Genome Improvement And Molecular Responses To Nutrient Deficiencies Of Fugacium Kawagutii

Zooxanthellae(dinoflagellates in the family Symbiodiniaceae)is a kind of unicellular algae that can establish symbiotic relationship with coral and other marine invertebrates.More than 100 species of zooxanthellae have been reported to establish symbiotic relationship with coral.The symbiotic relationship between zooxanthellae and corals are the foundation of the coral reef ecosystem,which has far-reaching significance for maintaining coral health and functional stability of the highly biodiverse ecosystem.However,with the impact of global climate changes and human activities,the coral reef ecosystem is facing many challenges,and coral bleaching is serious.The loss of the dinoflagellate symbionts and/or their pigment from the coral in response to environment stress can lead to coral bleaching and ultimately death of the coral and destruction of the reef.The internal molecular mechanism of coral bleaching is still unclear.Therefore,understanding zooxanthellae’s gene structure and gene expression responses to environmental stress is the key to understand whether corals and zooxanthellae can adapt to future climate changes.In this research,Fugacium kawagutii was studied in the following five aspects:1.Combining Hi-C,Illumina and pacbio sequencing technologies,the genome of F.kawagutii was re-sequenced and assembled.The N50 of the recombined genome reached 13533496 bp,and several scaffolds had telomere structure at both ends,indicating that the genome assembly reached the chromosome level.The gene set contains 45192 protein coding genes,of which 11984 are new predicted genes.The updated genome of F.kawagutii is of the best quality among the seven reported symbiodiniacean genomes,which provides a more accurate reference data set for the study of gene structure and gene expression in the future.2.By analyzing the transcriptome data of F.kawagutii under five trace metal deficiency conditions,we found differential influences of five trace metals,with the following ranking order:Fe>Mn>Zn>Cu>Ni.Under the deficiency of five trace metals,the genes encoding extracellular matrix(ECM),cell surface structure,cell adhesion and cell immunity were regulated.In addition,under iron deficiency,the antioxidant capacity of cells decreased,the production of reactive oxygen species increased,and the possibility of oxidative damage,metabolic disorder,cell damage and cell mutation increased.Therefore,the deficiency of trace metals(especially iron)seems to promote energy metabolism,innate immunity and cell adhesion,inhibit the cell growth and the ability to scavenge reactive oxygen species(ROS).When this stress environment occurs in the coral endoderm,it may cause the symbionts to be expelled by the coral host,thus leading to coral bleaching.3.The transcriptome data and physiological data of F.kawagutii under nitrogen deficiency were analyzed.The results showed that nitrogen deficiency can decrease cell growth,chlorophyll-a content,energy production,scavenging capacity of ROS and transport capacity of photosynthetic products.Under nitrogen deficiency,52 response genes related to nitrogen transport and transformation were screened.Among them,8 genes showed no differential expression to five trace metal ions,phosphorus and heat shock,which could be used as indicator genes of nitrogen stress.4.The differences of ammonium and nitrate uptake by F.kawagutii were compared by nutrient uptake kinetics and transcriptome analysis.The results showed that when both ammonium and nitrate were present in the medium,F.kawagutii preferentially utilized ammonium,and the genes involved in nutrient transport and nitrogen assimilation were down regulated in the ammonium-based condition,which indicated a reduced investment in nutrient transport and assimilation when ammonium is the source of N nutrient.Growing on ammonium produced a similar cell yield as nitrate,but the uptake rate of ammonium was faster than that of nitrate;yet at high concentrations ammonium exhibited inhibitory effects.5.Referring to the screening methods of the published core gene set,stable and highly expressed genes were screened across five trace metal deficiencies,nitrogen deficiency and ammonium treatment conditions.Combined with the published core gene set of F.kawagutii under phosphorus stress,high temperature stress and organic phosphorus treatment conditions,the latest version of the core gene set of F.kawagutii was generated.The new core gene set consists of 10 genes,which are stably expressed in 11 environmental conditions,and can be used as candidate reference genes,which lays a foundation for further research on gene expression.