基于线粒体基因组数据的扁甲系总科间系统发育关系分析
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摘要
扁甲系是鞘翅目多食亚目中最大的一个类群,具有重要的经济意义.尽管扁甲系昆虫的单系性得到广泛支持,但7个总科间的系统进化关系仍存在不确定性.为此,本研究测定了锈赤扁谷盗和锯谷盗的线粒体基因组,并联合已测的67个扁甲系昆虫线粒体基因组,构建了扁甲系昆虫总科间的系统发育关系,并采用似然值检验对不同的树拓扑结构进行了评价.结果表明,锈赤扁谷盗全线粒体基因组的大小为15497 bp,编码13个蛋白质编码基因、22个转运RNA基因和2个核糖体RNA基因.锯谷盗接近全长的线粒体基因长为13588 bp,编码34个基因,缺少trnI, trnQ和trnM等3个转运RNA基因.锈赤扁谷盗和锯谷盗线粒体基因的基因含量、基因排序、碱基组成、密码子使用等特征,与大多数已测鞘翅目昆虫的线粒体基因组高度相似.基于3个线粒体基因数据集及3种树构建方法的系统发育分析结果表明,瓢虫总科、叶甲总科、象甲总科、拟步甲总科和郭公虫总科等5个类群均为单系性,而扁甲总科始终为并系.树拓扑结构检验结果表明,扁甲系总科间的系统发育关系为((郭公虫总科+瓢虫总科)+(拟步甲总科+(扁甲总科(叶甲总科+象甲总科)))).尽管线粒体数据集的构成及系统发育分析方法对树拓扑结构具有重要影响,但线粒体基因组数据在扁甲系昆虫系统与进化研究方面具有重要应用价值.
Cucujiformia is the largest group in the Polyphaga of the Coleoptera, most of which are of economic importance. Although the monophyly of Cucujiformia has been widely supported, the phylogenetic relationships among seven superfamilies within Cucujiformia remain unresolved. In this study, mitochondrial genomes(mitogenomes) of Cryptolestes ferrugineus and Oryzaephilus surinamensis were sequenced. Combined with other 67 sequenced coleopteran mitogenomes, we reconstructed phylogenetic relationships among superfamilies of Cucujiformia and evaluated tree topologies by likelihood value tests. The results showed that the complete mitogenome of C. ferrugineus was 15497 bp long and encoded 13 protein-coding genes, 22 transfer RNA genes(tRNAs)and two ribosomal genes. The near complete mitogenome of O. surinamensis was 13588 bp long and encoded 34 mitochondrial genes, lacking three tRNAs(trnI, trnQ and trnM). General features of the two newly sequenced mitogenomes(gene content, gene arrangement, base composition and codon usage) were highly similar to that of previously sequenced beetles. Phylogenetic analyses based on three mitogenomic data and three analytical methods supported the monophyly of each of five superfamilies(Coccinelloidea, Chrysomeloidea, Curculionoidea, Tenebrionoidea and Cleroidea). The monophyly of Cucujoidea was never recovered in all the nine phylogenetic analyses. Tree topology tests statistically supported the superfamily-level relationships in Cucujiformia:((Cleroidea+Coccinelloidea)+(Tenebrionoidea+(Cucujoidea(Chrysomeloidea+Curculionoidea)))). Although both mitogenomic datasets and analytical methods have an important impact on tree topologies, mitogenomic data have important implications in evolutionary and phylogenetic studies of Cucujiformia.
Cucujiformia is the largest group in the Polyphaga of the Coleoptera, most of which are of economic importance. Although the monophyly of Cucujiformia has been widely supported, the phylogenetic relationships among seven superfamilies within Cucujiformia remain unresolved. In this study, mitochondrial genomes(mitogenomes) of Cryptolestes ferrugineus and Oryzaephilus surinamensis were sequenced. Combined with other 67 sequenced coleopteran mitogenomes, we reconstructed phylogenetic relationships among superfamilies of Cucujiformia and evaluated tree topologies by likelihood value tests. The results showed that the complete mitogenome of C. ferrugineus was 15497 bp long and encoded 13 protein-coding genes, 22 transfer RNA genes(tRNAs)and two ribosomal genes. The near complete mitogenome of O. surinamensis was 13588 bp long and encoded 34 mitochondrial genes, lacking three tRNAs(trnI, trnQ and trnM). General features of the two newly sequenced mitogenomes(gene content, gene arrangement, base composition and codon usage) were highly similar to that of previously sequenced beetles. Phylogenetic analyses based on three mitogenomic data and three analytical methods supported the monophyly of each of five superfamilies(Coccinelloidea, Chrysomeloidea, Curculionoidea, Tenebrionoidea and Cleroidea). The monophyly of Cucujoidea was never recovered in all the nine phylogenetic analyses. Tree topology tests statistically supported the superfamily-level relationships in Cucujiformia:((Cleroidea+Coccinelloidea)+(Tenebrionoidea+(Cucujoidea(Chrysomeloidea+Curculionoidea)))). Although both mitogenomic datasets and analytical methods have an important impact on tree topologies, mitogenomic data have important implications in evolutionary and phylogenetic studies of Cucujiformia.
引文
1 Robertson J A,?lipiński A,Moulton M,et al.Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea(Coleoptera:Cucujiformia).Syst Entomol,2015,40:745-778
2 Hunt T,Bergsten J,Levkanicova Z,et al.A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation.Science,2007,318:1913-1916
3 Bouchard P,Bousquet Y,Davies A E,et al.Family-group names in Coleoptera(Insecta).Zookeys,2011,88:1-972
4 Yuan M L,Zhang Q L,Zhang L,et al.High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences.Mol Phylogenets Evol,2016,104:99-111
5 Timmermans M J T N,Barton C,Haran J,et al.Family-level sampling of mitochondrial genomes in coleoptera:compositional heterogeneity and phylogenetics.Genome Biol Evol,2016,8:161-175
6 Bocak L,Barton C,Crampton-platt A,et al.Building the Coleoptera tree-of-life for>8000 species:composition of public DNA data and fit with Linnaean classification.Syst Entomol,2014,39:97-110
7 Lawrence J F,?lipiński A,Seago A E,et al.Phylogeny of the Coleoptera based on morphological characters of adults and larvae.Ann Zool,2011,61:1-217
8 Cameron S L.Insect mitochondrial genomics:implications for evolution and phylogeny.Annu Rev Entomol,2014,59:95-117
9 Boore J L.Animal mitochondrial genomes.Nucl Acids Res,1999,27:1767-1780
10 Simon C,Buckley T R,Frati F,et al.Incorporating molecular evolution into phylogenetic analysis,and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA.Annu Rev Ecol Evol Syst,2006,37:545-579
11 Wang I J.Recognizing the temporal distinctions between landscape genetics and phylogeography.Mol Ecol,2010,19:2605-2608
12 Yuan M L,Zhang Q L,Guo Z L,et al.Comparative mitogenomic analysis of the superfamily Pentatomoidea(Insecta:Hemiptera:Heteroptera)and phylogenetic implications.BMC Genom,2015,16:460
13 Yuan M L,Zhang Q L,Guo Z L,et al.The complete mitochondrial genome of Corizus tetraspilus(Hemiptera:Rhopalidae)and phylogenetic analysis of Pentatomomorpha.PLoS ONE,2015,10:e0129003
14 Lowe T M,Eddy S R.t RNAscan-SE:a program for improved detection of transfer RNA genes in genomic sequence.Nucl Acids Res,1997,25:955-964
15 Tamura K,Stecher G,Peterson D,et al.MEGA6:molecular evolutionary genetics analysis version 6.0.Mol Biol Evol,2013,30:2725-2729
16 Perna N T,Kocher T D.Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes.J Mol Evol,1995,41:353-358
17 Abascal F,Zardoya R,Telford M J.TranslatorX:multiple alignment of nucleotide sequences guided by amino acid translations.Nucl Acids Res,2010,38:W7-W13
18 Lanfear R,Calcott B,Ho S Y W,et al.Partitionfinder:combined selection of partitioning schemes and substitution models for phylogenetic analyses.Mol Biol Evol,2012,29:1695-1701
19 Miller MA,Pfeiffer W,Schwartz T.Creating the CIPRES Science Gateway for inference of large phylogenetic trees.New Orleans:Gateway Computing Environments Workshop(GCE),2010.1-8
20 Stamatakis A.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics,2014,30:1312-1313
21 Ronquist F,Teslenko M,van der Mark P,et al.MrBayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space.Syst Biol,2012,61:539-542
22 Trifinopoulos J,Nguyen L T,von Haeseler A,et al.W-IQ-TREE:a fast online phylogenetic tool for maximum likelihood analysis.Nucl Acids Res,2016,44:W232-W235
23 Shimodaira H,Hasegawa M.Multiple comparisons of log-likelihoods with applications to phylogenetic inference.Mol Biol Evol,1999,16:1114-1116
24 Kishino H,Hasegawa M.Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in hominoidea.J Mol Evol,1989,29:170-179
25 Shimodaira H.An approximately unbiased test of phylogenetic tree selection.Syst Biol,2002,51:492-508
26 Cameron S L,Whiting M F.The complete mitochondrial genome of the tobacco hornworm,Manduca sexta,(Insecta:Lepidoptera:Sphingidae),and an examination of mitochondrial gene variability within butterflies and moths.Gene,2008,408:112-123
27 Beckenbach A T.Mitochondrial genome sequences of Nematocera(lower Diptera):evidence of rearrangement following a complete genome duplication in a winter crane fly.Genom Biol Evol,2012,4:89-101
28 Roberti M,Polosa P L,Bruni F,et al.DmTTF,a novel mitochondrial transcription termination factor that recognises two sequences of Drosophila melanogaster mitochondrial DNA.Nucl Acids Res,2003,31:1597-1604
29 Hassanin A,Leger N,Deutsch J.Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa,and consequences for phylogenetic inferences.Syst Biol,2005,54:277-298
30 Ojala D,Montoya J,Attardi G.tRNA punctuation model of RNA processing in human mitochondria.Nature,1981,290:470-474
31 Lavrov D V,Boore J L,Brown W M.Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements:duplication and nonrandom loss.Mol Biol Evol,2002,19:163-169
32 Crampton-Platt A,Timmermans M J T N,Gimmel M L,et al.Soup to tree:the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample.Mol Biol Evol,2015,32:2302-2316
33 Marvaldi A E,Duckett C N,Kjer K M,et al.Structural alignment of 18S and 28S r DNA sequences provides insights into phylogeny of Phytophaga(Coleoptera:Curculionoidea and Chrysomeloidea).Zool Script,2009,38:63-77
34 Wei S J,Li Q,van Achterberg K,et al.Two mitochondrial genomes from the families Bethylidae and Mutillidae:independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera.Mol Phylogenet Evol,2014,77:1-10
35 Mao M,Gibson T,Dowton M.Evolutionary dynamics of the mitochondrial genome in the Evaniomorpha(Hymenoptera)-a group with an intermediate rate of gene rearrangement.Genom Biol Evol,2014,6:1862-1874
36 Leschen R A B,Lawrence J F,?lipiński S A.Classification of basal Cucujoidea(Coleoptera:Polyphaga):cladistic analysis,keys and review of new families.Invert Syst,2005,19:17-73
37 Mcelrath T C,Robertson J A,Thomas M C,et al.A molecular phylogenetic study of Cucujidae s.l.(Coleoptera:Cucujoidea).Syst Entomol,2015,40:705-718
2 Hunt T,Bergsten J,Levkanicova Z,et al.A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation.Science,2007,318:1913-1916
3 Bouchard P,Bousquet Y,Davies A E,et al.Family-group names in Coleoptera(Insecta).Zookeys,2011,88:1-972
4 Yuan M L,Zhang Q L,Zhang L,et al.High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences.Mol Phylogenets Evol,2016,104:99-111
5 Timmermans M J T N,Barton C,Haran J,et al.Family-level sampling of mitochondrial genomes in coleoptera:compositional heterogeneity and phylogenetics.Genome Biol Evol,2016,8:161-175
6 Bocak L,Barton C,Crampton-platt A,et al.Building the Coleoptera tree-of-life for>8000 species:composition of public DNA data and fit with Linnaean classification.Syst Entomol,2014,39:97-110
7 Lawrence J F,?lipiński A,Seago A E,et al.Phylogeny of the Coleoptera based on morphological characters of adults and larvae.Ann Zool,2011,61:1-217
8 Cameron S L.Insect mitochondrial genomics:implications for evolution and phylogeny.Annu Rev Entomol,2014,59:95-117
9 Boore J L.Animal mitochondrial genomes.Nucl Acids Res,1999,27:1767-1780
10 Simon C,Buckley T R,Frati F,et al.Incorporating molecular evolution into phylogenetic analysis,and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA.Annu Rev Ecol Evol Syst,2006,37:545-579
11 Wang I J.Recognizing the temporal distinctions between landscape genetics and phylogeography.Mol Ecol,2010,19:2605-2608
12 Yuan M L,Zhang Q L,Guo Z L,et al.Comparative mitogenomic analysis of the superfamily Pentatomoidea(Insecta:Hemiptera:Heteroptera)and phylogenetic implications.BMC Genom,2015,16:460
13 Yuan M L,Zhang Q L,Guo Z L,et al.The complete mitochondrial genome of Corizus tetraspilus(Hemiptera:Rhopalidae)and phylogenetic analysis of Pentatomomorpha.PLoS ONE,2015,10:e0129003
14 Lowe T M,Eddy S R.t RNAscan-SE:a program for improved detection of transfer RNA genes in genomic sequence.Nucl Acids Res,1997,25:955-964
15 Tamura K,Stecher G,Peterson D,et al.MEGA6:molecular evolutionary genetics analysis version 6.0.Mol Biol Evol,2013,30:2725-2729
16 Perna N T,Kocher T D.Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes.J Mol Evol,1995,41:353-358
17 Abascal F,Zardoya R,Telford M J.TranslatorX:multiple alignment of nucleotide sequences guided by amino acid translations.Nucl Acids Res,2010,38:W7-W13
18 Lanfear R,Calcott B,Ho S Y W,et al.Partitionfinder:combined selection of partitioning schemes and substitution models for phylogenetic analyses.Mol Biol Evol,2012,29:1695-1701
19 Miller MA,Pfeiffer W,Schwartz T.Creating the CIPRES Science Gateway for inference of large phylogenetic trees.New Orleans:Gateway Computing Environments Workshop(GCE),2010.1-8
20 Stamatakis A.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics,2014,30:1312-1313
21 Ronquist F,Teslenko M,van der Mark P,et al.MrBayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space.Syst Biol,2012,61:539-542
22 Trifinopoulos J,Nguyen L T,von Haeseler A,et al.W-IQ-TREE:a fast online phylogenetic tool for maximum likelihood analysis.Nucl Acids Res,2016,44:W232-W235
23 Shimodaira H,Hasegawa M.Multiple comparisons of log-likelihoods with applications to phylogenetic inference.Mol Biol Evol,1999,16:1114-1116
24 Kishino H,Hasegawa M.Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in hominoidea.J Mol Evol,1989,29:170-179
25 Shimodaira H.An approximately unbiased test of phylogenetic tree selection.Syst Biol,2002,51:492-508
26 Cameron S L,Whiting M F.The complete mitochondrial genome of the tobacco hornworm,Manduca sexta,(Insecta:Lepidoptera:Sphingidae),and an examination of mitochondrial gene variability within butterflies and moths.Gene,2008,408:112-123
27 Beckenbach A T.Mitochondrial genome sequences of Nematocera(lower Diptera):evidence of rearrangement following a complete genome duplication in a winter crane fly.Genom Biol Evol,2012,4:89-101
28 Roberti M,Polosa P L,Bruni F,et al.DmTTF,a novel mitochondrial transcription termination factor that recognises two sequences of Drosophila melanogaster mitochondrial DNA.Nucl Acids Res,2003,31:1597-1604
29 Hassanin A,Leger N,Deutsch J.Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa,and consequences for phylogenetic inferences.Syst Biol,2005,54:277-298
30 Ojala D,Montoya J,Attardi G.tRNA punctuation model of RNA processing in human mitochondria.Nature,1981,290:470-474
31 Lavrov D V,Boore J L,Brown W M.Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements:duplication and nonrandom loss.Mol Biol Evol,2002,19:163-169
32 Crampton-Platt A,Timmermans M J T N,Gimmel M L,et al.Soup to tree:the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample.Mol Biol Evol,2015,32:2302-2316
33 Marvaldi A E,Duckett C N,Kjer K M,et al.Structural alignment of 18S and 28S r DNA sequences provides insights into phylogeny of Phytophaga(Coleoptera:Curculionoidea and Chrysomeloidea).Zool Script,2009,38:63-77
34 Wei S J,Li Q,van Achterberg K,et al.Two mitochondrial genomes from the families Bethylidae and Mutillidae:independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera.Mol Phylogenet Evol,2014,77:1-10
35 Mao M,Gibson T,Dowton M.Evolutionary dynamics of the mitochondrial genome in the Evaniomorpha(Hymenoptera)-a group with an intermediate rate of gene rearrangement.Genom Biol Evol,2014,6:1862-1874
36 Leschen R A B,Lawrence J F,?lipiński S A.Classification of basal Cucujoidea(Coleoptera:Polyphaga):cladistic analysis,keys and review of new families.Invert Syst,2005,19:17-73
37 Mcelrath T C,Robertson J A,Thomas M C,et al.A molecular phylogenetic study of Cucujidae s.l.(Coleoptera:Cucujoidea).Syst Entomol,2015,40:705-718