Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae

Abstract

Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. While extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, LINE repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and non-mevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon

“…Our findings echo those of Watanabe et al (2016), that the relatively simple vegetative morphology characteristic of Hormotilopsis, especially the 2-4-celled packets, is repeatedly seen among phylogenetically distinct taxa in Chaetopeltidales. Analysis of 18S rDNA is very useful for placing green algae into major lineages, and even into less inclusive groups such as orders and families, but it can have less utility for species level identification as the 18S rDNA sequence can be identical or nearly so among closely related species (e.g., Lewis and Flechtner, 2002;Hall et al, 2010;Yang et al, 2021). The results of the 18S analysis presented here (Appendix S2) supports Gormaniella as a member of the Chaetopeltidales, with close affinity to Hormotilopsis gelatinosa (the type species) and Floydiella (a monotypic genus), but distinct from H. tetravacuolaris, Chaetopeltis, Pseudulvella, Koshicola, and Dichranochaete.…”

The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids

“…Another published genome of Vischeria alga ( V. sp. C74) [ 22 ] has a size of 106.5 Mb and contains 47.7% of the REs (Additional file 1 : Table S6). In contrast, the RE content was only 1.9–8.7% in species of Microchloropsis and Nannochloropsis with genome size from 26.9 to 35.5 Mb [ 5 – 8 ] (Additional file 1 : Table S6).…”

“…H4302, V . stellata , and twelve species with previously published genomes [ 6 – 8 , 22 , 44 , 78 – 80 ] (Additional file 1 : Table S8). If a gene had more than one transcript, the longest transcript was used.…”

Novel Insight of Nitrogen Deprivation Affected Lipid Accumulation by Genome-Wide Lactylation in Nannochloropsis oceanica

“…Under nitrogen stress, Nannochloropsis species store lipids as triacylglycerides (TAG), which may account for up to 60% of its dry weight. − More and more synthetic biologists are focusing on Nannochloropsis species because of its potential as a model organism and a source of future food, sustainable biodiesel production, and other high-value products. − The poor development under nitrogen deprivation (ND) or stress is a common problem for agricultural and industrial applications of Nannochloropsis spp. To maximize its photosynthetic output, it is crucial to have a firm grasp of the pathways involved in TAG biosynthesis and the activation of those processes in response to nitrogen deprivation at multiple levels. , In recent years, the omics tools of transcriptomes and proteomes were employed to understand the molecular mechanism of oil production under nitrogen stress. − Nannochloropsis species under ND have been the focus of much proteome-level research.…”