| Dunaliella salina is a single-celled organism in the Chlamydomonadales and has a layer of glycoprotein instread of cell walls.D.salina can grow up in the medium under the high concentration of NaCl from 0.05 M to saturated,thus it can be served as a model organism for studying the biological properties of halophiles.D.salina also contains a variety of substances,including glycerin,β-carotene,protein,and vitamins as well.Therefore,it has been considered as commercial resource for nutritional value.The analysis of the genome of D.salina is the basic foundation for studying its origin,evolution and important biological characteristics.In this study,in order to investigate the orgin of D.salina and the genetic basis of its key biological traits,we conducted a genome-wide analysis of D.salina(FACHB-435),and utilized the genome to analyze the D.salina under salt stress.The transcriptome is motivated to study the molecular mechanisms of its halophilicity.The main results of this study are as follows:(1)In order to analyze the genome of D.salina,we selected one of it which numbered FACHB-435 from the freshwater algae species library of the Chinese Academy of Sciences,as a research object,and assembled by modern high-throughput sequencing technology and bioinformatics analysis.As a result,the main genome assembly provides approximately 471 Mb arranged in 1623 scaffolds(N50=458 kb)with 49% G+C content.With a conservative annotation approach using transcriptome data,the presented draft genome revealed 30752 protein-coding genes.Based on the BUSCO analysis,D.salina genome were demonstrated to be high integrity,genome with the annotation integrity of 91.1%.(2)In order to study the evolutionary position of D.salina in the Chlamydomonadales,we use comparative genomics strategy to analyze the evolution of Chlamydomonas eustigma,Chlamydomonas reinhardtii,Gonium pectoral,Volvox carteri,D.salina.The results indicated that Arabidopsis thaliana and the Chlamydomonadales have a divergence time of 448.14 million years,and then the genus Dunaliella and the genus Chlamydomonas and other species in the Chlamydomonadales have a divergence time of 250 million years,and Chlamydomonas eustigma was in the 232.55 million years.Chlamydomonas reinhardtii and the multicellular algae were splitted about 159.54 million years,and Gonium pectoral and Volvox carteri have a divergence time of 150 million years.These results further illustrated the origin of multicellular species and extreme species in the Chlamydomonadales.(3)D.salina is a model organism for studying the biological characteristics of halophiles.To assess the quanlity of the genome in this study,we compared our genome with the published genome of CCAP19/18 by using them as reference to align the published salt stress transcriptome sequences.The results showed that our published genome have 90% of mapping rate while the published genome CCAP19/18 only has 7% of mapping rate for the transcriptome sequences,demonstrating the high quanlity of our genome.We obtained a subset of 727 and 497 differentially express genes at the time points 24 h after salinity increase and decrease,respectively.While obtaining a subset of the 330 and 553 differentially transcribed ESTs in response to salinity increase and decrease,respectively,by de novo assembling transcriptomic profiling of CCAP19/3.And then based on the FACHB-435 genome compared to CCAP19/3 of transcriptome sequences,which obtain differentially expressed genes,were analyzed by KEGG annotation.The transcriptome analysis showed that glycerol metabolism process involved in the response to salt stress in D.salina,such as Glyceraldehyde-phosphate dehydrogenase(GAPDH),Glycerate kinase,Phosphoglycerate kinase as well,supporting by the evidence that a related gene of which was identified.The use of the reference genome to analyze the transcriptome greatly reduces the no-reference analysis of gene expression redundancy caused by selective splicing. |
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