100 Algal genome project (ALG-ALL-CODE Project)-part-1-and part-2. Microalgae are integral primary producers for the global ecosystem and can produce diverse, commercially viable compounds. Due to their early recognition of potential value, thousands of species around the world have been acquired and maintained in collection centers. Many of these species' genomes hold the secrets to niche adaptation, salinity tolerance, toxic bloom formation, biotech commercialization, and bioremediation efforts, but few have been sequenced at the genomic level. To address this knowledge gap, we cultured and sequenced 100+ more microalgal species. Our culturing and sequencing project included Rhodophytes, Chlorophytes, Haptophytes, Cercozoans, and Chromophytes. Bioinformatics analyses of these assemblies reveals unique and shared genes, change in gene copy number, and lineage- and habitat-specific enrichment. We describe a vast network of endogenous viral elements characteristic of specific clades. We found core and accessory viral genes, incorporated into host microalgal genomes, consisting of diverse integral membrane proteins, including membrane transporters (sugars, amino acids, ions) and their linking ankyrins. These findings shed new light on the role of virus participation in microbial eukaryote speciation and help to clarify questions surrounding genomes from non-microalgal species, especially those from understudied clades and with essential roles in aquaculture, public safety, and bioremediation. The new genome collection will also facilitate research and utilization of non-model species, and their genes, with potential for biotech endeavors.