A high-quality genome assembly and an in-depth genome analysis of V. victoriae strain D19 are presented, establishing a valuable foundation for future functional studies and providing keys for developing a new chassis for potential industrial applications.
Abstract
Background
Vishniacozyma victoriae is a ubiquitous yeast isolated from various regions across the globe, especially in extreme environments. It can produce several interesting extracellular compounds, including carotenoids and cold-active hydrolytic enzymes, that confer high potential for industrial production and biotechnological applications. However, insufficient knowledge in its biology, genetics and genomics are the primary obstacle of its development as a new chassis. The aim of this study was to provide a high-quality genome assembly and an in-depth genome analysis of V. victoriae strain D19.
Results
We isolated V. victoriae D19 (CBS 19383) from Trondheimfjordens, Norway. Here we present its high-quality genome assembly, along with comprehensive structural and functional annotation of the genome. The assembly consists of 10 nuclear scaffolds with a cumulative size of 18.1 Mb, an N50 value of 1.7 Mb (L50 = 3) and a complete circular mitochondrial genome. A total of 7,853 protein-coding genes were predicted. Intron structure and other features, such as rRNA, tRNA, transposable elements, telomeric repeats were also analyzed to contribute to a deeper understanding of the V. victoriae genome architecture. Functional gene annotation, performed using the go-FAnnoT and BlastKOALA tools, enabled the reconstruction of key metabolic pathways, providing potential functions for 6,434 and 3,626 proteins, respectively. Moreover, the analysis of protein targeting and in silico secretome analysis, followed by CAZymes identification, helped us to understand the metabolic potential of this yeast.
Conclusion
These genomic resources establish a valuable foundation for future functional studies and provide keys for developing a new chassis for potential industrial applications.
An integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1, isolated from halophytic rice, and opens new avenues for exploring A. welwitschiae for sustainable agriculture and fungal biology.
Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin et al.· Microbial Genomics· 0 citations
Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, “Candidatus Abyssoplasma scotoplanesicola”, within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. “Candidatus Abyssoplasma scotoplanesicola” occupied 76.4–98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.
Members of the genus Marinobacterium are widely distributed in marine environments and contribute to diverse ecological processes; however, genomic information for several species remains limited. In this study, we report the complete genome sequence of Marinobacterium marisflavi strain IMCC4074ᵀ, originally isolated from coastal seawater of the Yellow Sea, to provide insights into its genomic features, metabolic potential, and environmental adaptation. The genome of strain IMCC4074ᵀ was sequenced using a combination of short- and long-read sequencing approaches and assembled into a single circular chromosome of 3,091,487 bp with a G + C content of 52.45%. Genome annotation revealed 2,974 protein-coding sequences, 15 rRNA genes, and 60 tRNA genes. Phylogenomic analyses confirmed its taxonomic placement within the genus Marinobacterium, while comparative genomic analysis revealed sufficient divergence (ANI ≤ 95%) from previously described species within the genus, supporting its distinction at the species level and representing the first genome report for this species. The availability of the complete genome provides a resource for understanding the potential ecological roles and adaptive strategies of M. marisflavi in marine ecosystems.
M. Rajeev, Yeonjung Lim, Ilnam Kang et al.· BMC Genomic Data· 0 citations
Microorganisms inhabiting cold and oligotrophic aquatic environments experience persistent physiological stress, necessitating genomic characterization to understand their survival strategies. Psychrotolerant strains have evolved diverse metabolic adaptations, including secondary metabolite biosynthesis, which may contribute to environmental fitness and offer potential for low-temperature biotechnological applications. However, the genus
Lacisediminihabitans
remains poorly represented at the genomic level, limiting our understanding of its ecological roles and metabolic potential. To address this gap, we generated a high-quality complete genome of a psychrotolerant
Lacisediminihabitans
strain isolated from Antarctic freshwater.
Lacisediminihabitans
sp. FW035 grew at 2 − 25 °C with an optimum at 20 °C. The genome of strain FW035 is 3,842,169 bp in size with a G+C content of 66.4%, encoding 3,592 protein-coding genes. Genome analysis revealed a complete C5–C20 isoprenoid biosynthesis pathway and multiple biosynthetic gene clusters, including terpene-associated clusters with low similarity to previously characterized pathways. These features indicate the presence of biosynthetic potential distinct from previously characterized pathways, particularly terpene-associated clusters, and highlight the dataset as a resource for future comparative genomic and functional analyses.
Minkyung Kim, A. Cho, Minjeong Kwon et al.· BMC Genomic Data· 0 citations
Rhizaria, one of the most species-rich and ecologically important eukaryotic supergroups, accommodates a newly discovered osmotrophic species, yet high-quality genomic resources remain scarce, limiting our understanding of their metabolic diversity and ecological functions. Here, we present the genome of Saccharomycomorpha psychra, the first rhizarian telomere-anchored assembly, to be explored as a model and reference for rhizarian ecology and evolution. The 62 Mb assembly, of which half comprises 22 telomere-to-telomere scaffolds, shows a BUSCO completeness of 94.2%, encodes 17,680 genes, and provides the genomic foundation for investigating rhizarian ecology and evolution. The genome of osmotrophic Saccharomycomorpha psychra reveals a functionally integrated secretome of 1,015 proteins dominated by carbohydrate-active enzymes (CAZymes), proteases, lipases, and oxidoreductases. Taken together with 303 predicted high-confidence membrane transporters of a total of 680, skewed toward H⁺-coupled secondary carriers, these features constitute the genomic signature of an extracellular digestive strategy convergent with saprotrophic fungi. Phenotypic MicroArrayTM assays confirmed active utilization of 17 carbon sources, including all six C5 pentose sugars tested, consistent with the predicted arabinose and ribokinase pathways among the most highly expressed metabolic genes in the transcriptome. These findings demonstrate that osmotrophic saprotrophy has evolved independently in Rhizaria with enzymatic solutions that closely parallel those of evolutionary distant fungal decomposers, highlighting the power of ecological context over phylogenetic heritage in shaping extracellular metabolic architecture.
Hüsna Öztoprak, Julia Graf, Robin Jacobs et al.· bioRxiv· 0 citations
Red algae (Rhodophyta) are an ancient lineage of photosynthetic eukaryotes that play important roles in marine ecosystems. However, genomic information for many species within the order Rhodymeniales remains limited, particularly for mitochondrial genomes. In this study, we sequenced, assembled, and analyzed the complete mitochondrial genome (mitogenome) of Rhodymenia intricata to investigate its genome organization, gene content, and phylogenetic position within Rhodymeniales. The mitogenome of R. intricata is a circular DNA molecule of 26,213 bp containing 49 genes, including 25 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes. The genome shows a strong A + T bias (70.9%) and positive AT and GC skews, typical of red algal mitogenomes. Comparative analysis with other Rhodymeniales mitogenomes revealed generally conserved gene content and organization, with several lineage-specific features such as the presence of the rpl20 gene, an additional open reading frame (orf148), and three rRNA genes (rnl, rns, and rns5). Codon usage analysis indicated a preference for leucine and isoleucine codons and dominant start and stop codons (ATG and TAA). Phylogenetic analysis based on a concatenated dataset of 23 mitochondrial PCGs strongly supported the monophyly of Rhodymeniales and confirmed the close relationship between R. intricata and R. pseudopalmata. Overall, this study presents the first complete mitogenome of R. intricata and expands mitogenomic resources for Rhodymeniales, providing new insights into mitogenome evolution and phylogenetic relationships in red algae.
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