Goemann, Calvin L.C.Wilkinson, RoyceHenriques, WilliamBui, HuyenGoemann, Hannah M.Carlson, Ross P.Viamajala, SridharGerlach, RobinWiedenheft, Blake2023-06-082023-06-082023-01Goemann, Calvin LC, Royce Wilkinson, William Henriques, Huyen Bui, Hannah M. Goemann, Ross P. Carlson, Sridhar Viamajala, Robin Gerlach, and Blake Wiedenheft. "Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04." Algal Research 69 (2023): 102943.2211-9264https://scholarworks.montana.edu/handle/1/17954© This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/Algae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments – high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Collectively, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequence-based methods.en-UScc-by-nc-ndhttps://creativecommons.org/licenses/by-nc-nd/4.0/Chlorella sp.Ultra-long-read sequencingComplete genomeProtein 3D structural annotationATP citrate lyaseSphingolipidsArticle