Phylogeny And Codon Usage Pattern Research Of Eukaryotic Algae Based On RbcL Gene

Algae plants have important economic value such as edible,medicinal,agricultural and industrial utilization.With the development of molecular biology,we can analyze their classification and phylogeny at the molecular level.Rubisco enzyme is the main soluble protein in chloroplast matrix,it contains 8 identical large subunits and 8 identical small subunits,and its catalytic site is mainly located on the large subunit,and the gene encoding the large subunit is the rbcL gene.To explore the taxonomic relationship of algae,the rbcL genes of Chlorophyta,Rhodophyta,Bacillariophyta,Euglenophyta,Phaeophyta,Cryptophyta and Dinophyta were selected from the NCBI database to establish phylogenetic tree to explor e the relationship among them.At the same time,the rbcL genes of seven algae were analyzed by bioinformatics methods.Finally,the codon preference of seven algae genes was analyzed to explore their codon usage patterns.The main results are as follows:1.Phylogenetic trees were constructed by Neighbor-Joining method for 184 rbcL gene sequences of 7 algal phylum groups.The algae of Chlorophyta and Euglenophyta were clustered into one branch,and the support rate was 100%.The algae of Rhodophyta and Cryptophyta were clustered into one branch,and the support rate was80%.Although the algae of Phaeophyta and Bacillariophyta were clustered into one branch,the support rate was only 56%.While the algae of Dinophyta became one branch inside Bacillariophyta,the support rate was 97%.2.Through the prediction of physicochemical properties,hydrophobicity and hydrophilicity,phosphorylation sites and secondary structure of the proteins encoded by the seven algae rbcL genes,the difference between the highest and lowest values of the grand average of hydropathicity of these amino acids was small,indicating that their hydrophobicity and hydrophilicity were very stable.Furthermore,the highest grand average of hydropathicity of amino acids encoded by the algae rbcL genes of Rhodophyta,Bacillariophyta,Phaeophyta,Cryptophyta and Dinophyta are all isoleucine on the 271 st position of the sequence,indicating that the site is extremely hydrophobic.The instability indices of the proteins encoded by the rbcL gene of the seven algae were less than 40,and it was assumed that all of these proteins were stable proteins.And their grand average of hydropathicity were negative,indicating that they were all hydrophilic,which provided the basis for the rbcL gene coding protein to play its own biological function.There were some differences in the number of phosphorylation sites of protein encoded by different algae rbcL genes,but they had similar characteristics in the species and distribution of phos phorylation sites,which might be related to the maintenance of unique biological functions of algae rbcL genes.The secondary structures of algae rbcL gene coding proteins were mainly ? helix and ?folding,indicating that the structures of these proteins were relatively stable.3.The codon usage pattern analysis of 266 rbcL gene sequences of 7 algal phylum groups was performed by Neutrality mapping analysis,ENC mapping analysis,PR2-Plot analysis,Correspondence analysis and Optimal codon analysis.The GC contents of rbcL genes in 7 algal phylum groups were lower than AT contents,and showed the GC1 was greater than GC2,and GC2 was greater than GC3.For Neutrality mapping analysis,the rbcL genes of most algae were distributed in the upper left of the regression curve.However,the factors affecting codon preference of algae rbcL genes were mainly natural selection,but the intensity of mutation pressure on it were weak.For ENC mapping analysis,most of the algal rbcL genes were distributed far below th e regression curve,showing discrete distribution,indicating that there were other factors affecting codon preference except for mutation pressure,such as natural selection for gene expression level and gene length and so on.For PR2-Plot analysis,most algal rbcL genes showed that the frequency of third codon A base was approximately equal to the trend of third codon T base,indicating that both mutation pressure and natural selection could affect the formation of codon usage bias of algae rbcL genes.According to Correspondence analysis,several groups of algae rbcL genes with similar distribution were determined,which provided important data basis for systematic taxonomy of algae.However,the rbcL genes of Cryptophyta and Dinophyta showed no obviously regular distribution.The codon distributions of 7 algal phylum groups had similar regularity,codons ending with A base or T base were closer to Axis1 than codons ending with G base or C base,indicating that mutation pressure still affected codon usage bias of algae rbcL genes.The optimal codons of rbcL genes o f 7 algal phylum groups were determined by optimal codon analysis,all of which tended to end with A base or T base.