Abstract
The Sphaeropleales are a dominant group of green algae, which contain species important to freshwater ecosystems and those that have potential applied usages. In particular, Raphidocelis subcapitata is widely used worldwide for bioassays in toxicological risk assessments. However, there are few comparative genome analyses of the Sphaeropleales. To reveal genome evolution in the Sphaeropleales based on well-resolved phylogenetic relationships, nuclear, mitochondrial, and plastid genomes were sequenced in this study. The plastid genome provides insights into the phylogenetic relationships of R. subcapitata, which is located in the most basal lineage of the four species in the family Selenastraceae. The mitochondrial genome shows dynamic evolutionary histories with intron expansion in the Selenastraceae. The 51.2 Mbp nuclear genome of R. subcapitata, encoding 13,383 protein-coding genes, is more compact than the genome of its closely related oil-rich species, Monoraphidium neglectum (Selenastraceae), Tetradesmus obliquus (Scenedesmaceae), and Chromochloris zofingiensis (Chromochloridaceae); however, the four species share most of their genes. The Sphaeropleales possess a large number of genes for glycerolipid metabolism and sugar assimilation, which suggests that this order is capable of both heterotrophic and mixotrophic lifestyles in nature. Comparison of transporter genes suggests that the Sphaeropleales can adapt to different natural environmental conditions, such as salinity and low metal concentrations.
Highlights
Genome evolution in the Sphaeropleales is little understood compared to that of the Chlamydomonadales
The cox2b gene is located in the nuclear genome, and it appears to have been transferred to the nuclear genome via an endosymbiotic gene transfer (EGT)[17]
In the Chlamydomonadales, both cox2a and cox2b are in the nuclear genome; the genes of T. obliquus are thought to be an intermediate character in EGT18
Summary
Genome evolution in the Sphaeropleales is little understood compared to that of the Chlamydomonadales. In the Chlamydomonadales, both cox2a and cox2b are in the nuclear genome; the genes of T. obliquus are thought to be an intermediate character in EGT18 These mitochondrial characters are conserved in the Sphaeropleales[17,19]. Well-resolved phylogenetic relationships have been recently reported for the Sphaeropleales, using plastid or mitochondrial genome-encoded proteins[19,20,23,24], the organellar genomes of R. subcapitata have not been sequenced. We sequenced the nuclear, mitochondrial, and plastid genomes of R. subcapitata, and compared them to other Sphaeropleales species genomes to reveal genome evolution in the order based on well-resolved phylogenetic relationships and to understand their genetic background in relation to high sensitivity to chemicals (e.g. metals). The nuclear genome of R. subcapitata is the most compact in this order, and comparison of proteins indicates that the Sphaeropleales can adapt to a variety of nutrient and environmental conditions
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