Journal of Genetics and Genomics

Drosophila has long been a successful model organism in multiple fields such as genetics and developmental biology. Drosophila genome is relatively smaller and less redundant, yet largely conserved with mammals, making it a productive model in studies of embryogenesis, cell signaling, disease mechanisms, etc. Spatial gene expression pattern is critical for understanding of complex signaling pathways and cell-cell interactions, whereas temporal gene expression changes need to be tracked during highly dynamic activities such as tissue development and disease progression. Systematic studies in Drosophila as a whole are still impeded by lack of these spatiotemporal transcriptomic information. Drosophila embryos and tissues are of relatively small size, limiting the application of current technologies to comprehensively resolve their spatiotemporal gene expression patterns. Here, utilizing SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq), we dissected the spatiotemporal transcriptomic changes of developing Drosophila with high resolution and sensitivity. Our data recapitulated the spatial transcriptomes of embryonic and larval development in Drosophila. With these data, we identified known and previously undetected subregions in several tissues during development, and revealed known and potential gene regulatory networks of transcription factors within their topographic background. We further demonstrated that Stereo-seq data can be used for 3D reconstruction of Drosophila embryo spatial transcriptomes. Our data provides Drosophila research community with useful resources of spatiotemporally resolved transcriptomic information across developmental stages.

Mapping genotype to phenotype is an essential topic in genetics and genomics research. As the Omics data become increasingly available, genome-wide association study (GWAS) has been widely applied to establish the relationship between genotype and phenotype. However, signals detected by GWAS usually span broad genomic regions with many underneath candidate genes, making it challenging to interpret and validate the molecular functions of the candidate genes. Under the context of genetics research, we hypothesized a causal chain from genotype to phenotype partially mediated by intermediate molecular processes, i.e., gene expression. To test this hypothesis, we applied the high dimensional mediation analysis, a class of causal inference method with an assumed causal chain from the exposure to the mediator to the outcome, and implemented it to the maize diversity panel (N=280 lines). Using 40 publicly available agronomic traits, 66 newly generated metabolic traits, and published RNA-seq data from seven different tissues, we detected N=736 unique mediating genes, explaining an average of 12.7% phenotypic variance due to mediation. Noticeably, 83/736 (11%) genes were identified in mediating more than one trait, suggesting the prevalence of pleiotropic mediating effects. Among those pleiotropic mediators, benzox-azinone synthesis 13 (Bx13), a well-characterized gene encoding a 2-oxoglutarate-dependent dioxygenase, was identified mediating 40 agronomic and metabolic traits in different tissues. Further genetic and genomic analyses of the Bx13 and adjacent mediating genes suggested a 3D co-regulation modulation likely affect their expression levels and eventually lead to phenotypic consequences. Our results suggested the genome-wide mediation analysis is a powerful tool to integrate Omics data in providing causal inference to connect genotype to phenotype.

Since Omicron variant of SARS-CoV-2 was first detected in South Africa (SA), it has now dominated in United Kingdom (UK) of Europe and United State (USA) of North America. A prominent feature of this variant is the gathering of spike protein mutations, in particularly at the receptor binding domain (RBD). These RBD mutations essentially contribute to antibody resistance of current immune approaches. During global spillover, combinations of RBD mutations may exist and synergistically contribute to antibody resistance in fact. Using three geographic-stratified genome wide association studies (GWAS), we observed that RBD combinations exhibited a geographic pattern and genetical associated, such as five common mutations in both UK and USA Omicron, six or two specific mutations in UK or USA Omicron. Although the UK specific RBD mutations can be further classified into two separated sub-groups of combination based on linkage disequilibrium analysis. Functional analysis indicated that the common RBD combinations (fold change, -11.59) alongside UK or USA specific mutations significantly reduced neutralization (fold change, -38.72, -18.11). As RBD overlaps with angiotensin converting enzyme 2(ACE2) binding motif, protein-protein contact analysis indicated that the common RBD mutations enhanced ACE2 binding accessibility and were further strengthened by UK or USA-specific RBD mutations. Spatiotemporal evolution analysis indicated that UK-specific RBD mutations largely contribute to global spillover. Collectively, we have provided genetic evidence of RBD combinations and estimated their effects on antibody evasion and ACE2 binding accessibility.

Legumes have evolved a unique manner of seed dispersal in that the seed pods explosively split open with helical tension generated by sclerenchyma on the endocarp. During domestication, azuki bean (Vigna angularis) and yard-long bean (Vigna unguiculata cv-gr. Sesquipedalis) have reduced or lost the sclerenchyma and lost the shattering behavior of seed pods. Here we performed fine-mapping with back-crossed populations and narrowed the candidate genomic region down to 4 kbp in azuki bean and 13 kbp in yard-long bean. Among genes located in these regions, we found MYB26 genes encoded truncated proteins in both the domesticated species. We also found in azuki bean and other legumes that MYB26 is duplicated and only the duplicated copy is expressed in seed pods. Interestingly, in Arabidopsis MYB26 is single copy and is specifically expressed in anther to initiate secondary wall thickening that is required for anther dehiscence. These facts indicated that, in legumes, MYB26 has been duplicated and acquired a new role in development of pod sclerenchyma. However, pod shattering is unfavorable phenotype for harvesting and thus has been selected against by human.

Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine ({Psi}), are critical regulators of plant development, stress responses, and environmental adaptation. The modifications m6A, m5C, and {Psi} were insufficiently studied in plant stress responses. To investigate the epitranscriptomic landscape of these modifications, we employed direct RNA sequencing (DRS) to analyze native RNA from the amphibious plant Riccia fluitans grown in both aquatic and terrestrial environments. Our study revealed the presence of {Psi}, m5C, and m6A modifications in R. fluitans transcriptomes from diverse environments. We observed correlations between the occurrence of these modifications and transcript length, as well as poly(A) tail length. Furthermore, we analyzed the expression of genes encoding {Psi} synthases and methyltransferases to gain initial insights into the regulatory mechanisms underlying these processes in R. fluitans. By understanding how RNA modifications are regulated in response to environmental changes, we can unlock the secrets of the remarkable adaptability of amphibious plants. This knowledge could have eventually led to the understanding of the mechanisms of plant land colonization.

The bam mutant ovary of Drosophila represents a classic tumor model caused by germline stem cell (GSC) differentiation defects. To date, its molecular and genetic features have rarely been characterized in detail at the single-cell resolution. Here, we performed single-cell RNA sequencing (scRNA-seq) to comprehensively delineate the transcriptomic landscape and identify distinct germline cell types in bam mutant ovaries by using in situ hybridization. Differentially expressed gene analysis and PAGA plots reveal different transcriptional profiles and developmental relationships in ovarian cells. Based on the expression pattern of eggpl, a useful marker for undifferentiated germ cell identity, and morphological differences in bam mutant ovarioles, two potentially distinct germ cell states are distinguished. Comparative single-cell analysis reveals the potential regulatory network and cellular communication in subclusters of undifferentiated germ cells, and contributes to the identification of gcrf1 as a novel marker gene for female GSC, which involves in the regulation of early germ cell proliferation and Drosophila fertility. Collectively, our study not only provides insights into tumorigenesis caused by GSC differentiation defects but also offers a valuable transcriptomic resource that can be mined for the reproductive features of bam mutant tumors by community.

Trisomy 18, commonly known as Edwards syndrome, is the second most common autosomal trisomy among live born neonates. Multiple tissues including cardiac, abdominal, and nervous systems are affected by an extra chromosome 18. To delineate the complexity of anomalies of trisomy 18, we analyzed amniotic fluid cells from two normal and three trisomy 18 samples using single-cell transcriptomics. We identified six cell groups, which function in major tissue development such as kidney, vasculature, and smooth muscle, and display significant alterations in gene expression detected by single-cell RNA-sequencing. Moreover, we demonstrated significant gene expression changes in previously proposed trisomy 18 critical regions, and identified three new regions such as 18p11.32, 18q11, 18q21.32, which are likely associated with trisomy 18 phenotypes. Our results indicate complexity of trisomy 18 at the gene expression level and reveal genetic reasoning of diverse phenotypes in trisomy 18 patients.

Craniofacial malformation (CFM) is a congenital defect encompassing a wide range of phenotypic presentations and is largely driven by genetics. Despite the discovery of more than 300 causal genes, there are a myriad of CFM cases with unknown genetic etiology. The complex gene regulations and heterogeneous cellular interactions in the developing head complicate disease-gene identification and prenatal genetic diagnosis. Recent progress in multiomic profiling of human embryogenesis enables the discovery of novel candidates from established GWAS data. Here, we developed an approach to prioritize GWAS variants using the epigenomes and single-cell transcriptomes of embryonic tissues and progenitor cells by implementing machine learning classifiers and combinatorial analysis. Systematic evaluation revealed significant improvement in the machine learning model performance after integrating transcriptome of neural crest cells (NCCs) and cranial placodes, as well as epigenomic profile of early craniofacial tissues. We identified 249 genes from the best-performing classifier, which include documented CFM-associated genes. Gene regulatory network (GRN) inference showed that 24 candidate genes were involved in NCC- and placode-specific regulons, of which 15 (F11R, ISL1, KANK4, L1TD1, LAMB1, MIA, PRDM1, S100A10, S100A11, STOM, STT3B, TESK2, USP43, WDR86, ZNF439) were novel candidates for human CFM. Motif analysis revealed putative functional SNPs contributing to CFM pathogenesis by disrupting transcription factor binding motifs in neural crest and placodes. Our analyses suggested that PRDM1 and ISL1 are strong candidates for human CFM, as supported by other animal functional studies. This study demonstrates a successful method for disease gene identification using epigenomic and single-cell transcriptomic profiles, and sheds light on the linkage between early cell lineages and the pathogenic process of CFM. Author SummaryCraniofacial malformation is one of the most common congenital disorders that affects food ingestion, speech and social interaction of the patients. The identification of craniofacial disease genes is difficult due to the dynamic gene expression and contribution from multiple cell types during embryonic development. In this study, we combine artificial intelligence with patient genetic and embryo multiomic information to identify new candidate genes for human craniofacial malformation. Using machine learning classifiers and combinatorial analyses, we prioritized single-nucleotide variants from patient datasets and identified 249 candidate genes. Annotation of the variants and candidate genes showed that some of them overlapped with known disease genes, demonstrating the efficacy of our approach. Further analyses using lineage reconstruction and motif analyses revealed a number of promising novel candidates, in particular PRDM1 and ISL1, are likely to be causative genes for human CFM. Our study has demonstrated a translatable approach for disease gene identification utilizing machine learning algorithm and multiomic data, and provides a gene list for improving diagnostic panels and understanding the pathogenic processes of craniofacial disorders.

Leaf angle is one of the key factors determining rice plant architecture. However, improvement of the leaf angle appears to be unsuccessful in practical breeding because of the simultaneous occurrence of unfavorable traits such as grain size reduction. In this study, we identified the pow1 (put on weight 1) mutant with enlarged grain size and leaf angle, typical brassinosteroid (BR)-related phenotypes caused by excessive cell proliferation and cell expansion. We show that POW1 encodes a novel protein functioning in grain size regulation by repressing the transcription activity of the interacting protein TAF2, a highly conserved member of the transcription initiation complex TFIID. Loss of function of POW1 increases the phosphorylation of OsBZR1 and decreases the inhibitory effect of OsBZR1 on the transcription of BR biosynthesis genes OsDWARF4 (D4) and D11, thus participates in BR-mediated leaf angle regulation. The separable functions of POW1 in grain size and leaf angle control provide a promising strategy to design high-yielding varieties in which both traits would be favorably developed, i.e., compact plant architecture and increased grain size, thus would promote the high-yield breeding a step forward in rice.

Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Telling apart the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression level dominance, transgressive expression, and homoeolog expression bias. We found that selfing syndrome, high pollen and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, transgressive expression and most down-regulated expression-level dominance were only found in natural allopolyploids. Natural allotetraploids also had more expression-level dominance toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of expression-level dominance in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of homoeolog expression bias among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

The early stages of embryonic development rely on maternal products for proper regulation. However, systematic screening for functional maternal-specific factors has been challenging due to the time- and labor-intensive nature of traditional approaches. Here, we combined a computational pipeline and F0 homozygous mutation technology to screen for functional maternal-specific chromatin regulators in zebrafish embryogenesis and identified Mcm3l, Mcm6l, and Npm2a as playing essential roles in DNA replication and cell division. Our results contribute to understanding the molecular mechanisms underlying early embryo development and highlight the importance of maternal-specific chromatin regulators in this critical stage.

Processing bodies (P-bodies) are the membraneless organelles that play critical roles in RNA storage and decay. Abnormalities in P-bodies contribute to diseases and developmental disorders. Huge efforts have been applied to the identification of the protein components in P-bodies, however, the dynamics of RNA components of P-bodies in human embryonic stem cells (hESCs) during maintenance and differentiation remain largely elusive. Here, we characterized the RNA profiles of P-bodies from HEK293T cells, hESCs, and hESC-derived mesodermal cells. The number of P-bodies decreases upon hESC differentiation towards mesodermal fate, accompanied with the decreased RNAs within P-bodies. By functional analysis of the P-body enriched and P-body depleted genes across different cell types, we discovered the cell type-specific enrichment of P-body-genes and the potential association with human diseases. We also captured the non-coding RNAs, including long intergenic non-coding RNAs and transposable elements in P-bodies in a cell type-specific manner. Furthermore, we verified the involvement P-bodies in regulating the differentiation of hESCs towards mesoderm by over-expression of LSM14A and knocking down of SPTAN1. In summary, we characterized the mRNAs and non-coding RNAs in P-bodies of hESCs and hESC-derived mesodermal cells, discovering the potential roles that P-bodies play for the precise differentiation of hESCs.

Ribonucleotide reductase (RNR), functioning in the de novo synthesis of dNTPs, is crucial for DNA replication and cell cycle progression. However, the knowledge about the RNR in plants is still limited. In this study, we isolated ylc1 (young leaf chlorosis 1) mutant, which exhibited many development defects such as dwarf stature, chlorotic young leaf, and smaller fruits. Map-based cloning, complementation, and knocking-out experiments confirmed that YLC1 encodes a large subunit of RNR (SlRNRL1), an enzyme involved in the de novo biosynthesis of dNTPs. Physiological and transcriptomic analyses indicate that SlRNRL1 plays a crucial role in the regulation of cell cycle, chloroplast biogenesis, and photosynthesis in tomato. In addition, we knocked out SlRNRL2 (a SlRNRL1 homolog) using CRISPR-Cas9 technology in the tomato genome, and found that SlRNRL2, possessing a redundant function with SlRNRL1, played a weak role in the formation of RNR complex due to its low expression intensity. Genetic analysis reveals that SlRNRL1 and SlRNRL2 are essential for tomato growth and development as the double mutant slrnrl1slrnrl2 is lethal. This also implies that the de novo synthesis of dNTPs is required for seed development in tomato. Overall, our results provide a new insight for understanding the SlRNRL1 and SlRNRL2 functions and the mechanism of de novo biosynthesis of dNTPs in plants.

Postzygotic mutations are acquired in all of the normal tissues throughout an individuals lifetime and hold clues for identifying mutagenesis causing factors. The process and underlying mechanism of postzygotic mutations in normal tissues is still poorly understood. In this study, we investigated postzygotic mutation spectra in healthy individuals by optimized ultra-deep exome sequencing of time series samples from the same volunteer and samples from different individuals. In cells of blood, sperm, and muscle, we resolved three common types of mutational signature. Two of them are known to represent clock-like mutational processes, and their proportions in mutation profiles associated with polymorphisms of epigenetic regulation genes, suggesting the contribution of personal genetic backgrounds to underlying biological process. Notably, the third signature, characterized by C>T transitions at GpCpN sites, tends to be a feature of diverse normal tissues. Mutations of this type were likely to occur early in embryo development even before the tissue differentiation, as indicated by their relatively high allele frequencies, sharing variants between multiple tissues, and lacking of age-related accumulation. Almost all tumors shown in public datasets did not have this signature detected except for 19.6% of clear cell renal cell carcinoma samples, which featured by activation of the hypoxia-induced signaling pathway. Moreover, in vitro activation of HIF signaling pathway successfully introduced the corresponding mutation profile of this signature in a culture-expanded human embryonic stem cell line. Therefore, embryonic hypoxia may explain this novel signature across multiple normal tissues. Our study suggest hypoxic conditions in the early stage of embryo development may be a crucial factor for the C>T transitions at GpCpN sites and individual genetic background also related to shaping human postzygotic mutation profiles.

Using bioinformatic pipelines and Bayseian phylogenetic analyses, we characterized a SARS-CoV-2 variant designated by the World Health Organization as a variant under monitoring in August 2023. Here we analyze the genomes of this SARS-CoV-2 variant, BA.2.86, deposited into GISAID within the two weeks of its emergence (2023-08-14 first submission to 2023-08-31), including the first BA.2.86 genome reported from a traveler originating from Japan. We present bioinformatics methods using publicly available tools to help analysts identify the lineage-defining 12 nucleotide insertion (S:Ins16MPLF), which is often masked by most bioinformatics pipelines. We also applied maximum-likelihood and Bayesian phylogenetics to demonstrate the high mutational rate of the tree branch leading to the emergence of BA.2.86, hinting at possible origins, and predict that BA.2.86 emerged around May 2023 and spread globally rapidly. Taken together, these results provide a framework for more rigorous bioinformatics approaches for teams performing genomic surveillance on viral respiratory pathogens.

O_LIACTIN DEPOLYMERIZING FACTORS (ADFs) are key regulators of actin cytoskeletal dynamics and plant immunity. C_LIO_LIWe predicted the potential immune-associated function of 38 genes from Arabidopsis using gene expression values from 24,123 RNA-Seq datasets and 34 single-cell datasets through machine learning algorithms. C_LIO_LIThe evolutionary relationships of ADF family members from 38 eukaryotic species were evaluated, including an assessment of the sub-function(s) of these members. C_LIO_LIOur results show that the ADF clade in plant and other kingdoms are separated, with ADF3, 5, 7, 9, and 10 possessing collinear relationships within species, and ADF 2,3,4,6,7, and 10 possessing evolved, new, sub-functions related to response to Fe, copper-deficiency, and ABA signaling in Arabidopsis. Expanded, multiple, roles for ADF1,4, and 6 were also identified. C_LIO_LIThis study not only provides an analysis of the expanded role for the ADF family of genes/proteins, but also provides insight into, and a framework for, the identification and study of the evolutionary history of genes having putative roles in immune signaling. C_LI

Lycophytes and euphyllophytes (ferns and seed plants) are the two surviving lineages of vascular plants. The modern lycophytes (clubmosses) are herbaceous found either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). The contrasting genome size between homosporous and heterosporous plants has long been an attractive topic. Most clubmosses are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimers disease, but the evolutionary trajectory of which in land plants is unexplored. To better understand these fundamental questions, the genome data of a homosporous lycophyte is urgently required. We generated the Lycopodium clavatum L. genome by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is LTR. Two whole genome duplications (WGDs) are rigorously detected. The content of LTR-RTs was more than ten times higher in homosporous lycophytes than heterosporous ones, although most appeared within one Mya. Then, we find that the LTR-RTs birth-death mode (a much greater birth and extremely slower death) contributes the accumulation of LTR-RTs resulting homosporous lycophyte genome expansion, while in heterosporous lycophytes, the mode is exactly the opposite. Furthermore, the five necessary enzymes of the HupA biosynthetic pathway were identified in the L. clavatum genome, but absent in the other land plants. This decoded genome data will be a key cornerstone to elucidating the fundamental aspects of lycophyte biology and land plant evolution.

Selaginellaceae exhibit extraordinary evolutionary history in which they survived and thrived during the Permian-Triassic extinction and did not undergo polyploidization. Here, we reconstructed the phylogenetic relationships of Selaginellaceae by applying large-scale nuclear genes from RNA-seq, and found that each group showed phylogenetic incongruences among single-gene trees with different frequencies. In particular, three different phylogenetic positions of the sanguinolenta group were recovered by different nuclear gene sets. We evaluated the factors that might lead to the phylogenetic incongruence of the sanguinolenta group and concluded that hybridization between each ancestor of two superclades is the most likely cause. We presented the supporting evidence from gene flow test, species network inference, and plastome-based phylogeny. Furthermore, morphological characters and chromosomal evidence also lend support to the hybrid origin of this group. The divergence time estimations, using two gene sets respectively, indicated the splits between the sanguinolenta group and each related superclade happened around the same period, implying that the hybridization event probably occurred during the Early Triassic. This study reveals an ancient allopolyploidization with integrative evidence and robust analyses, which sheds new light on the recalcitrant phylogenetic problem of the sanguinolenta group and reports the polyploidization in the basal vascular plants, Selaginellaceae.

Callose is a plant cell wall polymer in the form of {beta}-1,3-glucan, which regulates symplasmic channel size at plasmodesmata (PD). It plays a crucial role in a variety of processes in plants through the regulation of intercelluar symplasmic continuity. However, how to maintain callose homeostasis at PD in the molecular levels is poorly understood. To further elucidate the mechanism of PD callose homeostasis, we screened and identified an Arabidopsis mutant plant that exhibited excessive callose deposition at PD. Based on the Next-generation sequencing (NGS)-based mapping, other mutant allele analysis, and complementation assay, the mutated gene was shown to be 1-COP, which encodes a member of the COPI coatomer complex comprised of , {beta}, {beta}', {gamma}, {delta}, {varepsilon}, and {zeta} subunits. Since there is no report on the link between COPI and callose/PD, it was extremely curious to know the roles of 1-COP or COPI in PD regulation through callose deposition. Here, we report that loss-of-function of 1-COP directly elevates the callose accumulation at PD by affecting subcellular protein localization of callose degradation enzyme PdBG2. This process is linked to ERH1, an inositol phosphoryl ceramide synthase (IPCS), and glucosylceramide synthase (GCS) functions through physical interactions with the 1-COP protein. In addition, the loss-of-function of 1-COP also alters the subcellular localization of ERH1 and GCS proteins, results in a reduction of GlcCers and GlcHCers molecules, which are the key SL species for lipid raft formation. According to our findings, we propose that 1-COP protein, together with the SL modifiers controlling lipid raft compositions, regulates the function of GPI-anchored PD proteins and hence the callose turnover at PD and symplastic movement of biomolecules. Our findings provide the first key clue to link the COPI-mediated intracellular trafficking pathway to the callose-mediated intercellular signaling pathway through PD. One-sentence summaryPlant-specific coatomer protein functions as a negative regulator of callose accumulation by regulating the translocation of sphingolipid enzymes.