cis-regulatory landscapes are essential for accurate enhancer prediction and disease variant mapping. Although cis-regulatory element (CRE) resources exist for most tissues and organs, many rare - yet functionally important - cell types remain overlooked. Despite representing only a small fraction of the heart's cellular biomass, the cardiac conduction system (CCS) unfailingly coordinates every life-sustaining heartbeat. To globally profile the mouse CCS cis-regulatory landscape, we genetically tagged CCS component-specific nuclei for comprehensive assay for transposase-accessible chromatin-sequencing (ATAC-Seq) analysis. Thus, we established a global CCS-enriched CRE database, referred to as CCS-ATAC, as a key resource for studying CCS-wide and component-specific regulatory functions. Using transcription factor (TF) motifs to construct CCS component-specific gene regulatory networks (GRNs), we identified and independently confirmed several specific TF sub-networks. Highlighting the functional importance of CCS-ATAC, we also validated numerous CCS-enriched enhancer elements and suggested gene targets based on CCS single-cell RNA-Seq data. Furthermore, we leveraged CCS-ATAC to improve annotation of existing human variants related to cardiac rhythm and nominated a potential enhancer-target pair that was dysregulated by a specific SNP. Collectively, our results established a CCS-regulatory compendium, identified novel CCS enhancer elements, and illuminated potential functional associations between human genomic variants and CCS component-specific CREs.

Characterization and necrosis-inducing activity of necrosis- and ethylene-inducing peptide 1-like proteins from Colletotrichum australisinense, the causative agent of rubber tree anthracnose.

Colletotrichum australisinense, a member of the Colletotrichum acutatum species complex, is an important pathogen causing rubber tree anthracnose. Genome-wide comparative analysis showed this species complex contains more genes encoding necrosis- and ethylene-inducing peptide 1-like proteins (NLPs) than other Colletotrichum species complexes, but little is known about their necrosis-inducing roles in host. The aim of this study was to analyze NLPs number and type in C. australisinense, and characterize their necrosis-inducing activity in host or non-host. According to phylogenetic relationship, conserved the cysteine residues and the heptapeptide motif (GHRHDWE), 11 NLPs were identified and classified into three types. Five of the eleven NLPs were evaluated for necrosis-inducing activity. CaNLP4 (type 1) could not induce necrosis in host or non-host plants. By contrast, both CaNLP5 and CaNLP9 (type 1) induced necrosis in host and non-host plants, and necrosis-inducing activity was strongest for CaNLP9. CaNLP10 (type 2) and CaNLP11 (type 3) induced necrosis in host but not non-host plants. Substitution of key amino acid residues essential for necrosis induction activity led to loss of CaNLP4 activity. Structural characterization of CaNLP5 and CaNLP9 may explain differences in necrosis-inducing activity. We evaluated the expression of genes coding CaNLP by reverse transcription polymerase chain reaction (RT-PCR) and quantitative real-time PCR (qRT-PCR) at different time-points after pathogen infection. It was found that genes encoding CaNLPs with different activities exhibited significantly different expression patterns. The results demonstrate that CaNLPs are functionally and spatially distinct, and may play different but important roles in C. australisinense pathogenesis.

Single-Cell Genomics: Catalyst for Cell Fate Engineering.

As we near a complete catalog of mammalian cell types, the capability to engineer specific cell types on demand would transform biomedical research and regenerative medicine. However, the current pace of discovering new cell types far outstrips our ability to engineer them. One attractive strategy for cellular engineering is direct reprogramming, where induction of specific transcription factor (TF) cocktails orchestrates cell state transitions. Here, we review the foundational studies of TF-mediated reprogramming in the context of a general framework for cell fate engineering, which consists of: discovering new reprogramming cocktails, assessing engineered cells, and revealing molecular mechanisms. Traditional bulk reprogramming methods established a strong foundation for TF-mediated reprogramming, but were limited by their small scale and difficulty resolving cellular heterogeneity. Recently, single-cell technologies have overcome these challenges to rapidly accelerate progress in cell fate engineering. In the next decade, we anticipate that these tools will enable unprecedented control of cell state.

Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease.

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.