EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data.

SUMMARY: Recent technical advancements in single-cell chromatin accessibility sequencing (scCAS) have brought new insights to the characterization of epigenetic heterogeneity. As single-cell genomics experiments scale up to hundreds of thousands of cells, the demand for computational resources for downstream analysis grows intractably large and exceeds the capabilities of most researchers. Here, we propose EpiCarousel, a tailored Python package based on lazy loading, parallel processing, and community detection for memory- and time-efficient identification of metacells, i.e. the emergence of homogenous cells, in large-scale scCAS data. Through comprehensive experiments on five datasets of various protocols, sample sizes, dimensions, number of cell types, and degrees of cell-type imbalance, EpiCarousel outperformed baseline methods in systematic evaluation of memory usage, computational time, and multiple downstream analyses including cell type identification. Moreover, EpiCarousel executes preprocessing and downstream cell clustering on the atlas-level dataset with 707 043 cells and 1 154 611 peaks within 2 h consuming <75 GB of RAM and provides superior performance for characterizing cell heterogeneity than state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: The EpiCarousel software is well-documented and freely available at https://github.com/biox-nku/epicarousel. It can be seamlessly interoperated with extensive scCAS analysis toolkits.

scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders.

Recent advancements for simultaneously profiling multi-omics modalities within individual cells have enabled the interrogation of cellular heterogeneity and molecular hierarchy. However, technical limitations lead to highly noisy multi-modal data and substantial costs. Although computational methods have been proposed to translate single-cell data across modalities, broad applications of the methods still remain impeded by formidable challenges. Here, we propose scButterfly, a versatile single-cell cross-modality translation method based on dual-aligned variational autoencoders and data augmentation schemes. With comprehensive experiments on multiple datasets, we provide compelling evidence of scButterfly's superiority over baseline methods in preserving cellular heterogeneity while translating datasets of various contexts and in revealing cell type-specific biological insights. Besides, we demonstrate the extensive applications of scButterfly for integrative multi-omics analysis of single-modality data, data enhancement of poor-quality single-cell multi-omics, and automatic cell type annotation of scATAC-seq data. Moreover, scButterfly can be generalized to unpaired data training, perturbation-response analysis, and consecutive translation.

scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data.

Single-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity and gene regulation. However, scCAS data inherently suffers from limitations such as high sparsity and dimensionality, which pose significant challenges for downstream analyses. Although several methods are proposed to enhance scCAS data, there are still challenges and limitations that hinder the effectiveness of these methods. Here, we propose scCASE, a scCAS data enhancement method based on non-negative matrix factorization which incorporates an iteratively updating cell-to-cell similarity matrix. Through comprehensive experiments on multiple datasets, we demonstrate the advantages of scCASE over existing methods for scCAS data enhancement. The interpretable cell type-specific peaks identified by scCASE can provide valuable biological insights into cell subpopulations. Moreover, to leverage the large compendia of available omics data as a reference, we further expand scCASE to scCASER, which enables the incorporation of external reference data to improve enhancement performance.

Morphological and molecular analyses reveal two new species of Grifola (Polyporales) from Yunnan, China.

Species of Grifola are famous edible mushrooms and are deeply loved by consumers around the world. Most species of this genus have been described and recorded in Oceania, Europe and South America, with only Grifolafrondosa being recorded in Asia. In this study, two novel species of Grifola from southwestern China (Asia) are introduced. Macro and micromorphological characters are described. Grifolaedulissp. nov. present medium-size basidiomata with gray to gray-brown lobes upper surface, mostly tibiiform or narrowly clavate, rarely narrowly lageniform or ellipsoid chlamydospores, cuticle hyphae terminal segments slightly enlarged. Grifolasinensissp. nov. has white to grayish white lobes upper surface, mostly ellipsoid, rarely narrowly utriform chlamydospores, and broadly ellipsoid to ellipsoid basidiospores (4.6-7.9 × 3.0-5.9 µm). The two new species are supported by phylogenetic analyses of combined nuclear rDNA internal transcribed spacer ITS1-5.8S-ITS2 rDNA (ITS) and ß-tubulin (TUBB). Moreover, the genetic distance between TUBB sequences of those specimen from GenBank was 1.76-1.9%. Thus, the conspecificity relationship of our specimens remains uncertain, and further specimens are required to conclusively confirm its identity.

Morphological and molecular analyses reveal two new species of Termitomyces (Agaricales, Lyophyllaceae) and morphological variability of T.intermedius.

Two new species, Termitomycestigrinus and T.yunnanensis are described based on specimens collected from southwestern China. Termitomycesyunnanensis is morphologically characterized by a conspicuously venose pileus surface that is grey, olive grey, light grey to greenish grey at center, light grey towards margin, and a cylindrical white stipe. Termitomycestigrinus is morphologically characterized by a densely tomentose to tomentose-squamulose pileus showing alternating greyish white and dark grey zones, and a stipe that is bulbous at the base. The two new species are supported by phylogenetic analyses of combined nuclear rDNA internal transcribed spacer ITS1-5.8S-ITS2 rDNA (ITS), the mitochondrial rDNA small subunit (mrSSU) and the nuclear rDNA large subunit (nrLSU). The morphological variability of T.intermedius, including five specimens newly collected from Yunnan Province, China, is also discussed. The collections showed variability in colour of the stipe surface and in the shape of cheilocystidia when compared to the original description. Full descriptions of the two new species and of T.intermedius, as well as a taxonomic key to the 14 Termitomyces species reported from China are provided.

New species of Hydnotrya (Ascomycota, Pezizomycetes) from southwestern China with notes on morphological characteristics of 17 species of Hydnotrya.

More specimens of Hydnotrya have been collected from southwestern China in recent years. Morphological and molecular analyses showed that they belonged to three species of Hydnotrya, of which two are new to science, H.oblongispora and H.zayuensis. The third one was H.laojunshanensis, previously reported in 2013. The new species are described, and their relationship to other species of Hydnotrya is discussed. H.laojunshanensis is re-described in more detail. The main morphological characters of 17 species of Hydnotrya are compared and a key to them is provided as well.

Species diversity of Ganoderma (Ganodermataceae, Polyporales) with three new species and a key to Ganoderma in Yunnan Province, China.

Ganoderma is a globally distributed genus that encompasses species with forestry ecological, medicinal, economic, and cultural importance. Despite the importance of this fungus, the studies on the species diversity of Ganoderma in Yunnan Province, China (YPC) have poorly been carried out. During this study, opportunistic sampling was used to collect 21 specimens of Ganoderma from YPC. Morphology and multigene phylogeny of the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nrLSU), the translation elongation factor 1-α gene (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2) were used to identify them. Morphological and molecular characterization of the 21 specimens showed that they belong to 18 species of Ganoderma, of which three are novel viz. G. artocarpicola, G. obscuratum and G. yunnanense. Ganoderma artocarpicola is characterized by the sessile and concrescent basidiomata, reddish brown to yellowish brown pileus surface, heterogeneous context, wavy margin, and ovoid basidiospores. Ganoderma obscuratum is distinguished by small pores (6-9 per mm), dorsolaterally sub-stipitate basidiomata which become greyish-brown when dry, and narrow ellipsoid basidiospores. Ganoderma yunnanense is characterized by cream color pore surface and context, centrally to laterally stipitate basidiomata with reddish-brown to violet-brown strongly laccate pileus surface, and broadly ellipsoid basidiospores. With the help of an extensive literature survey and the results of this study, a checklist of 32 Ganoderma species from YPC was established, which accounts for 71.11% of the known species in China. In addition, a key to the Ganoderma in YPC is also provided.

Phylogenetic analyses and morphological characters reveal two new species of Ganoderma from Yunnan province, China.

Ganodermadianzhongense sp. nov. and G.esculentum sp. nov. are proposed as two new species based on both phenotypic and genotypic evidences. Ganodermadianzhongense is characterized by the stipitate basidiomata, laccate and oxblood red pileus, gray white pore surface, duplex context and broadly ellipsoid basidiospores (9.0-12.5 × 6.5-9.0 µm) with coarse interwall pillars. Ganodermaesculentum is characterized by its basidiomata with slender stipe, white pore surface, homogeneous pileus context, and slightly truncate, narrow basidiospores (8.0-12.5 × 5.0-8.0 µm). Phylogenetic analyses were carried out based on the internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α) and the second subunit of RNA polymerase II (RPB2) sequence data. The illustrations and descriptions for the new taxa are provided.

Comprehensive Review of Tolypocladium and Description of a Novel Lineage from Southwest China.

Tolypocladium, a diverse genus of fungicolous fungi belonging to Ophiocordycipitaceae, includes saprotrophic soil inhabitants, plant endophytes and pathogens of insects, nematodes, rotifers, and parasites of truffle-like fungi. Here, we review the research progress achieved for Tolypocladium regarding its taxonomy, species diversity, geographic distribution, host affiliations and ecological diversity. Furthermore, an undescribed taxon from China was established using morphology and multi-gene phylogeny. Tolypocladium inusitaticapitatum is introduced as a new species parasitizing ectomycorrhizal Elaphomyces species. It is diagnosed by its irregularly enlarged fertile heads and lemon, yellow-to-dark-brown, smooth and nearly cylindrical stipe. Phylogenetic analyses based on SSU, LSU, ITS, TEF1-α and RPB2 sequence data showed T. inusitaticapitatum to be an independent lineage separated from T. flavonigrum in the clade comprising T. capitatum, T. fractum and T. longisegmentatum. A key for identifying the sexual Tolypocladium species is also provided.