Comparative Genomics Study Of The TPS Family Of Cruciferous Plants

Terpenoids have important physiological,ecological and medicinal value,which are the precursors of plant hormone,they involved in the regulation of plant growth and development,such as strigolactones,ABA,as well as to attract pollinators and against pathogens or herbivores,such as(E)-a-bergamotene and(E)-?-farnesene.Terpenoid synthases are key enzyme in the synthesis of terpenoids.Terpenoids can be synthesized by two pathways:mevalonate(MVA)pathway and 2-C-methyl-D-erythritol-4-phosph-ate(MEP)pathway.The TPS gene family have be identified and analyzed in Arabidopsis thaliana,Vitis vinifera,Populus tremula,Oryza sativa,Solanum lycopersicum,Gossypium spp,Sorghum bicolor,Zea mays,Glycine max,physcomitrella patens and Selaginella moellendorffli genome-wide.Brassicaceae species have high economic value and closely related to human life,including oil crops,vegetable plants,ornamental plants and medicinal plants.There are many terpenoids have be identified in Brassicaceae species,such as(E,E)-geranyllinalool,nerolidol et al.Consider the importance of terpenoids and the key role of TPS in synthesis of terpenoids,the TPS family has been studied systematically in the model plant Arabidopsis thaliana.However,the research of other Brassicaceae species is still rare.With more and more genome have been sequenced from Brassicaceae species,it is possible for us to identify TPS systematically and conduct comparative analysis by bioinformatics.Our research is the first time using comparative genomics approach to systematic study on the terpenoid synthase gene families from 12 Brassicaceae species which have completed the sequencing Aethionema arabicum,Arabidopsis thaliana,Arabidopsis lyrata,Capsella rubella,Eutrema salsugineum,Brassica rapa,Brassica oleracea,Brassica napus,Leavenworthia alabamica,Sisymbrium irio and Schrenkiella parvula and Carica papaya(as an outgroup).Firstly,we identified TPS genes from 13 species,moreover,we explored the gene feature of TPS and studied the evolution and the distribution of the TPS gene from the perspective of the genome,the last but not least,we analyzed the co-linear relationship of TPS genes from Brassicaceae.Our research will provide a theoretical basis for further experimental study of TPS gene function of Brassicaceae species,the results show:1.Our study identified 335 full-length TPS genes from 13 plants by HMM prediction model,of which 325 from Brassicaceae species,10 from Carica papaya,the number of TPS in each species is 10-68,Carica papaya have the minimum number 10 and Camelina sativa have the maximum number 68.2.The result of genetic information and chromosomal localization.The study showed that there is little differentiation of the TPS gene sequence length between the different species,the length of the protein sequence is about between 426?822aa,the average length of the coding sequence is about between 1718?193 6nt,the length of the gene sequence is about between 3166?5624nt.The study of chromosomal location found that there are 46 TPS gene copy series,which involving in 108 TPS genes,we speculated that the gene tandem duplication is the main way of the TPS gene amplification.3.The result of Genetic characteristics and structural analysis.Through a number of characteristic values calculated of TPS family genes,such as GC content,GC3,ENc and CAI,GC content and GC3 values are about 0.4,ENc are all greater than 4.0,the value of CAI is about 0.2.The results revealed that TPS genes are conservative during evolution.The proportion of TPS genes which contain exon number between 5 to 10 is maximum,can reach more than 50%of the total number of TPS genes in each species,Arabidopsis lyrata,Arabidopsis thaliana,Sisymbrium irio do not containing TPS genes with exon number<5.4.The result of phylogenetic and protein domains analysis.TPS genes show that TPS genes can be divided into five subfamilies,TPS-a,TPS-b,TPS-c,TPS-e/f and TPS-g.TPS-a and TPS-b contain the largest number of TPS,account for 80.6%of the total number,TPS-g subfamily have the least number of TPS and lost during the evolution-in some species..For.different subfamilies,we further analyzed the protein domain,the number;of motif in,each,subfamily mostly between 7-10,the number of each subfamily Motif and the regularity of the distribution of TPS genes verify that TPS genes can be divided into five subfamilies.5.The result of collinearity analysis.Our study selccted 9 known function TPS genes from Arabidopsis thaliana and analyzed its co-linear relationship with other Brassicaceae genes,the number of collinearity genes of each gene is between 78-155,which suggested that there is certain relevance in evolution among species,this revealed the conservation of TPS genes once again.Conclusion:In this study,we use bioinformatics tools to predict and analyze the TPS genes from Brassicaceae species and Carica papaya and identified 335 full-length TPS genes,which will provide us theoretical basis for further screening function TPS.Although our prediction model can't fully explain the evolutionary mechanism of TPS family genes,but our study will help people learn more about the family gene for TPS.