Secondary Structural Characteristics And Phylogenetic Signals Of 16S RRNA In The Basal Lineages Of Hymenoptera

The basal Symphyta clade(Insecta: Hymenoptera)consists of 633 genera in 14 families.In this study,there are 14 families,85 genera and 125 species,covering all families of the basic groups of Hymenoptera,including the majority of the genera of Blasticotomidae and Cimbicidae,13 subfamilies of Tenthredinidae.To better study the16 Sr RNA comparative genomics of the basal group of Hymenoptera,we have also added 7 families,10 genera,and 14 species to the basal cladistic group of Apocrita.In this study,based on the mitochondrial ribosomal large subunit 16 S r RNA gene fragment of Hymenoptera,the characteristics of its secondary structure were studied,and its applicability in reconstructing the phylogenetic relationship was found by splitting the stem-loop of 16 S r RNA secondary structure,and the phylogenetic relationship of the basal group of Hymenoptera was inferred by the NJ method.The results show that:1.Based on the prediction and analysis of the secondary structure of mitochondrial ribosomal large subunit 16 Sr RNA in 139 groups of Hymenoptera.The model of 16 S r RNA secondary structure of the base group of Hymenoptera was determined.Many conserved sites were found to be associated with the biological functions of the ribosome.The secondary structure model of 16 S r RNA are divided into 6 domains with 44-45 stems or stem-loops,among which some stems or stem-loops in regions IV,V and VI are relatively conservative.Domain I contains three stem-loops(H183-H461).The pairing number(1-3 pairs)and base composition of H183 vary greatly among families,but are stable within families.There are six pairs of H235 in all families,but the number of bases of hairpin loop and internal loop is slightly different.Except for corynis zhengi of Cimbicidae,the number of bases of hairpin-loops of H461 are the same.H461 is involved in the exit channel of the polypeptide.Domain ? contains 16-17 stem-loops(H533-H1196),and the number of pairs was stable except H837 and H1196.H563 is the most conservative structure in Domain II,and the six stem-loops H579,H671,H736,H777,and H946 are relatively conservative,with little difference within and among families.These relatively conserved stem-loops are involved in the exit channel of the polypeptide.Domain ? contains 10 stem-loops(H1648-H2023).The internal loop of H1648 is unstable,and the 1-4 and 8th pairs are variable.The most conservative stem is H1775,which is composed of 15 bp bases.H1875 contains 7-8 pairs(Siricidae,Blasticotomidae and Cladiinae have 7 pairs).The several sties of H1648,H1764,and H1775 stems are involved in the exit channel of the polypeptide,and the partial sties of H1906 was related to the P-site,the partial sties of the hairpin loop was related to Asite,and the partial sties of single between H1925 and H1935 was related to A-site.There were 12 stem-loops(H2043-H2588)in the V Domain.The lateral bulge and internal loop of H2043 are consistent with the eighth to tenth pairs in all families.Except for H2077,H2347,and H2395,most of the stems are stable.Many stems of domain V are involved in the composition of polypeptide exit channels,and many Asite,P-site,E-site,and antibiotic resistance sites are located in domain V.There are three stem-loops(H2646?H2735)in the ? domain.Only H2646 is stable.The pairing numbers of H2647 and H2735 were the same in all species,but the differences of pairing bases and hairpin-loops,and they were only stable within the genus.2.By visualizing the secondary structure stem-loop comparisons of 85 genera in14 families,24 stem-loop were found(H533,H536,H579,H671,H687,H736,H777,H812,H822,H946,H991,H1057,H1648,H1764,H1792,H1835,H1906 H1935,H2023,H2043,H2259,H2455,H2520,H2547)for some sites containing phylogenetic signals.The first four bases of H183(CAAU)and the first pair of H533(U-U pair)are the synapomorphy of Xyelidae,the second site of H563 hairpin loop(U)is the synapomorphy of Pamphilioidea and Unicalcarida,the first pair of H579(G-U pair)and the second pair of H991(C-G pair)are the synapomorphy of Blasticotomidae,and the eighth pair of H2455(A-U pair)is the synapomorphy of Cephidae.3.Phylogenetic relationships of 16 S r RNA were inferred by BI,ML,and NJ methods,show that:The phylogenetic relationships inferred by BI and NJ methods shows that(Pamphilioidea + Unicalcarida)and Tenthredinoidea are sister groups,the phylogenetic relationships inferred by ML method shows that Pamphilioidea and Unicalcarida +Tenthredinoidea)are sister groups.In Unicalcarida,the phylogenetic relationships inferred by BI and ML methods shows that(Orussidae +(Siricoidea + Apocrita))and(Cephoidea + Xiphydrioidea)are sister groups,but by NJ method shows that(Cephoidea + Orussidae)and(Siricoidea +(Apocrita + Xiphydrioidea)are sister groups.In Tenthredinoidea,the phylogenetic relationships inferred by the three methods shows that Blasticotomidae and other groups of Tenthredinoidea are sister groups,Pergidae and Argidae are sister groups,Athaliinae and Cimbicidae?Diprionidae?Heptamelidae?Tenthredinidae are sister groups,and the phylogenetic relationships of BI and NJ shows that Cimbicidae and Diprionidae are sister groups,but by ML method shows Cimbicidae and Heptamelidae are sister groups.In Tenthredinidae,the phylogenetic relationships inferred by the three methods shows that(Rocaliinae + Selandriinae)and Dolerinae are sister groups,(Nematinae +Hoplocampinae)and Cladiinae are sister groups.The phylogenetic relationships inferred by NJ shows that(((Nematinae + Hoplocampinae)+ Cladiinae)+(((Dolerinae+ Selandriinae)+ Rocaliinae)+(Megabelesinae +(((Blennocampinae + Fenusinae)+((Allantinae + Caliroinae)+ Belesinae)+ Tenthredininae)))).The phylogenetic relationships inferred by BI shows that(Nematinae + Hoplocampinae)and Cladiinae are sister groups,(Rocaliinae + Selandriinae)and Dolerinae are sister groups,and Megabelesinae and Tenthredininae ? Belesinae ? Allantinae ? Fenusinae ?Blennocampinae?Caliroinae are sister groups,and the phylogenetic relationships among Tenthredininae?Belesinae?Allantinae?Fenusinae?Blennocampinae?Caliroinae could not be resolved.The phylogenetic relationships inferred by ML shows that(((Nematinae + Hoplocampinae)+ Cladiinae)+((Dolerinae + Selandriinae)+Rocaliinae))+((Allantinae + Caliroinae)+(Belesinae +((Megabelesinae +(Blennocampinae + Fenusinae))+ Tenthredininae))))).4.The phylogenetic relationship among the genera is consistent with the results of current studies on the basal groups of Hymenoptera.Therefore,this study considers that the sequence of 16 S r RNA is suitable for the inference of the phylogenetic relationship of low-order taxons.