The genome of the diatom Chaetoceros tenuissimus carries an ancient integrated fragment of an extant virus

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.

Whole-genome scanning reveals selection mechanisms in epipelagic Chaetoceros diatom populations

“…The genomes we considered for the present study have been generated from the Tara Oceans metagenomic reads and displayed the same magnitude in size, number of protein-coding genes and G+C content as the newly published Chaetoceros tenuissimus genome (Hongo et al 2021), pointing out the accuracy of the MAG reconstruction methods. Several studies have investigated the link between genome size compared to cell morphology and metabolism and have found that both cell size and growth rate are, respectively, proportional and inversely proportional to genome size (Williams 1964; Holm-Hansen 1969; Shuter et al 1983; Veldhuis et al 1997; Cavalier-Smith 2005; Von Dassow et al 2008).…”

“…For this, we selected the MAGs that were present in at least three different stations or depths and with a variance superior to zero, namely MAGs ARC_116, ARC_217 and SOC_37, all of them having populations in the Arctic Ocean. Pairwise-FST values between the MAG populations were modelled depending on a range of environmental parameters and Euclidean distance by applying a linear mixed model (LMM), as described in Laso-Jadart et al (2021), to perform a variance partitioning analysis. The fixed part of the unexplained variance was below 10% for the three analyses, and was therefore considered negligible.…”

“…In a second step, the estimation of the relative effects of abiotic parameters and geographic distance on the genomic differentiation of MAGs was undertaken. For this, a linear mixed model from the R package 'MM4LMM' (Laporte and Mary-Huard 2021) was used as previously applied by Laso-Jadart et al (2021) on marine plankton. As an input dataset for abiotic parameters, median values of different environmental parameters were extracted from the PANGAEA database (Ardyna et al 2017;Guidi, Morin, et al 2017;Guidi, Picheral, et al 2017) and for each sampling site, namely oxygen, salinity, temperature, and nutrient concentrations of ammonium, iron, nitrate, nitrite, phosphate and silicate.…”

“…The 'pcadapt' R package v4.0.2 (Luu et al 2017) was applied to detect selection among populations using the B-allele frequency (BAF) matrix, on 'pool-seq' mode with a minimal allele frequency of 0.05 within the populations, as was done in Laso-Jadart et al (2021). Based on the PCA results, two samples from one station (194 SUR and DCM) of the MAG ARC_116 exhibited very distinct variation patterns (Supplementary Figure S24A), leading to a very high number of outliers (12,954) and were therefore removed from the analysis (Supplementary Figure 24B) to avoid false positive inflation.…”

Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros

“…Reference diatom genomes for P. tricornutum CCAP 1055 and T. pseudonana CCMP 1335 were also considered to provide a comparison with the Chaetoceros MAGs and were both retrieved from the Joint Genome Institute [16,17]. The genome of Chatoceros tenuissimus NIES-3715 was retrieved from the DDBJ repository (https://www.ddbj.nig.ac.jp) [81]. Information about their completion level, gene length, and percentage of G+C were obtained with the aforementioned methods, except for C. tenuissimus for which the genes were not available.…”