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Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat‐driven genome size evolution in diatoms

Wade R. Roberts,Matthew Parks,Marissa Ashner,Matthew P Ashworth,Nina Denne,Elizabeth C. Ruck,Elias Spiliotopoulos,Anni Wang,Shady A. Amin,S. Schaack,N. Wickett,Andrew J. Alverson

Published 2025 in Journal of Phycology

ABSTRACT

We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain‐forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ‐proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under‐described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.

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