DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.

Recent nanopore sequencing system (R10.4) has enhanced base calling accuracy and is being increasingly utilized for detecting CpG methylation state. However, the robustness and universality of the methylation calling model in officially supplied Dorado remains poorly tested. In this study, we obtained heterogeneous datasets from human and plant sources to carry out comprehensive evaluations, which showed that Dorado performed significantly different across datasets. We therefore developed deep neural networks and implemented several optimizations in training a new model called DeepBAM. DeepBAM achieved superior and more stable performances compared with Dorado, including higher area under the ROC curves (98.47% on average and up to 7.36% improvement) and F1 scores (94.97% on average and up to 16.24% improvement) across the datasets. DeepBAM-based whole genome methylation frequencies have achieved >0.95 correlations with BS-seq on four of five datasets, outperforming Dorado in all instances. It enables unraveling allele-specific methylation patterns, including regions of transposable elements. The enhanced performance of DeepBAM paves the way for broader applications of nanopore sequencing in CpG methylation studies.

MIKC type MADS-box transcription factor LcSVP2 is involved in dormancy regulation of the terminal buds in evergreen perennial litchi (Litchi chinensis Sonn.).

SHORT VEGETATIVE PHASE (SVP), a member of the MADS-box transcription factor family, has been reported to regulate bud dormancy in deciduous perennial plants. Previously, three LcSVPs (LcSVP1, LcSVP2 and LcSVP3) were identified from litchi genome, and LcSVP2 was highly expressed in the terminal buds of litchi during growth cessation or dormancy stages and down-regulated during growth stages. In this study, the role of LcSVP2 in governing litchi bud dormancy was examined. LcSVP2 was highly expressed in the shoots, especially in the terminal buds at growth cessation stage, whereas low expression was showed in roots, female flowers and seeds. LcSVP2 was found to be located in the nucleus and have transcription inhibitory activity. Overexpression of LcSVP2 in Arabidopsis thaliana resulted in a later flowering phenotype compared to the wild-type control. Silencing LcSVP2 in growing litchi terminal buds delayed re-entry of dormancy, resulting in significantly lower dormancy rate. The treatment also significantly up-regulated litchi FLOWERING LOCUS T2 (LcFT2). Further study indicates that LcSVP2 interacts with an AP2-type transcription factor, SMALL ORGAN SIZE1 (LcSMOS1). Silencing LcSMOS1 promoted budbreak and delayed bud dormancy. Abscisic acid (200 mg/L), which enforced bud dormancy, induced a short-term increase in the expression of LcSVP2 and LcSMOS1. Our study reveals that LcSVP2 may play a crucial role, likely together with LcSMOS1, in dormancy onset of the terminal bud and may also serve as a flowering repressor in evergreen perennial litchi.

Tunable multicolor supramolecular assemblies based on phosphorescence cascade energy transfer for photocatalytic organic conversion and anti-counterfeiting.

Making full use of the captured energy by phosphorescence light-harvesting systems (PLHSs) and the tunable photoluminescence in energy transfer process to realize the multiple applications is still the challenge of PLHSs research. In this study, we have successfully constructed a highly effective PLHS with tunable multicolor luminescence and efficient conversion of photosensitizer types, which can further be used in photocatalytic organic conversion, information anti-counterfeiting and storage. The supramolecular polymer of BDBP-CB[8], which is generated by cucurbit[8]uril (CB[8]) and 4-(4-bromophenyl)-pyridine derivative (BDBP), realizes a phosphorescence emission and a change in luminescence color. Notably, white light emission was achieved and the logic gate systems were constructed utilizing the application of adjustable luminescence color. More interestingly, PLHS can be constructed by employing BDBP-CB[8] as energy donors, Sulforhodamine 101 (SR101) and Cyanine5 (Cy5) as energy acceptors, which results in a remarkably tunable multicolor photoluminescence to achieve the information storage. Furthermore, we have also found that BDBP-CB[8] can serve as type II photosensitizer for the effective production of singlet oxygen (1O2) during the photooxidation process of styrene in aqueous environments, attaining a remarkable output rate reaching as high as 89 %. Particularly, compared with 1O2 produced by type II photosensitizer BDBP-CB[8], the construction of PLHS can effectively convert type II photosensitizer to type I photosensitizer and efficiently generate superoxide anion radical (O2•-), which can be used for photocatalytic cross-dehydrogenative coupling (CDC) reaction in the aqueous solution with a yield of 90 %. Thus, we have created a PLHS that not only achieves tunable multicolor emission for information anti-counterfeiting and storage, but also realizes the conversion of reactive oxygen species (ROS) for different types photocatalytic oxidation reactions.