Genome Annotation and Differential Expression Analysis of Green Algae Chlorella spp.

The unicellular photosynthetic green algae (Trebouxiophyceae) Chlorella finds application in several fields including renewable energy and as source of animal feed. High growth rates and the ability to cope with high light conditions are traits that are considered of great interest. An annotated genome can help to detect genes that are linked to favourable traits. We annotated the genomes of the green algae Chlorella spp. C. vulgaris 264, C. vulgaris C-1, C. vulgaris 211-11b and C. sorokiniana 211-8k using the genome annotation pipelines BRAKER1 and MAKER2 and evaluated the performance with BUSCO and BLAST. RNA-Seq reads of algae cultivated under low light (LL) and high light (HL) conditions were mapped to the genome and analysed for differential expression. The number of significant differentially expressed genes varied between 1226 and 3457. We assigned Human Readable Descriptions (HRD) and Gene Ontology (GO) terms to the predicted protein-encoding genes and differentially expressed genes using AHRD. About 99% of the predicted genes, and 92% of the differentially expressed genes were assigned putative functions.