The Nannochloropsis oceanica (Yellow Sea, Qingdao) genome: gene mining by comparative genomics and RNA sequencing
December 18, 2013 4:57: pm | by Matthew Hills
Thomas Mock (UEA), Vincent Moulton (UEA), Mario Caccamo (TGAC)
Nannochloropsis belongs to the group of Heterokontophyta, a diverse algal group that includes brown algae and diatoms. The plastid of this alga is surrounded by four membranes derived from a secondary endosymbiotic event. Strains from this genus have been investigated for their lipid composition and lipid accumulation. In addition, the biomass production by strains of Nannochloropsis grown under different conditions has been increasingly studied in recent years. Nannochloropsis species grow in fresh and salt water and can even be grown heterotrophically on glucose, sodium acetate and Na2CO3. Almost all species from this genus are characterized by high lipid content, especially triacylglycerols. Given the potential of this alga as an industrial feedstock and the progress made in developing homologous gene replacement, several research groups have set out to sequence the genome of different Nannochloropsis strains and draft genomes of Nannochloropsis oceanica and Nannochloropsis gaditana have recently become available. The genomes of Nannochloropsis species are <30Mb in size.
- Comparative genomics with all available Nannochloropsis genomes to identify species-specific differences in gene content and genes that are shared.
- RNA-seq under different growth conditions relevant for understanding the biology of this genus and for optimising biotechnological applications.
This is a collaborative project between Norwich Research Park, the University of Konstanz in Germany (Prof. Peter Kroth) and the Ocean University of China in Qingdao (Prof. Guanpin Yang). Specific emphasis will be given on the analysis of the Nannochloropsis oceanica strain from our Chinese project partner. Comparative genome and transcriptome analyses will be conducted at The Genome Analysis Centre (TGAC), the School of Computing Sciences and the School of Environmental Sciences at the University of East Anglia.