Development And Application Of Bioinformatics In Research Of Marine Dinoflagellates

Dinoflagellates are primary producer in ecosystem with a special phylogenetic position as well as several unusual genomic features including extremely huge size of genome.In addition,dinoflagellates are of ecological significance.Some species can cause harmful algal blooms,which can bring diaster to the ecosystem as well as econimic activities.And Symbiodium,a distinct group of dinoflagellates with complicated genetic diversity,are essential endosymbionts of reef building corals;disruption of its symbiosis with corals leads to coral bleaching.Based on these,research on dinoflagellates is critically importantThe development of Next-Generation Sequencing has provided innovative techniques for ecological research,and has produced large amount of data.This research aims to apply and develope bioinformatics methodology,by metabarcoding and transcriptomic data mining and analysis,to gain understanding on the relationship between dinoflagellates,genes and ecological environments.We adopted metabarcoding methodology to study the genetic diversity of Symbiodinium in South China Sea.Our major accomplishments included:1)We surveyed the genetic diversity of Symbiodinium associated with coral in South China Sea,and the results showed that the Clade C and Clade D were dominant,which were similar to what have been reported in Indo-Pacific corals;2)We detected several clades such as Clade E,Clade F that have been rarely found to be associated with corals.This indicated that traditional methods including ITS2-DGGE underestimated the genetic diversity associated with coral;3)We found that Symbiodinium genetic diversity within clade C showed some geographic or coral host specificity;4)Our results also indicated that Symbiodnium-specific primers and metabarcoding methods developed in this study is well-suited to study Symbiodinium diversity.Besides,this study also explored taxonomic distribution of mycosporine-like amino acids(MAAs)synthesis genes by colletcing and mining existing genomic and transcriptomic data.MAAs are a seires of UV-absrobing chemical compounds that are critical for the aquatic ecosystem to resist UV radiation.Our results include:1)We detected MAAs synthesis genes across multiple taxonomic groups including Cyanobacteria,Actinobacteria,Proteobacteria,Fungi,dinoflagellates,diatoms,red algae,Raphidophyceae as well as cnidaria.From this taxonomic distribution,we explored the origin and evolution of the synthesis machinery of MAAs in aquatic ecosystem;2)We found that previous research had documented variability in the ability in Symbiodinium to produce MAAs.In this study,we screened three existing genomes of Symbiodinium for MAAs synthesis genes,and only Symbiodinium microadriaticum showed the presence of these genes while no above-mentioned genes were found in S.minutum or S.kawagutii.This result is consistent with culture experiment results reported previously,and provides genetic evidence for the above-mentioned varibility in Symbiodinium;3)All the results indicate that the capacity of eukaryotic algae to produce MAAs may have been acquired from Cyanobacteria by endosymbiosis.