广西扇棘单睾吸虫5.8S rRNA序列和二级结构研究
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摘要
目的:研究广西扇棘单睾吸虫和其它人体吸虫5.8S rRNA序列和二级结构,探讨人体吸虫二级结构的特征,揭示单睾吸虫之间的亲缘关系。
方法:采集广西扶绥县扇棘单睾吸虫,提取其DNA,PCR扩增5.8S rDNA序列并测序。另外选用Genbank登录的7种人体吸虫5.8S rDNA序列进行研究,包括:扇棘单睾吸虫、钩棘单睾吸虫、巨片形吸虫、裂体吸虫、獾似颈吸虫、卷棘口吸虫和猫后睾吸虫。应用DNAman软件把上述人体吸虫5.8SrDNA基因转换成5.8S rRNA。应用RNAstructure3.2软件,根据最小自由能原理,采用Zuker算法,构建5.8S rRNA分子二级结构。应用SPSSv14.0软件对5.8S rRNA一级结构和二级结构组成进行统计分析,人工比对分析部分人体吸虫5.8S rRNA序列和二级结构特征。
结果:对广西扇棘单睾吸虫与Dzikowski等报道的扇棘单睾吸虫5.8SrRNA序列进行比较,显示第81、83、84、129、143位碱基发生变异,但这些突变碱基均位于5.8S rRNA二级结构未配对碱基区,碱基突变并未影响5.8S rRNA二级结构。对广西扇棘单睾吸虫与钩棘单睾吸虫5.8S rRNA序列进行比较,发现既存在未配对碱基区的变异又存在配对碱基区的变异,配对区碱基的变异使两者5.8S rRNA二级结构呈现较大差异。对复殖目部分吸虫5.8S rRNA二级结构进行比对分析,结果显示:5.8S rRNA二级结构具有相同的基本结构模式;Ⅰ分支具有1个保守模序为5′-GUGUCGAUG:CAUCGACAU-3′(钩棘单睾吸虫为5′-GUGUCGAUG:CAUCGAUAU-3′)。Ⅱ分支具有1个保守发卡结构,该发卡结构的茎是由9个碱基对组成的保守模序,S.sp保守模序为5′-GGCUACGGG:CCUGUGGCC-3′,其它7种保守模序为5′-GGCCAUGGG:CCUGUGGCC-3′;发卡环为富含尿嘧啶的6元环。在8种人体吸虫中,除裂体吸虫和猫后睾吸虫外,其它6种吸虫5.8SrRNA 5′端均有1段单链序列。在8种人体吸虫中,除钩棘单睾吸虫外,其余吸虫Ⅰ分支均有保守模序5′-GCAG:CUGC-3′。钩棘单睾吸虫和裂体吸虫与其它6种吸虫具有不同的H部和多分支环。巨片形吸虫、獾似颈吸虫和卷棘口吸虫Ⅰ分支尾端具有一个保守发卡结构。碱基的替代、丢失和插入多发生于5.8S rRNA二级结构单链区,双链区的替代、丢失和插入则往往会引起二级结构的较大变异。
结论:本研究首次获得广西扇棘单睾吸虫5.8S rRNA基因序列,发现人体吸虫5.8S rRNA二级结构的一些特征。根据单睾吸虫二级结构特征,本研究还发现广西扇棘单睾吸虫与Dzikowski等报道的扇棘单睾吸虫亲缘关系比较近,与钩棘单睾吸虫亲缘关系比较远。
OBJECTIVE:The The sequence and secondary structure of Haplorchis taichui from Guangxi and other Digenea Trematodes 5.8S rRNA are investigated to explore the kinships of Haplorchis trematodes and the secondary structure characters of Digenea Trematodes 5.8S rRNA.
METHODS:Haplorchis taichuis were collected from Fusui county in Guangxi.The genomic DNA of Haplorchis taichui from Guangxi was extracted. The 5.8S rDNA was amplified by PCR and the sequences of PCR products were obtained by the sequencing reaction The 5.8S rDNAs of Haplorchis taichui,Haplorchis pumilio,Fasciola gigantica,Schistosoma sp,Isthmiophora melis,Echinostoma revolutum,Opisthorchis felineus from Genebank were investigated too.The 5.8S rDNAs of the above Trematodes are all transformed into the 5.8S rRNAs.The secondary structure of the 5.8S rRNAs were constructed using RNAstructure3.2 software according to the theory of minimally free energy with Zuker method.The composition of the sequence structures and the secondary structures of the 5.8S rRNAs were analyzed with SPSS v14.The sequences and secondary structures of Digenea Trematodes 5.8S rRNA were compared to explore their characters.
RESULTS:Sequence comparing was performed between the 5.8S rRNA of Haplorchis taichui from Guangxi and that previously studied by Dzikowski,with the results showing some point mutations sites in the 81th, 83nd,84th,129th and 143th nucleotide.Those sites locate in unpaired regions so that they don't affect on the secondary structural characters of the 5.8S rRNA. Sequence comparing between Haplorchis taichui from Guangxi and Haplorchis pumilio showed mutation sites which not only locate in unpaired regions but also in pared regions.The mutationof the nucleotides locating in pared regions cause more differences in 5.8S rRNA secondary structures between Haplorchis taichui from Guangxi and Haplorchis pumilio.The secondary structures of 5.8S rRNA in several Digenea Trematodes are all composed of main structure models. BranchⅠhas one conservative motif,5'-GUGUCGAUG:CAUCGACAU-3' (5'-GUGUCGAUG:CAUCGAUAU-3' in Haplorchis pumilio).BranchⅡhas a conservative hairpin,which consists of nine basepairs5'-GGCCAUGGG: CCUGUGGCC-3'(5'-GGCUACGGG:CCUGUGGCC-3' in Schistosoma sp) The hairpin loop is a six-membered ring of U rich.There is a single strand sequence in the 5' end of 5.8S rRNA among the above Trematodes except Schistosoma sp and Opisthorchis felineus.The Trematodes except Haplorchis taichui have a conservative motif(5'-GCAG:CUGC-3')in branchⅠ. Haplorchis taichui and Schistosoma sp have a different handle and multibranch loop,compared with other six Trematodes.The branchⅠend of Fasciola gigantica,Isthmiophora melis and Echinostoma revolutum have a conservative hairpin.Replacement,deletion and insertion of bases mostly occur in the single strand region of the secondary structure of the 5.8S rRNAs.While these occurre in double strand,the secondary structure changes tremendously.
CONCLUSION:It was the first time that this study had obtainded 5.8S rRNA gene sequence of Haplorchis taichui from Guangxi.The secondary structure characters of 5.8S rRNA were discovered in Digenea Trematodes. According to their secondary structure characters of 5.8S rRNA,the kinship between Haplorchis taichui from Guangxi and that previously studied by Dzikowski is nearer while the kinship between Haplorchis taichui from Guangxi and Haplorchis pumilio is more far away.
方法:采集广西扶绥县扇棘单睾吸虫,提取其DNA,PCR扩增5.8S rDNA序列并测序。另外选用Genbank登录的7种人体吸虫5.8S rDNA序列进行研究,包括:扇棘单睾吸虫、钩棘单睾吸虫、巨片形吸虫、裂体吸虫、獾似颈吸虫、卷棘口吸虫和猫后睾吸虫。应用DNAman软件把上述人体吸虫5.8SrDNA基因转换成5.8S rRNA。应用RNAstructure3.2软件,根据最小自由能原理,采用Zuker算法,构建5.8S rRNA分子二级结构。应用SPSSv14.0软件对5.8S rRNA一级结构和二级结构组成进行统计分析,人工比对分析部分人体吸虫5.8S rRNA序列和二级结构特征。
结果:对广西扇棘单睾吸虫与Dzikowski等报道的扇棘单睾吸虫5.8SrRNA序列进行比较,显示第81、83、84、129、143位碱基发生变异,但这些突变碱基均位于5.8S rRNA二级结构未配对碱基区,碱基突变并未影响5.8S rRNA二级结构。对广西扇棘单睾吸虫与钩棘单睾吸虫5.8S rRNA序列进行比较,发现既存在未配对碱基区的变异又存在配对碱基区的变异,配对区碱基的变异使两者5.8S rRNA二级结构呈现较大差异。对复殖目部分吸虫5.8S rRNA二级结构进行比对分析,结果显示:5.8S rRNA二级结构具有相同的基本结构模式;Ⅰ分支具有1个保守模序为5′-GUGUCGAUG:CAUCGACAU-3′(钩棘单睾吸虫为5′-GUGUCGAUG:CAUCGAUAU-3′)。Ⅱ分支具有1个保守发卡结构,该发卡结构的茎是由9个碱基对组成的保守模序,S.sp保守模序为5′-GGCUACGGG:CCUGUGGCC-3′,其它7种保守模序为5′-GGCCAUGGG:CCUGUGGCC-3′;发卡环为富含尿嘧啶的6元环。在8种人体吸虫中,除裂体吸虫和猫后睾吸虫外,其它6种吸虫5.8SrRNA 5′端均有1段单链序列。在8种人体吸虫中,除钩棘单睾吸虫外,其余吸虫Ⅰ分支均有保守模序5′-GCAG:CUGC-3′。钩棘单睾吸虫和裂体吸虫与其它6种吸虫具有不同的H部和多分支环。巨片形吸虫、獾似颈吸虫和卷棘口吸虫Ⅰ分支尾端具有一个保守发卡结构。碱基的替代、丢失和插入多发生于5.8S rRNA二级结构单链区,双链区的替代、丢失和插入则往往会引起二级结构的较大变异。
结论:本研究首次获得广西扇棘单睾吸虫5.8S rRNA基因序列,发现人体吸虫5.8S rRNA二级结构的一些特征。根据单睾吸虫二级结构特征,本研究还发现广西扇棘单睾吸虫与Dzikowski等报道的扇棘单睾吸虫亲缘关系比较近,与钩棘单睾吸虫亲缘关系比较远。
OBJECTIVE:The The sequence and secondary structure of Haplorchis taichui from Guangxi and other Digenea Trematodes 5.8S rRNA are investigated to explore the kinships of Haplorchis trematodes and the secondary structure characters of Digenea Trematodes 5.8S rRNA.
METHODS:Haplorchis taichuis were collected from Fusui county in Guangxi.The genomic DNA of Haplorchis taichui from Guangxi was extracted. The 5.8S rDNA was amplified by PCR and the sequences of PCR products were obtained by the sequencing reaction The 5.8S rDNAs of Haplorchis taichui,Haplorchis pumilio,Fasciola gigantica,Schistosoma sp,Isthmiophora melis,Echinostoma revolutum,Opisthorchis felineus from Genebank were investigated too.The 5.8S rDNAs of the above Trematodes are all transformed into the 5.8S rRNAs.The secondary structure of the 5.8S rRNAs were constructed using RNAstructure3.2 software according to the theory of minimally free energy with Zuker method.The composition of the sequence structures and the secondary structures of the 5.8S rRNAs were analyzed with SPSS v14.The sequences and secondary structures of Digenea Trematodes 5.8S rRNA were compared to explore their characters.
RESULTS:Sequence comparing was performed between the 5.8S rRNA of Haplorchis taichui from Guangxi and that previously studied by Dzikowski,with the results showing some point mutations sites in the 81th, 83nd,84th,129th and 143th nucleotide.Those sites locate in unpaired regions so that they don't affect on the secondary structural characters of the 5.8S rRNA. Sequence comparing between Haplorchis taichui from Guangxi and Haplorchis pumilio showed mutation sites which not only locate in unpaired regions but also in pared regions.The mutationof the nucleotides locating in pared regions cause more differences in 5.8S rRNA secondary structures between Haplorchis taichui from Guangxi and Haplorchis pumilio.The secondary structures of 5.8S rRNA in several Digenea Trematodes are all composed of main structure models. BranchⅠhas one conservative motif,5'-GUGUCGAUG:CAUCGACAU-3' (5'-GUGUCGAUG:CAUCGAUAU-3' in Haplorchis pumilio).BranchⅡhas a conservative hairpin,which consists of nine basepairs5'-GGCCAUGGG: CCUGUGGCC-3'(5'-GGCUACGGG:CCUGUGGCC-3' in Schistosoma sp) The hairpin loop is a six-membered ring of U rich.There is a single strand sequence in the 5' end of 5.8S rRNA among the above Trematodes except Schistosoma sp and Opisthorchis felineus.The Trematodes except Haplorchis taichui have a conservative motif(5'-GCAG:CUGC-3')in branchⅠ. Haplorchis taichui and Schistosoma sp have a different handle and multibranch loop,compared with other six Trematodes.The branchⅠend of Fasciola gigantica,Isthmiophora melis and Echinostoma revolutum have a conservative hairpin.Replacement,deletion and insertion of bases mostly occur in the single strand region of the secondary structure of the 5.8S rRNAs.While these occurre in double strand,the secondary structure changes tremendously.
CONCLUSION:It was the first time that this study had obtainded 5.8S rRNA gene sequence of Haplorchis taichui from Guangxi.The secondary structure characters of 5.8S rRNA were discovered in Digenea Trematodes. According to their secondary structure characters of 5.8S rRNA,the kinship between Haplorchis taichui from Guangxi and that previously studied by Dzikowski is nearer while the kinship between Haplorchis taichui from Guangxi and Haplorchis pumilio is more far away.
引文
[1]黎学铭,杨益超,蓝春庚,等。广西发现扇棘单睾吸虫.中国寄生虫学与寄生虫病杂志,2004,22(1):61-62.
[2]Dzikowski R,Levy MG,Poore MF,Flowers JR,Paperna I.Use of rDNA polymorphism for identification of Heterophyidae infecting.freshwater fishes.Dis Aquat Organ.2004 Apr 21;59(1):35-41.
[3]Bargues,M.D.and Mas-Coma,S.molecular characterization of Fasciolid liver flukes from Egypt.www.ncbi.nlm.nih.gov/entrez/viewer.fcgi.
[4]Morgan JA,DeJong RJ,Kazibwe F,Mkoji GM,Loker ES.A newlyidentified lineage of Schistosoma.Int J Parasitol.2003 Aug;33(9):977-85.
[5]Kostadinova A,Herniou EA,Barrett J,Littlewood DT.Phylogenetic relationships of Echinostoma Rudolphi,1809(Digenea:Echinostomatidae)and related genera re-assessed via DNA and morphological analyses.Syst Parasitol.2003 Mar;54(3):159-76.
[6]Sorensen RE,Curtis J,Minchella DJ.Intraspecific variation in the rDNA its loci of 37-collar-spined echinostomes from North America:implications for sequence-based diagnoses and phylogenetics.Parasitol.1998 Oct;84(5):992-7.
[7]Shekhovtsov,S.V.,Katokhin,A.V.andMordvinov,V.A.Molecular-genetic studies of Opisthorchis felineus,www.ncbi.nlm.nih.gov/entrez/viewer.fcgi.
[8]Billoud B,Guerrucci MA,Masselot M,Deutsch JS.Cirripede phylogeny using a novel approach:molecular morphometrics.Mol Biol Evol.2000Oct;17(10):1435-45.
[9]Schmitz J,Moritz RF.Molecular phylogeny of Vespidae(Hymenoptera)and the evolution of sociality in wasps.Mol Phylogenet Evol.1998 Apr; 9(2):183-91.
[10] Ouvrard D, Campbell BC, Bourgoin T, Chan KL. 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera). Mol Phylogenet Evol. 2000 Sep;16(3):403-17.
[11] Kjer KM. Use of rRNA secondary structure in phylogenetic studiesto identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phylogenet Evol. 1995 Sep; 4 (3):314-30.
[12] Lenaers G, Bhaud M. Molecular phylogeny of some polychaete annelids: an initial approach to the Atlantic-Mediterranean speciation problem. J Mol Evol. 1992 Nov; 35(5):429-35.
[13] Gagnon S, Bourbeau D, Levesque RC. Secondary structures and features of the 18S, 5.8S and 26S ribosomal RNAs from the Apicomplexan parasite Toxoplasma gondii. Gene. 1996 Sep 16;173(2):129-35.
[14] Flook PK, Rowell CH. The effectiveness of mitochondrial rRNA gene sequences for the reconstruction of the phylogeny of an insect order (Orthoptera).Mol Phylogenet Evol. 1997 Oct;8(2): 177-192.
[1] Dixon MT, Hillis DM. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis.Mol Biol Evol. 1993 Jan; 10(1):256-67.
[2] Kjer KM. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phylogenet Evol. 1995 Sep; 4 (3):314-30.
[3] Belshaw RQuicke DL. A molecular phylogeny of the Aphidiinae (Hymenoptera: Braconidae). Mol Phylogenet Evol. 1997 Jun;7(3):281-93.
[4] Matejusova I, Cunningham CO. The first complete monogenean ribosomal RNA gene operon: sequence and secondary structure of the Gyrodactylus salaris Malmberg, 1957, large subunit ribosomal RNA gene. J Parasitol. 2004 Feb; 90(1): 146-51.
[5] Hancock JM, Vogler AP. How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction. Mol Phylogenet Evol. 2000 Mar; 14(3):366-74.
[6] Billoud B, Guerrucci MA, Masselot M, Deutsch JS. Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol. 2000 Oct; 17(10):1435-45.
[7] Ouvrard D, Campbell BC, Bourgoin T, Chan KL. 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera). Mol Phylogenet Evol. 2000 Sep;16(3):403-17.
[8] Gillespie JJ, McKenna CH, Yoder MJ, Gutell RR, Johnston JS, Kathirithamby J, Cognato AI. Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera). Insect Mol Biol. 2005 Dec; 14(6):625-43.
[9] Chiotis M, Jermiin LS, Crozier RH. A molecular framework for the phylogeny of the ant subfamily dolichoderinae. Mol Phylogenet Evol. 2000 Oct; 17(1):108-16.
[10] Okamoto K, Sekito T, Yoshida K. The secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei. Genes Genet Syst. 1996 Apr; 71(2):69-74.
[11] Gonzalez P, Labarere J. Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains. Microbiology. 2000 Jan; 146 (Ptl):209-21.
[12] Page RD. Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching. Nucleic Acids Res. 2000 Oct 15;28(20):3839-45.
[13] Chilton NB, Hoste H, Newton LA, Beveridge I, Gasser RB. Common secondary structures for the second internal transcribed spacer pre-rRNA of two subfamilies of trichostrongylid nematodes. Int J Parasitol. 1998 Nov; 8(11):1765-73.
[14] Morgan JA, Blair D. Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. J Mol Evol. 1998 Oct; 47(4):406-19.
[15] Chilton NB, Newton LA, Beveridge I, Gasser RB. Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data. Mol Phylogenet Evol. 2001 Jun; 19(3):367-86.
[16] Marc Gottschling and JoE rg PloE tner. Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates. Nucleic Acids Research, 2004, Vol. 32, No. 1, 307-315.
[17] Wang S, Bao Z, Li N, Zhang L, Hu J. Analysis of the Secondary Structure of ITS1 in Pectinidae: Implications for Phylogenetic Reconstruction and Structural Evolution. Mar Biotechnol (NY). 2007 Mar; 9(2):231-242.
[2]Dzikowski R,Levy MG,Poore MF,Flowers JR,Paperna I.Use of rDNA polymorphism for identification of Heterophyidae infecting.freshwater fishes.Dis Aquat Organ.2004 Apr 21;59(1):35-41.
[3]Bargues,M.D.and Mas-Coma,S.molecular characterization of Fasciolid liver flukes from Egypt.www.ncbi.nlm.nih.gov/entrez/viewer.fcgi.
[4]Morgan JA,DeJong RJ,Kazibwe F,Mkoji GM,Loker ES.A newlyidentified lineage of Schistosoma.Int J Parasitol.2003 Aug;33(9):977-85.
[5]Kostadinova A,Herniou EA,Barrett J,Littlewood DT.Phylogenetic relationships of Echinostoma Rudolphi,1809(Digenea:Echinostomatidae)and related genera re-assessed via DNA and morphological analyses.Syst Parasitol.2003 Mar;54(3):159-76.
[6]Sorensen RE,Curtis J,Minchella DJ.Intraspecific variation in the rDNA its loci of 37-collar-spined echinostomes from North America:implications for sequence-based diagnoses and phylogenetics.Parasitol.1998 Oct;84(5):992-7.
[7]Shekhovtsov,S.V.,Katokhin,A.V.andMordvinov,V.A.Molecular-genetic studies of Opisthorchis felineus,www.ncbi.nlm.nih.gov/entrez/viewer.fcgi.
[8]Billoud B,Guerrucci MA,Masselot M,Deutsch JS.Cirripede phylogeny using a novel approach:molecular morphometrics.Mol Biol Evol.2000Oct;17(10):1435-45.
[9]Schmitz J,Moritz RF.Molecular phylogeny of Vespidae(Hymenoptera)and the evolution of sociality in wasps.Mol Phylogenet Evol.1998 Apr; 9(2):183-91.
[10] Ouvrard D, Campbell BC, Bourgoin T, Chan KL. 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera). Mol Phylogenet Evol. 2000 Sep;16(3):403-17.
[11] Kjer KM. Use of rRNA secondary structure in phylogenetic studiesto identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phylogenet Evol. 1995 Sep; 4 (3):314-30.
[12] Lenaers G, Bhaud M. Molecular phylogeny of some polychaete annelids: an initial approach to the Atlantic-Mediterranean speciation problem. J Mol Evol. 1992 Nov; 35(5):429-35.
[13] Gagnon S, Bourbeau D, Levesque RC. Secondary structures and features of the 18S, 5.8S and 26S ribosomal RNAs from the Apicomplexan parasite Toxoplasma gondii. Gene. 1996 Sep 16;173(2):129-35.
[14] Flook PK, Rowell CH. The effectiveness of mitochondrial rRNA gene sequences for the reconstruction of the phylogeny of an insect order (Orthoptera).Mol Phylogenet Evol. 1997 Oct;8(2): 177-192.
[1] Dixon MT, Hillis DM. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis.Mol Biol Evol. 1993 Jan; 10(1):256-67.
[2] Kjer KM. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol Phylogenet Evol. 1995 Sep; 4 (3):314-30.
[3] Belshaw RQuicke DL. A molecular phylogeny of the Aphidiinae (Hymenoptera: Braconidae). Mol Phylogenet Evol. 1997 Jun;7(3):281-93.
[4] Matejusova I, Cunningham CO. The first complete monogenean ribosomal RNA gene operon: sequence and secondary structure of the Gyrodactylus salaris Malmberg, 1957, large subunit ribosomal RNA gene. J Parasitol. 2004 Feb; 90(1): 146-51.
[5] Hancock JM, Vogler AP. How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction. Mol Phylogenet Evol. 2000 Mar; 14(3):366-74.
[6] Billoud B, Guerrucci MA, Masselot M, Deutsch JS. Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol. 2000 Oct; 17(10):1435-45.
[7] Ouvrard D, Campbell BC, Bourgoin T, Chan KL. 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera). Mol Phylogenet Evol. 2000 Sep;16(3):403-17.
[8] Gillespie JJ, McKenna CH, Yoder MJ, Gutell RR, Johnston JS, Kathirithamby J, Cognato AI. Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera). Insect Mol Biol. 2005 Dec; 14(6):625-43.
[9] Chiotis M, Jermiin LS, Crozier RH. A molecular framework for the phylogeny of the ant subfamily dolichoderinae. Mol Phylogenet Evol. 2000 Oct; 17(1):108-16.
[10] Okamoto K, Sekito T, Yoshida K. The secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei. Genes Genet Syst. 1996 Apr; 71(2):69-74.
[11] Gonzalez P, Labarere J. Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains. Microbiology. 2000 Jan; 146 (Ptl):209-21.
[12] Page RD. Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching. Nucleic Acids Res. 2000 Oct 15;28(20):3839-45.
[13] Chilton NB, Hoste H, Newton LA, Beveridge I, Gasser RB. Common secondary structures for the second internal transcribed spacer pre-rRNA of two subfamilies of trichostrongylid nematodes. Int J Parasitol. 1998 Nov; 8(11):1765-73.
[14] Morgan JA, Blair D. Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. J Mol Evol. 1998 Oct; 47(4):406-19.
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