| The freshwater red algae is a special and rare lineage in freshwater algal evolution.Batrachospermaceae is the most important group.The rbcL gene,psbA gene and psaA gene are three genes with important biological functions in chloroplasts of Batrachospermaceae.The rbcL gene encode the large subunit of Ribulose-1,5 bisphosphate carboxylase/oxygenase(Rubisco);psbA gene encode PS? reaction center Q? protein,namely the D1 protein;psaA gene encode the central protein A of the photosystem ?(PS ?)transmembrane complex,also known as P700 apoproteinA.Consideringthe important biological functions of the three genes,in order to explore the molecular mechanism of them to adapt to the special living environment and understand their evolution history,the adaptive evolution and co-evolution of these three genes were analyzed in this paper.The phylogenetic trees were constructed based on Maximum Likelihood method using target sequenced gene sequences and the related genes in Genbank.Based on gene sequences and phylogenetic tree,software PAML4.8 was used to run the site model,branch model,and branch-site model to analyze the adaptive evolution of the three genes.Based on gene sequences and three-dimensional structure of protein constructed by homology modeling,the co-evolutionary analysis of the three genes was performed using software CAPS based on Pearson correlation coefficient method,parametric test method,and mutual information method.The specific findings are as follows:(1)In the analysis of adaptive evolution and co-evolution of the rbcL gene of Batrachospermaceae using software PAML4.8,the six branches of the intrinsic cluster were selected in the phylogenetic tree constructed based on Maximum Likelihood method.Cluster A is Bangia atropurpurea,B is Batrachospermum gelatinosum,C is Batrachospermum.helminthosum,D is the genus Kumanoa,E is the genus Sirodotia,and F is Sheathia arcuata;350S,277 L,and 280 L are identified as positive selection sites on three branches in the branch-site model;Mark positive selection sites in constructed reference three-dimensional model of the Rubisco large subunit.277 L and 280 L are located in a loop between the 7th ? helix and the 7th ?sheet of the conserved ?/?-barrel domain that consists of 8 ?-helices and 8?-sheets at the C-terminus,and 350 S is located on an ? helix in the C-terminus adjacent to the ?/?-barrel domain.This results revealed that the rbcL gene has undergone adaptive evolution,which has been beneficial to Batrachospermaceae for the adaption to the special living environment.The amino acid co-evolution relationship within Rubisco large subunits was analyzed using software CAPS.Six co-evolution groups(35 pairs of co-evolution sites)were identified based on the correlation coefficients of amino acids.Based on the amino acid hydrophobicity correlation values,6co-evolution groups(35 pairs of co-evolution sites)were identified,and 6co-evolution groups(35 pairs of co-evolution sites)were identified based on the amino acid molecular weight correlation values.All co-evolution groups(pairs)of Rubisco large subunits were significantly related to the hydrophobicity and molecular weight of amino acids,suggesting that they are co-evolutionary in the evolution of the protein and are important for maintaining the functional structure of the protein.(2)In the analysis of adaptive evolution and co-evolution of the psaA gene of Batrachospermaceae using software PAML4.8,no statistically significant positive selection sites were detected in the selected 9 branches,suggesting psaA gene is under strong negative selection in various groups.Its high degree of conservation maintains its important biological functions.These results are consistent with existing studies and are consistent with the high conservation of the chloroplast genome.In view of the highly conserved nature of psaA gene,based on previous phylogenetic studies,it is suggested that the gene is suitable for phylogenetic relationships among genus and higher taxonomic level and it has potential as a taxonomic marker for algaesystematics.In addition,the amino acid co-evolutionary relationship within center proteinA of PS ? was analyzed using software CAPS.Five co-evolution groups(20 pairs of co-evolution sites)were identified based on the correlation coefficients of amino acids.Based on the amino acid hydrophobicity correlation values,5 co-evolution groups(12 pairs of co-evolution sites)were identified,and 5 co-evolution groups(15 pairs of co-evolution sites)were identified based on the amino acid molecular weight correlation values.15 pairs of co-evolution sites of center proteinA of PS?were significantly related to the hydrophobicity and molecular weight of amino acids,suggesting that they are co-evolutionary in the evolution of the protein and are important for maintaining the functional structure of the protein.(3)In theanalysis of adaptive evolution and co-evolution of the psbA gene of Batrachospermaceae using software PAML4.8,no statistically significant positive selection sites were detected in the selected 9 branches,suggesting psbA gene is similar with psaA gene and both are under strong negative selection in various groups.The amino acid co-evolutionary relationship within D1 protein was analyzed using software CAPS.There was no co-evolution group(pair),and we consider this result is unreliable,probably because the sequence data used for the analysis were properly edited and were not complete.The psbA gene needs to be combined with multiple genes to perform its function.Therefore,a one analysis of the coevolutionary relationship of single gene is not sufficient.The molecular mechanism of the evolution process of organisms is extremely complicated,especially for special plants such as freshwater red algae.Therefore,in order to reveal its evolutionary history and explain how it can adapt to a particular living environment,it is necessary to conduct further study on more genes.These research hopes to further deepen the understanding of the molecular mechanisms in adaptive evolution of chloroplast genesto living conditions. |
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