The findings link genome reduction to host-dependent carboxylic acid metabolism in a quarantine-relevant phytoplasma, establishing a framework for comparative and functional studies of 16SrIX phytoplasmas and providing a basis for future investigations of AlmWB ecology and pathogenicity.
Abstract
Phytoplasmas are wall-less plant pathogens characterized by highly reduced genomes and limited metabolic capabilities, leading to an obligate host dependency. Since phytoplasma axenic cultivation has not yet been achieved, genomic approaches are essential to unravelling their biological and pathogenic traits. However, such insights are currently hindered by the scarcity of complete genomes and the lack of data for several clades, as is the case for the quarantine-relevant 'Candidatus Phytoplasma phoenicium' (group 16SrIX-B), the causal agent of the severe stone-fruit disease almond witches' broom (AlmWB). In this study, we present the complete genome sequence of the Lebanese strain F1A, which consists of a 552,248 bp chromosome with a 24.29% GC content and encodes 450 protein-coding genes. Comparative analyses with 16SrIX group draft genomes revealed high conservation among Lebanese AlmWB strains; however, comparisons with related 16SrIX-C phytoplasmas were limited by their low assembly completeness. Beyond providing a complete reference genome for this phytoplasma group, the F1A chromosome revealed distinct metabolic features. Strain F1A lacks the upper glycolytic pathway, indicating a metabolism that relies on glycerol-3-phosphate uptake and carboxylic acid fermentation. Notably, in addition to the conserved malate-to-acetate pathway, F1A encodes a complete citrate lyase complex, suggesting the potential for citrate utilization. Phylogenetic analysis of the associated 2-hydrocarboxylate symporter revealed the widespread occurrence of two phylogenetically distinct variants in phytoplasmas. Apart from the deduced metabolic capacities, the predicted effector repertoire shows similarities with those of other phytoplasmas, including proteins associated with branch proliferation and witches' broom symptoms. Overall, these findings link genome reduction to host-dependent carboxylic acid metabolism in a quarantine-relevant phytoplasma, establishing a framework for comparative and functional studies of 16SrIX phytoplasmas and providing a basis for future investigations of AlmWB ecology and pathogenicity.
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.
Bartosz Wąsik, Patryk Kupaj, Paweł Moroz et al.· BMC Genomics· 0 citations
Aspergillus welwitschiae is a widespread fungus with diverse roles as a plant mutualist, opportunistic human pathogen and industrial enzyme producer. The endophytic strain AwOcstreb1, isolated from halophytic rice (Oryza coarctata), promotes growth in commercial rice under normal and saline conditions. Despite its significance, genomic and metabolic resources for A. welwitschiae remain limited, with no complete genome information available for endophytic strains within the species. Moreover, the close relationship of this species to Aspergillus niger complicates its taxonomic resolution. We performed whole-genome and transcriptomic sequencing of AwOcstreb1 cultured on potato dextrose agar, along with -MS-based volatile metabolite profiling. Comparative analyses included simple sequence repeat (SSR), transposable element (TE; including starships) and carbohydrate-active enzyme (CAZyme) profiling across A. welwitschiae strains. Evolutionary relationships with A. niger were examined using average nucleotide identity (ANI) and orthologous gene clustering, supported by phylogenomic reconstruction. Genes for mycotoxin production and plant growth-promoting traits were also searched in this strain. The AwOcstreb1 genome is 37.7 Mb with 13,242 predicted genes, of which 66.6% were actively expressed under potato dextrose agar growth. The genome harbours 5,126 SSRs, 19,434 TEs and a CAZyme composition similar to other A. welwitschiae strains. Although established marker genes such as CaM and β-tubulin identify AwOcstreb1 as A. welwitschiae, whole-genome ANI and orthologous gene-based analyses place A. welwitschiae strains within the broader A. niger species complex, suggesting that it represents a population-level group rather than a clearly separated species, a view that is still not widely adopted. Synteny analysis showed that the AwOcstreb1 genes are highly collinear with those of A. niger. Genes involved in phosphate and zinc solubilization and siderophore biosynthesis were detected, whereas ochratoxin A biosynthetic genes were absent. Although the presence of fumonisin genes was detected, only a trace amount of the toxin was detected both in culture as well as rice grains. Among 172 strain-specific orthogroups, several encode intrinsically disordered, secreted or membrane-associated proteins that are potentially linked to endophytic lifestyle adaptations. Volatile metabolite profiling identified compounds such as 17-pentatriacontene, eicosane and octanal, each linked to known biological sources and potential functions, such as antifungal, antibacterial and anti-inflammatory activities. Several additional metabolites were also identified, whose biological roles need further investigation. This integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1. This work 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.
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
Penitrem A is a toxic secondary metabolite (SM) produced by
Penicillium crustosum
(
P. crustosum
) on various foods such as nuts, dairy products, and fruits. However, the biosynthetic gene clusters (BGCs) responsible for SMs including penitrem A in
P. crustosum
isolated from pears is largely unexplored.
In the current study, we performed whole-genome sequencing of
P. crustosum
KACC 411287, which can produce penitrem A and roquefortine C, and identified its SM BGCs including BGCs of the toxins. Furthermore, we conducted a comparative analysis of the penitrem A and roquefortine C BGCs against those in other fungal strains. We also analyzed the carbohydrate-active enzyme-(CAZyme-) encoding genes in
P. crustosum
KACC 411287, and compared with those of other closely related fungal strains.
The
P. crustosum
KACC 411287 genome is composed of five chromosomes, totaling approximately 32.37 Mb in size. Gene Ontology analysis using 8,520 functionally annotated proteins exhibited that the genome of
P. crustosum
KACC 411287 contains a significant abundance of genes involved in degradation of organonitrogen compounds including amino acids or carbohydrates and fungal self-protective mechanisms including SM biosynthesis. Of the 8,520 functionally annotated proteins, 546 predicted CAZymes were identified in
P. crustosum
KACC 411287. We also detected 68 SM BGCs including penitrem A and roquefortine C BGCs in
P. crustosum
KACC 411287. Furthermore, the conserved functionality analyses exhibited that each gene within the penitrem A BGC in
P. crustosum
KACC 411287 is highly conserved with the corresponding gene in four other penitrem A-producing
Penicillium
strains (above 77% amino acid sequence identity) except for
ptmH
in
P. flavigenum
IBT 14082 (20%). In contrast, the sequence identity decreased significantly (0–69% identity) in two penitrem A non-producing
Penicillium
strains.
Our data strongly indicate that the penitrem A BGCs were highly conserved among
P. crustosum
KACC 411287 and three other penitrem A-producing
Pencillium
strains. Our findings expand our knowledge about the biosynthesis of SMs including penitrem A and roquefortine C in
P. crustosum
KACC 411287 that causes blue mold rot on pears. These results could provide new insight into the biosynthesis of penitrem A and roquefortine C in
P. crustosum
KACC 411287 to find potential approaches for alleviating penitrem A or roquefortine C contamination on pears.