Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration.

With the tremendous increase of publicly available single-cell RNA-sequencing (scRNA-seq) datasets, bioinformatics methods based on gene co-expression network are becoming efficient tools for analyzing scRNA-seq data, improving cell type prediction accuracy and in turn facilitating biological discovery. However, the current methods are mainly based on overall co-expression correlation and overlook co-expression that exists in only a subset of cells, thus fail to discover certain rare cell types and sensitive to batch effect. Here, we developed independent component analysis-based gene co-expression network inference (ICAnet) that decomposed scRNA-seq data into a series of independent gene expression components and inferred co-expression modules, which improved cell clustering and rare cell-type discovery. ICAnet showed efficient performance for cell clustering and batch integration using scRNA-seq datasets spanning multiple cells/tissues/donors/library types. It works stably on datasets produced by different library construction strategies and with different sequencing depths and cell numbers. We demonstrated the capability of ICAnet to discover rare cell types in multiple independent scRNA-seq datasets from different sources. Importantly, the identified modules activated in acute myeloid leukemia scRNA-seq datasets have the potential to serve as new diagnostic markers. Thus, ICAnet is a competitive tool for cell clustering and biological interpretations of single-cell RNA-seq data analysis.

[Main sources of soil phosphorus and their seasonal changes across different vegetation restoration stages in karst region of southwest China]. / è¥¿å—å–€æ–¯ç‰¹åŒºåŸŸä¸åŒæ¤è¢«æ¢å¤é˜¶æ®µåœŸå£¤ç£·ä¸»è¦æ¥æºåŠå ¶å­£èŠ‚å˜åŒ–.

Investigating the main sources of soil phosphorus and their seasonal variations across different vegetation restoration stages in karst region of southwest China can deepen our understanding of soil phosphorus cycling during vegetation restoration, and provide scientific reference for the controlling of rocky desertification. Taking the typical karst ecosystems at different vegetation restoration stages in Guilin, Guangxi as the research objects, we conducted a one-year field experiment with three treatments: vegetation restoration for about 10 years (R10), 30 years (R30) and 50 years (R50). We collected rainfall based on precipitation frequency, as well as soil, fresh litter and root samples in each season to measure the concentrations of total phosphorus (TP) in rainfall, the contents of TP and available phosphorus (AP) in soil, and the contents of TP in fresh litter and roots. In combination with litter phosphorus storage and soil microbial biomass phosphorus (MBP), we analyzed the contributions of phosphorus input to soil from different phosphorus sources. The results showed that soil TP content increased initially and then decreased with vegetation restoration, with a seasonal pattern of autumn > summer > spring > winter. Soil AP content was low in all treatments, with higher levels in summer and winter than in spring and autumn. Soil MBP content increased with vegetation restoration, with a seasonal variation pattern of spring >autumn > summer > winter. The annual phosphorus input from rainfall was 0.78 kg·hm-2 with the highest value in spring. The annual phosphorus input from fresh litter in the R10, R30, and R50 treatments was 2.42, 10.64 and 5.03 kg·hm-2. Phosphorus storage in litter was 1.23, 5.32 and 3.45 kg·hm-2. The annual phosphorus input from plant roots was 5.18, 12.65, and 5.96 kg·hm-2, respectively. The highest levels of the above parameters always occurred in the R30 treatment. There was a significant positive correlation between soil TP content and plant root phosphorus input, and a significant negative correlation between soil AP content and rainfall phosphorus input. In summary, the contribution of phosphorus input from different sources to soil phosphorus pool varied across different vegetation restoration stages in the karst region of southwest China. Roots are the main source of soil phosphorus, followed by litters. Phosphorus entering the soil through wet deposition is very limited. Soil microorganisms also contribute to soil phosphorus reserve.