Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.

Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen's pangenomic landscape and aiding in the development of novel disease management strategies. Database URL: http://www.fopgdb.site.

De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus).

Chinese motherwort (Leonurus japonicus), a member of Lamiaceae family, is a commonly used medicinal herb for treating obstetrical and gynecological diseases, producing over 280 officinal natural products. Due to limited genomic resources, little progress has been made in deciphering the biosynthetic pathway of valuable natural products in L. japonicus. Here, we de novo assembled the L. japonicus genome using high-coverage ONT long reads and Hi-C reads. The chromosome-level genome assembly contained ten chromosomes representing 99.29% of 489.34 Mb genomic sequence with a contig and scaffold N50 of 7.27 Mb and 50.86 Mb, respectively. Genome validations revealed BUSCO and LAI score of 99.2% and 21.99, respectively, suggesting high quality of genome assembly. Using transcriptomic data from various tissues, 22,531 protein-coding genes were annotated. Phylogenomic analysis of 13 angiosperm plants suggested L. japonicus had 58 expanded gene families functionally enriched in specialized metabolism such as diterpenoid biosynthesis. The genome assembly, annotation, and sequencing data provide resources for the elucidation of biosynthetic pathways behind natural products of pharmaceutical applications in L. japonicus.

Bacillus megaterium: a Potential and an Efficient Bio-Degrader of Polystyrene

Abstract This research has been conducted to investigate the biodegradation of polystyrene (PS) by isolated strain Bacillus megaterium from Zophobas morio's. The viability and metabolic activity of Bacillus megaterium utilizing emulsified PS in liquid carbon free basal medium as sole carbon source was confirmed using redox probe 2,3,5-triphenyltetrazolium chloride (TTC). Bacillus megaterium showed prominent result with TTC, which forms red colored insoluble TPF (triphenyl formazan) within four to seven days. The formation of TPF confirmed the metabolism activity of the cell using PS as source of carbon. The biodegradation activity of Bacillus megaterium on PS film was also confirmed by FTIR analysis, the result showed changes in functional groups due to microbial activities. FESEM analysis was carried out on the PS surface, revealing the formation of bacterial biofilm as well as occurrence of porosity and fragility of the bacterial deteriorate surface compared to control. Overall, the identification of plastic degrading bacteria (PDB) will become a fundamental platform promoting more in-depth research for optimal plastic waste management to switch from the conventional landfilling to enzymatic biodegradation. In the long run, it is to regulate the current global plastic waste accumulation on Earth which poses potent ecological threat.