Elucidating phylogenetic relationships within the genus Curcuma through the comprehensive analysis of the chloroplast genome of Curcuma viridiflora Roxb. 1810 (Zingiberaceae).

Curcuma viridiflora Roxb., a plant species of significant pharmaceutical interest, has been the subject of limited chloroplast genomic research. In this study, we present the sequencing and assembly of the C. viridiflora chloroplast genome, which is characterized by a circular chromosome spanning 162,212 base pairs and a GC content of 36.20%. The genome encodes 87 protein-coding genes (PCGs), 38 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted, incorporating eight related species, and based on the complete chloroplast genome and protein-coding DNA sequences of six related taxa within the genus. Outgroup species Zingiber zerumbet and Zingiber officinale were also included in the analysis. The results indicate a close relationship between C. viridiflora and Curcuma phaeocaulis, Curcuma sichuanensis, and Curcuma yunnanensis. This study provides the first chloroplast genome of C. viridiflora, thereby contributing a valuable genomic resource for future research on medicinal plants within the Curcuma genus.

MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.

DNA methylation plays a crucial role in tumorigenesis and tumor progression, sparking substantial interest in the clinical applications of cancer DNA methylation biomarkers. Cancer-related whole-genome bisulfite sequencing (WGBS) data offers a promising approach to precisely identify these biomarkers with differentially methylated regions (DMRs). However, currently there is no dedicated resource for cancer DNA methylation biomarkers with WGBS data. Here, we developed a comprehensive cancer DNA methylation biomarker database (MethMarkerDB, https://methmarkerdb.hzau.edu.cn/), which integrated 658 WGBS datasets, incorporating 724 curated DNA methylation biomarker genes from 1425 PubMed published articles. Based on WGBS data, we documented 5.4 million DMRs from 13 common types of cancer as candidate DNA methylation biomarkers. We provided search and annotation functions for these DMRs with different resources, such as enhancers and SNPs, and developed diagnostic and prognostic models for further biomarker evaluation. With the database, we not only identified known DNA methylation biomarkers, but also identified 781 hypermethylated and 5245 hypomethylated pan-cancer DMRs, corresponding to 693 and 2172 genes, respectively. These novel potential pan-cancer DNA methylation biomarkers hold significant clinical translational value. We hope that MethMarkerDB will help identify novel cancer DNA methylation biomarkers and propel the clinical application of these biomarkers.

Simultaneous quantification of alpha-tocopherol and four major carotenoids in botanical materials by normal phase liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry.

A rapid and sensitive method for the simultaneous quantification of alpha-tocopherol, beta-carotene, beta-cryptoxanthin, lutein and zeaxanthin in botanical materials has been developed using normal phase liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry (NP-LC-APCI-MS/MS). A systematic extraction procedure for different botanical materials was described and the extraction solvents were matched with normal-phase LC requirement. Quantification was performed by using the external standards and standard calibration curves were linear between 35 and 8505 ng/mL for alpha-tocopherol, 64-15,552 ng/mL for beta-carotene, 40-9720 ng/mL for beta-cryptoxanthin, 70-17,010 ng/mL for lutein and 64-15,552 ng/mL for zeaxanthin with regression coefficient r2 > 0.9996. The limits of quantification (LOQ) were 35, 64, 40, 70 and 66 ng/mL for alpha-tocopherol, beta-carotene, beta-cryptoxanthin, lutein and zeaxanthin, respectively.