A pan-genome perspective uncovers the core genetic basis and evolutionary adaptation of lipid synthesis and vesicular transport in Nannochloropsis.

Genome mining and comparative genome analysis of Pseudomonas fluorescens revealed diverse biosynthetic and metabolic potential

Understanding of the metabolic capabilities and genomic landscape of the P. fluorescens species is enhanced, providing a foundation for natural product discovery using bioinformatic approaches.

Genome analysis of the glycosphingolipid-producing green alga Tetraselmis sp. NKG400013.

Microalgae are gaining attention as sustainable resources for the production of valuable compounds, including biofuels, pigments, and bioactive metabolites. To support metabolic engineering and genome editing approaches aimed at enhancing these traits, high-quality genome assemblies are essential; however, genomic information remains limited for many microalgal lineages. Tetraselmis sp. NKG400013 is a green alga known for high glycosphingolipid accumulation with distinctive structural features. Here, we report a draft genome assembly of this strain generated using PacBio HiFi sequencing and transcriptome-supported annotation. The assembled genome spans 423.7 Mbp, with 74.5% repetitive sequences and 15,322 predicted protein-coding genes. Comparative analyses across 11 green algal species revealed a positive correlation between genome sizes and repeat contents, indicating that transposable element expansion, particularly long terminal repeat retrotransposons, has substantially contributed to genome enlargement in Tetraselmis. Genome-wide functional annotation and ortholog inference identified core enzymes required for glycosylceramide biosynthesis. Both sphingolipid Δ4 and Δ8 desaturases were identified in Tetraselmis. and their coexistence suggests an expanded capacity for long-chain base modification that may underlie its distinctive glycosphingolipid profile. These results establish a genomic framework for understanding the high glycosphingolipid-producing capacity of NKG400013 and provide insights into the evolutionary diversification of sphingolipid metabolism in green algae.

A pan-genomic perspective: comprehensive dissection of the FIG superfamily unravels its evolution, expansion, and environmental adaptation in wheat.

BACKGROUND As a major global food crop, wheat faces dual pressures from population growth and deteriorating agricultural environments in efforts to increase its yield. The members of the FIG superfamily are associated with photosynthetic carbon metabolism and stress-responsive pathways in plants. RESULTS In this study, we conducted the first systematic pan-genomic analysis to investigate the evolution and function of the FIG superfamily in wheat. The results revealed that this family underwent significant expansion during plant evolution from aquatic to terrestrial habitats and from lower to higher forms, with functional divergence apparently predating the green algal stage as inferred from phylogenetic patterns. The members of this family were primarily derived from three ancestral species, and their expansion was largely driven by whole-genome duplication. Most members were found to be under purifying selection, whereas the TaVTC4-4B was subjected to positive selection. This gene is constitutively highly expressed in green tissues, and its promoter is enriched with cis-regulatory elements associated with light responsiveness, JA/ABA signaling, and stress responses. Expression analysis indicated its strong responsiveness to salt stresses. CONCLUSIONS This study elucidates the evolutionary trajectory and functional landscape of the wheat FIG superfamily, laying a theoretical foundation for the potential genetic improvement of photosynthetic efficiency and stress resilience in wheat.

Integrated Genomic, Transcriptomic and Metabolomic Analyses Identify Key Genetic Determinants and Regulatory Networks for Salinity Tolerance in Macrobrachium rosenbergii

Pangenome Dynamics and Functional Diversification in the Marine Genus Pseudoalteromonas: Association to Colony Pigmentation

Pseudoalteromonas species are ecologically versatile marine bacteria widely recognized for their capacity to synthesize diverse bioactive metabolites and psychrophilic enzymes with biotechnological relevance. Here, we present a comprehensive comparative genomic analysis of 53 reference genomes to elucidate the dynamics, functional diversity, and biosynthetic potential of this genus. Reference genomes representing each deposited species were selected in order to avoid bias associated with unequal numbers of genomes per species. Pangenome reconstruction revealed an open structure comprising a small core genome (1,350 gene families) and a large proportion of accessory and strain-specific genes, reflecting extensive genomic plasticity. Functional annotation indicated that accessory regions are enriched for genes involved in secondary metabolism, stress adaptation, and environmental resilience. Notably, biosynthetic gene cluster (BGC) mining uncovered a rich repertoire of potentially novel RiPPs and other secondary metabolite clusters, underscoring Pseudoalteromonas as a promising source of unexplored bioactive compounds. Statistical analyses revealed that pigmented strains harbor significantly higher numbers of BGCs compared to non-pigmented strains, while only a weak and non-significant correlation was observed between BGC abundance and carbohydrate-active enzyme (CAZyme) content. No significant effect of the isolation source was detected on either BGC or CAZyme distributions. Together, these findings provide new insights into the genomic basis of ecological adaptation and metabolic diversification in Pseudoalteromonas, supporting the role of pigmentation as a proxy for enhanced biosynthetic potential, while carbohydrate utilization capabilities evolve more independently and offering a framework for targeted bioprospecting of marine-derived metabolites with industrial and environmental applications.

Integrated Pangenomic and Systems Biology Analyses Reveal the Genomic Basis of Virulence and Adaptation in Bipolaris sorokiniana

The first comprehensive species-wide pangenomic and systems-level analyses of B. sorokiniana are presented, providing vital insights into the evolutionary architecture of pathogenicity, adaptation, and genome diversification and providing a valuable genomic resource for disease surveillance and functional characterization of virulence determinants.