The first comparative genomic analysis of multiple isolates of a single chytrid species infecting the cyanobacterium Planktothrix agardhii is presented, suggesting that chytrids consistently express high levels of cytoskeletal genes, alongside numerous hypothetical proteins, and that zoospores may upregulate carbohydrate-binding proteins implicated in host recognition.
Abstract
Chytrids (phylum Chytridiomycota) are zoosporic fungi that play key roles as parasites of aquatic microorganisms, yet they are understudied and genomic resources for algal-infecting chytrids remain scarce. Here, we present the first comparative genomic analysis of multiple isolates of a single chytrid species (order Rhizophydiales) infecting the cyanobacterium Planktothrix agardhii. Isolates were collected from Sandusky Bay, Lake Erie, across two bloom years (2018 and 2019). Using single cell sequencing and metagenomic assembly, we generated individual genomes averaging 15.36 ± 0.12 Mbp in size with ~ 75% completeness, and a pangenome. Gene ontology analyses highlighted the presence of categories related to cellular structure, biosynthetic regulation, and interspecies interactions. As a preliminary exploration of gene expression during infection, we also performed RNA sequencing on a subset of size-sorted samples. These data suggest that chytrids consistently express high levels of cytoskeletal genes, alongside numerous hypothetical proteins, and that zoospores may upregulate carbohydrate-binding proteins implicated in host recognition. On the host side, P. agardhii showed transcriptional shifts in pathways associated with buoyancy and nutrient acquisition, patterns that could represent defensive adjustments or parasite-driven manipulation. Together, this study generates reference genomes for Planktothrix-infective chytrids, identifies conserved gene content across isolates from different bloom years, and provides preliminary transcriptomic insights into parasite and host responses. These resources lay the foundation for deeper investigations into chytrid genome evolution, infection biology, and their ecological roles in shaping cyanobacterial bloom dynamics.
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
The plastids of peridinin-containing dinoflagellates ultimately derive from a red alga acquired by secondary endosymbiosis, an event that required extensive endosymbiotic gene transfer (EGT) from the endosymbiont to the host nucleus. Although many individual studies have recovered a red-algal phylogenetic signal in nucleus-encoded, plastid-targeted dinoflagellate proteins, this evidence remains scattered across genome papers, transcriptome surveys, plastid-proteome predictions and single-gene phylogenies, and has never been compiled systematically. Conducted and reported in accordance with the PRISMA 2020 guideline adapted for evolutionary genomics, this systematic review aimed to map and grade that evidence at the level of individual genes, lineages and functional categories. Bibliographic databases and sequence repositories, including Web of Science, Scopus, PubMed, MMETSP and EukProt, were searched up to 31 January 2026, and a four-tier evidence-grading scheme (strong, moderate, weak, ambiguous) together with a phylogenomic risk-of-bias appraisal was applied. Twenty-four studies met the eligibility criteria. The strongest and most consistent red-algal signals were recovered among nucleus-encoded proteins of the photosynthetic electron-transport chain, the Calvin–Benson cycle, tetrapyrrole and carotenoid biosynthesis, and plastid gene expression, consistent with a chromalveolate origin of the peridinin plastid. Peridinean lineages carried the clearest red-derived signal, whereas haptophyte-derived (Kareniaceae) and diatom-derived (dinotom) lineages showed a younger layer of donor-specific ancestry that frequently obscured the original red signal. The number of recovered EGT candidates was also an order of magnitude greater in secondary than in tertiary plastid contexts.
Anssam Hassan Ali, Amjad Abd Ali· International Journal of Sci...· 0 citations
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.
A genome-resolved reference framework is established for the cultivable bacteria and yeasts isolates obtained from healthy A. diaperinus larvae in the present study and provides genomic resources for future ecological and functional investigations.
Gisele Ivonne Antonuccio, Pablo Julián López, M. Berretta et al.· Insects· 0 citations
Mycoparasitic fungi in the
Hypocreaceae
family are ecologically and economically significant, yet genomic resources for many lineages remain limited. This is particularly true for
Hypomyces
and some related genera, which include causative agents of cobweb and web bubble diseases in commercial mushroom farms. Here, we present high-quality genome assemblies and annotations for two mycoparasitic
Hypocreaceae
fungi,
Hypomyces semicircularis
X01500 and
Mycogone
sp. X01501 representing a distinct phylogenetic lineage within
Mycogone
. Using a hybrid sequencing approach (Illumina and ONT), we generated chromosome-scale assemblies for X01501 (32,977,754 bp, 8 contigs, N50 = 4,917,145 bp) and X01500 (39,466,758 bp, 8 contigs, N50 = 5,660,398 bp), with BUSCO completeness > 99.7%. We annotated 9,717 and 11,121 protein-coding genes in genomes of X01501 and X01500, respectively, the majority of which received functional annotation. The metrics indicate high assembly continuity, completeness, and accuracy, with seven nuclear contigs and one mitochondrial contig recovered for each strain. These genomes provide a foundation for future research into the evolution and mechanisms of mycoparasitism within this understudied clade.
Fan Yi, Yuanchao Liu, Huiping Hu et al.· Scientific Data· 0 citations