The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes

Abstract

The genome of the marine alga Ulva compressa was assembled using long and short reads. The genome assembly was 80.8 Mb in size and encoded 19,207 protein-coding genes. Several genes encoding antioxidant enzymes and a few genes encoding enzymes that synthesize ascorbate and glutathione were identified, showing similarity to plant and bacterial enzymes. Additionally, several genes encoding signal transduction protein kinases, such as MAPKs, CDPKS, CBLPKs, and CaMKs, were also detected, showing similarity to plants, green microalgae, and bacterial proteins. Regulatory transcription factors, such as ethylene- and ABA-responsive factors, MYB, WRKY, and HSTF, were also present and showed similarity to plant and green microalgae transcription factors. Genes encoding enzymes that synthesize ACC and ABA-aldehyde were also identified, but oxidases that synthesize ethylene and ABA, as well as enzymes that synthesize other plant hormones, were absent. Interestingly, genes involved in plant cell wall synthesis and proteins related to animal extracellular matrix were also detected. Genes encoding cyclins and CDKs were also found, and CDKs showed similarity to animal and fungal CDKs. Few genes encoding voltage-dependent calcium channels and ionotropic glutamate receptors were identified as showing similarity to animal channels. Genes encoding Transient Receptor Potential (TRP) channels were not identified, even though TRPs have been experimentally detected, indicating that the genome is not yet complete. Thus, protein-coding genes present in the genome of U. compressa showed similarity to plant and green microalgae, but also to animal, bacterial, and fungal genes.

Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta)

“…This strong selection of A + T preference seen in plastomes does not appear in nuclear genomes of Ulva species (e.g. 57.2% in U. mutabilis and 57.3% in U. compressa ) ( De Clerck et al., 2018 ; Osorio et al., 2022 ).…”

Transcriptomic analyses reveal increased expression of dioxygenases, monooxygenases, and other metabolizing enzymes involved in anthracene degradation in the marine alga Ulva lactuca

“…However, these 2-OGDOs do not participate in the hydroxylation of phytohormones such as gibberellins since these phytohormones may not be present in U. lactuca , as it has been shown in U. mutabilis (De Clerck et al, 2018 ). In addition, the genome of another Ulvophyceae, U. compressa , was recently sequenced, and genes encoding enzymes involved in the synthesis of auxin, gibberellins, and cytokinins were not identified (Osorio et al, 2022 ). Thus, probably 2-OGDOs are not required for phytohormone activation synthesis in U. lactuca .…”

Ulva: An emerging green seaweed model for systems biology

“…The wild‐type genome (mt(−); strain 1–41) was the first whole‐genome sequence of a green seaweed (De Clerck et al, 2018). More recently, the genome of a Chilean Ulva compressa isolate has been reported (Osorio et al, 2022). Whereas the genomes have not been completed at a chromosomal level, comparison of both genomes reveal substantial differences in genome size (98.5 vs. 80.8 Mb), protein‐coding genes (12,924 vs. 19,207), and repetitive elements (35% vs. 19%; Osorio et al, 2022).…”

“…More recently, the genome of a Chilean Ulva compressa isolate has been reported (Osorio et al, 2022). Whereas the genomes have not been completed at a chromosomal level, comparison of both genomes reveal substantial differences in genome size (98.5 vs. 80.8 Mb), protein‐coding genes (12,924 vs. 19,207), and repetitive elements (35% vs. 19%; Osorio et al, 2022). Flow cytometry‐based genome size estimates from French (120 Mb) and Japanese (135 Mb) U. compressa strains further suggest significant genome size variation (Kagami et al, 2005; Le Gall et al, 1993).…”