We present a tool that combines fast mapping, error correction, and de novo assembly (MECAT; accessible at https://github.com/xiaochuanle/MECAT) for processing single-molecule sequencing (SMS) reads. MECAT's computing efficiency is superior to that of current tools, while the results MECAT produces are comparable or improved. MECAT enables reference mapping or de novo assembly of large genomes using SMS reads on a single computer.

Although a few studies have investigated the intestinal microbiota of women with polycystic ovary syndrome (PCOS), the functional and metabolic mechanisms of the microbes associated with PCOS, as well as potential microbial biomarkers, have not yet been identified. To address this gap, we designed a two-phase experiment in which we performed shotgun metagenomic sequencing and monitored the metabolic parameters, gut-brain mediators, and sex hormones of PCOS patients. In the first stage, we identified an imbalance in the intestinal microbiota of the PCOS patients, observing that Faecalibacterium, Bifidobacterium, and Blautia were significantly more abundant in the control group, whereas Parabacteroides and Clostridium were enriched in the PCOS group. In the second stage, we monitored the impact of the probiotic Bifidobacterium lactis V9 on the intestinal microbiome, gut-brain mediators, and sex hormones of 14 PCOS patients. Notably, we observed that the levels of luteinizing hormone (LH) and LH/follicle-stimulating hormone (LH/FSH) decreased significantly in 9 volunteers, whereas the levels of sex hormones and intestinal short-chain fatty acids (SCFAs) increased markedly. In contrast, the changes in the indices mentioned above were indistinct in the remaining 5 volunteers. The results of an analysis of the number of viable Bifidobacterium lactis V9 cells in the two groups were highly consistent with the clinical and SCFA results. Therefore, effective host gut colonization of the probiotic Bifidobacterium lactis V9 was crucial for its ability to function as a probiotic. Finally, we propose a potential mechanism describing how probiotics regulate the levels of sex hormones by manipulating the intestinal microbiome in PCOS patients. IMPORTANCE Polycystic ovary syndrome (PCOS) is a common metabolic disorder among women of reproductive age worldwide. Through a two-phase clinical experiment, we first revealed an imbalance in the intestinal microbiome of PCOS patients. By binning and annotating shotgun metagenomic sequences into metagenomic species (MGS), 61 MGSs were identified as potential PCOS-related microbial biomarkers. In the second stage, we monitored the impact of the probiotic Bifidobacterium lactis V9 on the intestinal microbiota, metabolic parameters, gut-brain mediators, and sex hormones of PCOS patients. Notably, we observed that the PCOS-related clinical indices and the intestinal microbiotas of the participating patients exhibited an inconsistent response to the intake of the B. lactis V9 probiotic. Therefore, effective host gut colonization of the probiotic was crucial for its ability to function as a probiotic. Finally, we propose a potential mechanism by which B. lactis V9 regulates the levels of sex hormones by manipulating the intestinal microbiome in PCOS patients.

DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets. MethSMRT is the first resource hosting DNA 6mA and 4mC methylomes. All the data sets were processed using the same analysis pipeline with the same quality control. The current version of the database provides a platform to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms (SNP) and genomic annotation. Furthermore, the database provides a quick summary of statistics of methylome of 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use restriction.

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Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and phenotypic data were applied to multi-locus genome-wide association studies (GWAS) with the mrMLM software. A total of 42 SNPs were identified to be associated with the five forage quality-related traits. Moreover, three and two quantitative trait nucleotides (QTNs) were simultaneously detected among them by three and two multi-locus methods, respectively. One QTN on chromosome 5 was found to be associated simultaneously with CP, NDF, and ADF. Furthermore, 3, 2, 2, 5, and 2 candidate genes were identified to be responsible for CP, NDF, ADF, HC, and CL contents, respectively. These results provided insightful information of the forage quality-related traits and would facilitate the genetic improvement of sorghum forage quality in the future.

The environment of Lake Taihu has changed a great deal in recent decades. Wetland plant restoration is considered an efficient way to keep it healthy. However, restoration efforts are affected by environmental factors which have important influences on wetland plant growth. In order to study the mutual effects of water depth and sediment type on the growth of aquatic plants, the impacts of the two environmental factors on root morphology of the submerged plant Vallisneria natans were investigated in an outdoor pond experiment. Treatments included three levels of water depth (60, 120 and 180 cm) and two sediment types (clay and sandy loam). Results showed that root/leaf mass ratio and root morphological parameters (root diameter, root length, root area, root volume, specific root length and specific root area) of the plant generally decreased with increasing water depth, with reductions of 12.64% in root diameter and 97.40% in root mass in clay and 28.82% in root diameter and 97.98% in root volume in sandy loam. Root/leaf mass ratio in low nutrient sediment (sandy loam) was higher than that in the more nutrient-rich sediment (clay). However, the other four morphological parameters were higher in clay at any water depths. Results of two-way analysis of variance (ANOVA) showed that water depth impacted the biomass allocation and root morphology of V. natans significantly, while sediment type only had significant impact on root/leaf mass ratio and root diameter. The results indicate that a considerable variation in root morphology of the submerged plant V. natans exists in response to water depth and sediment type, and water depth is the key ecological factor affecting root growth of the plant. This study can provide useful information in aquatic plant restoration and management.

Chromophoric dissolved organic matter (CDOM) is a key component with a critical role in the littoral zones of eutrophic shallow lakes; yet the characteristics of CDOM in these zones remain seldom systematically reported. In this study, the differences in sources, biogeochemical characteristics, and fates of CDOM between the littoral zones of eutrophic lakes Taihu (LLT; frequently occurring algal blooms and longer lake residence time) and Hongze (LLH; no obvious algal blooms and shorter residence time) were compared during the algal bloom season using ultraviolet-visible spectra and excitation and emission matrix spectroscopy combined with parallel factor analysis. Three humic-like fluorescent dissolved organic matter (FDOM) components (C1, C3, and C4) and one protein-like component (C2) were identified. Results showed that FDOM components were dominated by protein-like fluorescent substances in LLT, and humic-like materials in LLH, respectively. The CDOM in LLT had a lower relative aromaticity and molecular weight, humification degree and a higher autotrophic productivity because of algal blooms. Furthermore, CDOM depletion rates in LLT were higher than those in LLH due to a longer lake residence time in LLT. In addition, CDOM shifted from high molecular weight to low molecular weight as the humification degree decreased during the CDOM depletion process. This comparative study showed that algal blooms and lake residence time were the significant factors for distinguishing characteristics of CDOM between littoral zones of shallow lakes on a similar trophic level. This study provides field-based knowledge for remote sensing CDOM measurement and serves as a reference for lakeshore aquatic environmental management.