Reveal The Factors That Influence The Reconstruction Of Phylogenetic Tree Of Gnetophytes Based On Chloroplast Genome Data

The chloroplast genome of plants is small,high copy number,conserved structure and contains important genes of plant photosynthesis and plastid semi-autonomous inheritance.Chloroplast genes and genome provide important information for molecular evolution research,and it is often used in plant molecular systematics.Gnetophytes is a unique group among extant gymnosperms with the characteristics of angiosperm,it is of great value to study the origin and evolution of seed plants,and the phylogenetic relationships of gnetophytes still remains unclear.In this paper,the CDS(Coding sequence)of common chloroplast genes was extracted from chloroplast genomes to construct data matrixs,with Maximum likelihood(ML)analyses,Maximum parsimony(MP)analyses,Bayesian inference(BI)and Neighbor-joining(NJ)analyses to reconstruct the phylogenetic tree of each gene.Compared and analysed the effects of different genes and different methods on reconstructed phylogenetic tree.Then,to select different molecular characters(base substitutions,indels and the first,the second and the third bases of codons)reconstruct phylogenetic tree and the effects of these characters on reconstructed tree were studied.Concluded as follow:(1)57 common chloroplast-encoded genes were filtrated by four different methods.The topologies of gene trees are different.Among them,the ML analyses found there are 28 genes support gnetophytes as sister to cupressophytes,and 25 genes support the relationship between gnetophytes and Pinaceae as a sister group,4 genes support the gnetophytes as sister to conifers.In MP analyses,32 genes support the relationship between gnetophytes and cupressophytes as a sister group,19 genes support gnetophytes and Pinaceae as a sister group,6 genes support gnetophytes and conifers as a sister group.In BI analyses,there are 26 genes support gnetophytes as sister to cupressophytes.22 genes support gnetophytes as sister to Pinaceae and 9 genes support gnetophytes as sister to conifers.Finally,in NJ analyses,there are 34 genes support the gnetophytes as sister to cupressophytes.15 genes support gnetophytes as sister to Pinaceae.There also are 8 genes as sister group to conifers.(2)With different chloroplast genes sequences were used to constructed phylogenetic tree,the corresponding results show that the position of the reconstructed tree of gnetophytes has changed.There are 19 genes,including psaC,psbH,atpA,atpF,rbcL,petA,petG,rpl22,rpl36,rps2,rps3,rps4,rps19,rpoA,rpoB,rpoC1,infA,cemA and ycf2 were not affected by the four methods,gnetophytes still as sister to cupressophytes.However,the phylogenetic trees of 7 genes,psaB,psbF,psbN,ycf3,ycf4,rpl14 and rps8,gnetophytes were sister to Pinaceae.Phylogenetic trees of psbE and petB show gnetophytes were sister to conifers.The gnetophytes were sister to cupressophytes were surported by more genes.(3)To most genes support the topology that gnetophytes as sister to cupressophytes and take the result of the reconstructed tree is not affected by the four methods into consideration.Then,to select related genes and the sequences of these genes are concatenated into combined data sets,which are analyzed by using ML,MP,BI and NJ respectively.In addition,the sequence matrixs of base substitutions,indels and codons of three different bases are constructed based on the combined data sets.Once again,it's used four methods to analyse these matrixs.Results show that in the ML,MP and BI analyses,the phylogenetic placements of the gnetophytes were not changed it is almost imperceptibly influenced by different molecular characters,but the bootstrap is reduced.In contarst,to analyses the first and the second bases of different positions of codons in NJ,the gnetophytes were sister to conifers,but reconstructed phylogenetic tree by the third base of the codon,shows that the gnetophytes were sister to cupressophytes.