Abstract
Diatoms are one of the most prominent oceanic primary producers and are now recognized to be distributed throughout the world. They maintain their population despite predators, infections, and unfavourable environmental conditions. One of the smallest diatoms, Chaetoceros tenuissimus, can coexist with infectious viruses during blooms. To further understand this relationship, we sequenced the C. tenuissimus strain NIES-3715 genome. A gene fragment of a replication-associated gene from the infectious ssDNA virus (designated endogenous virus-like fragment, EVLF) was found to be integrated into each 41 Mb of haploid assembly. In addition, the EVLF was transcriptionally active and conserved in nine other C. tenuissimus strains from different geographical areas, although the primary structures of their proteins varied. The phylogenetic tree further suggested that the EVLF was acquired by the ancestor of C. tenuissimus. Additionally, retrotransposon genes possessing a reverse transcriptase function were more abundant in C. tenuissimus than in Thalassiosira pseudonana and Phaeodactylum tricornutum. Moreover, a target site duplication, a hallmark for long interspersed nuclear element retrotransposons, flanked the EVLF. Therefore, the EVLF was likely integrated by a retrotransposon during viral infection. The present study provides further insights into the diatom-virus evolutionary relationship.
Highlights
The virus resistance mechanisms of eukaryotic microalgae have been reported by numerous researchers, e.g., variation in susceptibility in the host c ell[12,13,14], blockade of intracellular virus genome replication[15], bacterially mediated virus r esistance[16], and host cell physiological b arriers[17,18]
Knowledge on the relationship between C. tenuissimus and its viruses has gradually accumulated from the viewpoint of growth-physiology studies based on traditional culture experiments[17,34], studies focusing on the aspect of cell biology are lacking
The haploid genome size and its heterozygosity were estimated at 39.7 Mb and 1.56%, respectively (Supplementary Fig. 1) using the kmer-based statistic, and the size corresponding to the assembly
Summary
The virus resistance mechanisms of eukaryotic microalgae have been reported by numerous researchers, e.g., variation in susceptibility in the host c ell[12,13,14], blockade of intracellular virus genome replication[15], bacterially mediated virus r esistance[16], and host cell physiological b arriers[17,18]. The marine planktonic diatom, Chaetoceros tenuissimus Meunier (Bacillariophyta, Centrales), is rectangular in the girdle view and is one of the smallest (~ 5 μm) diatoms. This species is widely distributed and is observed in Japanese coastal w aters[10], the Narraganset B ay[29], the Mediterranean S ea[30,31], and the San Matıas G ulf[32]. The tolerance to viral infection, along with their high growth rate, suggests that C. tenuissimus is to be a successful and ubiquitous species for maintaining primary productions in coastal environments. We believe that novel genomic discoveries can provide critical insights into the evolution of the diatom-virus relationship
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