Joint Genome Institute

The biogeography of giant viruses and interactions with Eukaryotes across European lakes

Abstract Advances in genomics have revealed a diversity of nucleocytoplasmic large DNA viruses (phylum Nucleocytoviricota) that infect eukaryotes, but their ecology beyond the oceans remains poorly understood. We recover 208 Nucleocytoviricota genomes, including 205 putative new...

The chromosomal genome sequence of the boulder star coral, Orbicella franksi (Gregory, 1895) (Scleractinia: Merulinidae)

We present a genome assembly from a specimen of Orbicella franksi (boulder star coral; Cnidaria; Anthozoa; Scleractinia; Merulinidae). The genome sequence has a total length of 496.97 megabases. Most of the assembly (95.24%) is scaffolded into 15 chromosomal pseudomolecules. The...

Multi-omics analysis reveals Protein Kinase A-associated regulatory remodeling during adaptation of Trichoderma reesei to lignocellulosic substrate

The filamentous fungus Trichoderma reesei is a major industrial source of holocellulolytic enzymes, and its response to complex carbon sources is regulated by nutrient-sensing mechanisms, including the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway...

A genomic catalog of Earth’s bacterial and archaeal symbionts

1 SUMMARY Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict symbiotic lifestyles in hundreds of thousands of microbial genomes fr...

Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina

Dikaryotic rust fungi maintain two distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora lar...

Genomic catalogue of giant viruses reveals expanded diversity and functional potential

Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727...

Evidence for the acquisition of a proteorhodopsin-like rhodopsin by a chrysophyte-infecting giant virus

ABSTRACT Chrysophytes are nanoflagellate protists widespread in aquatic ecosystems with diverse trophic roles as primary producers and bacterivores. Molecular evidence suggests that chrysophytes are commonly infected by giant viruses, but isolates of such virus-host systems have...