木犀科植物叶绿体基因组结构特征和系统发育关系
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摘要
木犀科11属19个种叶绿体基因组的一般特征和变异特征的比较分析显示,结果表明,该科叶绿体基因组大小为154–165kb,其差异主要是大单拷贝(LSC)长度的差异所致。Jasminum属3个物种的叶绿体基因组长度与其余物种有较大差异,该属clpP基因内含子和accD基因丢失。共线性分析表明, Jasminum属3个物种多个基因出现基因重排现象,倒位可能是重排的主要原因。Jasminum属在IRb/SSC和SSC/IRa边界的基因均与其它物种不同;重复序列与SSR数量检测结果表明,Jasminum属与其余物种在数量及重复长度上差异较大。基于CDS数据构建的系统发育树表明, Abeliophyllum distichum和Forsythia suspensa为木犀科中较早分化的类群。
In this study, the chloroplast genomes from 19 species(11 genera) in Oleaceae were compared to reveal the general characteristics and structural variations. The chloroplast genome sizes in Oleaceae were 154-165 kb, and the differences were mainly caused by the length of large single-copy regions. The chloroplast genome sizes of 3 species from the genus Jasminum differed greatly from that for other species; in addition, the introns from the clp P and accD genes were lost in Jasminum. Synteny analyses showed several gene rearrangements in 3 Jasminum species that were probably caused by inversions. The boundary genes between IRb/small single copy(SSC) and SSC/IRa regions in 3 Jasminum species differed from others. Repeat sequences and simple sequence repeat detection demonstrated that Jasminum had significant differences in repeat number and repeat length as compared with other genera. On the basis of shared protein-coding genes among 19 species, Abeliophyllum distichum and Forsythia suspensa were the early-diverging clades in Oleaceae.
In this study, the chloroplast genomes from 19 species(11 genera) in Oleaceae were compared to reveal the general characteristics and structural variations. The chloroplast genome sizes in Oleaceae were 154-165 kb, and the differences were mainly caused by the length of large single-copy regions. The chloroplast genome sizes of 3 species from the genus Jasminum differed greatly from that for other species; in addition, the introns from the clp P and accD genes were lost in Jasminum. Synteny analyses showed several gene rearrangements in 3 Jasminum species that were probably caused by inversions. The boundary genes between IRb/small single copy(SSC) and SSC/IRa regions in 3 Jasminum species differed from others. Repeat sequences and simple sequence repeat detection demonstrated that Jasminum had significant differences in repeat number and repeat length as compared with other genera. On the basis of shared protein-coding genes among 19 species, Abeliophyllum distichum and Forsythia suspensa were the early-diverging clades in Oleaceae.
引文
李巧丽,延娜,宋琼,郭军战(2018).鲁桑叶绿体基因组序列及特征分析.植物学报53,94-103.
唐萍,阮秋燕,彭程(2011).禾本科植物叶绿体基因组结构的系统进化研究.中国农学通报27(30),17.
Baali-Cherif D,Besnard G(2005).High genetic diversity and clonal growth in relict populations of Olea europaea subsp.laperrinei(Oleaceae)from Hoggar,Algeria.Ann Bot 96,823-830.
Benson G(1999).Tandem repeats finder:a program to analyze DNA sequences.Nucleic Acids Res 27,573-580.
Besnard G,de Casas RR,Christin PA,Vargas P(2009).Phylogenetics of Olea(Oleaceae)based on plastid and nuclear ribosomal DNA sequences:tertiary climatic shifts and lineage differentiation times.Ann Bot 104,143-160.
Besnard G,Hernández P,Khadari B,Dorado G,Savolainen V(2011).Genomic profiling of plastid DNA variation in the mediterranean olive tree.BMC Plant Biol 11,80.
Besnard G,Khadari B,Baradat P,BervilléA(2002).Olea europaea(Oleaceae)phylogeography based on chloroplast DNA polymorphism.Theor Appl Genet 104,1353-1361.
Blazier JC,Ruhlman TA,Weng ML,Rehman SK,Sabir JSM,Jansen RK(2016).Divergence of RNA polymeraseαsubunits in angiosperm plastid genomes is mediated by genomic rearrangement.Sci Rep 6,24595.
Chumley TW,Palmer JD,Mower JP,Fourcade HM,Calie PJ,Boore JL,Jansen RK(2006).The complete chloroplast genome sequence of Pelargonium x hortorum:organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.Mol Biol Evol 23,2175-2190.
Darling ACE,Mau B,Blattner FR,Perna ANT(2004).Mauve:multiple alignment of conserved genomic sequence with rearrangements.Genome Res 14,1394-1403.
Dong WP,Xu C,Cheng T,Lin K,Zhou SL(2013).Sequencing angiosperm plastid genomes made easy:a complete set of universal primers and a case study on the phylogeny of Saxifragales.Genome Biol Evol 5,989-997.
Flora of China Editorial Committee(1995).Flora of China,Vol.16.Beijing&St.Louis:Science Press&Missouri Botanical Garden Press.pp.143-188.
Flora of China Editorial Committee(1996).Flora of China,Vol.15.Beijing&St.Louis:Science Press&Missouri Botanical Garden Press.pp.272-319.
Frazer KA,Pachter L,Poliakov A,Rubin EM,Dubchak I(2004).Vista:computational tools for comparative genomics.Nucleic Acids Res 32,W273-W279.
Gao L,Su YJ,Wang T(2010).Plastid genome sequencing,comparative genomics,and phylogenomics:current status and prospects.J Syst Evol 48,77-93.
Gray BN,Ahner BA,Hanson MR(2009).Extensive homologous recombination between introduced and native regulatory plastid DNA elements in transplastomic plants.Transgenic Res 18,559-572.
Greiner S,Wang X,Rauwolf U,Silber MV,Mayer K,Meurer J,Haberer G,Herrmann RG(2008).The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera,subsection Oenothera.I.Sequence evaluation and plastome evolution.Nucleic Acids Res 36,2366-2378.
Guisinger MM,Kuehl JV,Boore JL,Jansen RK(2011).Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae:rearrangements,repeats,and codon usage.Mol Biol Evol 28,583-600.
Hansen DR,Dastidar SG,Cai ZQ,Penaflor C,Kuehl JV,Boore JL,Jansen RK(2007).Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms:Buxus(Buxaceae),Chloranthus(Chloranthaceae),Dioscorea(Dioscoreaceae),and Illicium(Schisandraceae).Mol Phylogenet Evol 45,547-563.
He YX,Liu LX,Yang SH,Dong MF,Yuan WJ,Shang FD(2017).Characterization of the complete chloroplast genome of chinese fringetree(Chionanthus retusus).Conserv Genet Resour 9,431-434.
Hirao T,Watanabe A,Kurita M,Kondo T,Takata K(2008).Complete nucleotide sequence of the Cryptomeria japonica D.Don.chloroplast genome and comparative chloroplast genomics:diversified genomic structure of coniferous species.BMC Plant Biol 8,70.
Hiratsuka J,Shimada H,Whittier R,Ishibashi T,Sakamoto M,Mori M,Kondo C,Honji Y,Sun CR,Meng BY,Li YQ,Kanno A,Nishizawa Y,Hirai A,Shinozaki K,Sugiura M(1989).The complete sequence of the rice(Oryza sativa)chloroplast genome:intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals.Mol Gen Genet 217,185-194.
Hu YC,Zhang Q,Rao GY,Sodmergen(2008).Occurrence of plastids in the sperm cells of Caprifoliaceae:biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance.Plant Cell Physiol 49,958-968.
Huang H,Shi C,Liu Y,Mao SY,Gao LZ(2014).Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing:genome structure and phylogenetic relationships.BMC Evol Biol 14,151.
Jeandroz S,Roy A,Bousquet J(1997).Phylogeny and phylogeography of the circumpolar genus Fraxinus(Oleaceae)based on internal transcribed spacer sequences of nuclear ribosomal DNA.Mol Phylogenet Evol 7,241-251.
Katayama H,Ogihara Y(1996).Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA.Curr Genet 29,572-581.
Khakhlova O,Bock R(2006).Elimination of deleterious mutations in plastid genomes by gene conversion.Plant J46,85-94.
Kim C,Kim HJ,Do HDK,Jung J,Kim JH(2018).Characterization of the complete chloroplast genome of Fraxinus chiisanensis(Oleaceae),an endemic to Korea.Conserv Genet Resour 11,63-66.
Kim HW,Lee HL,Lee DK,Kim KJ(2016).Complete plastid genome sequences of Abeliophyllum distichum Nakai(Oleaceae),a Korea endemic genus.Mitochondr DNAPart B 1,596-598.
Knox EB,Downie SR,Palmer JD(1993).Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors.Mol Biol Evol 10,414-430.
Kurtz S,Choudhuri JV,Ohlebusch E,Schleiermacher C,Stoye J,Giegerich R(2001).Reputer:the manifold applications of repeat analysis on a genomic scale.Nucleic Acids Res 29,4633-4642.
Lee HL,Jansen RK,Chumley TW,Kim KJ(2007).Gene relocations within chloroplast genomes of Jasminum and Menodora(Oleaceae)are due to multiple,overlapping inversions.Mol Biol Evol 24,1161-1180.
Li JH,Alexander JH,Zhang DL(2002).Paraphyletic Syringa(Oleaceae):evidence from sequences of nuclear ribosomal DNA ITS and ETS regions.Syst Bot 27,592-597.
Maier RM,Neckermann K,Igloi GL,K?sel H(1995).Complete sequence of the maize chloroplast genome:gene content,hotspots of divergence and fine tuning of genetic information by transcript editing.J Mol Biol 251,614-628.
Ogihara Y,Terachi T,Sasakuma T(1988).Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species.Proc Natl Acad Sci USA 85,8573-8577.
Palmer JD(1985).Comparative organization of chloroplast genomes.Annu Rev Genet 19,325-354.
Posada D(2008).jModeltest:phylogenetic model averaging.Mol Biol Evol 25,1253-1256.
Ronquist F,Huelsenbeck JP(2003).Mrbayes 3:Bayesian phylogenetic inference under mixed models.Bioinformatics 19,1572-1574.
Stamatakis A,Hoover P,Rougemont J(2008).A rapid bootstrap algorithm for the raxml web servers.Syst Biol57,758-771.
Thiel T,Michalek W,Varshney R,Graner A(2003).Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley(Hordeum vulgare L.).Theor Appl Genet 106,411-422.
Van de Paer C,Bouchez O,Besnard G(2018).Prospects on the evolutionary mitogenomics of plants:a case study on the olive family(Oleaceae).Mol Ecol Res 18,407-423.
Wallander E(2008).Systematics of Fraxinus(Oleaceae)and evolution of dioecy.Plant Syst Evol 273,25-49.
Wallander E,Albert VA(2000).Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data.Am J Bot 87,1827-1841.
Wang WB,Yu H,Wang JH,Lei WJ,Gao JH,Qiu XP,Wang JS(2017).The complete chloroplast genome sequences of the medicinal plant Forsythia suspensa(Oleaceae).Int J Mol Sci 18,2288.
Weng ML,Blazier JC,Govindu M,Jansen RK(2014).Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements,repeats,and nucleotide substitution rates.Mol Biol Evol 31,645-659.
Zhang TW,Fang YJ,Wang XM,Deng X,Zhang XW,Hu SN,Yu J(2012).The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica:insights into the evolution of plant organellar genomes.PLoS One 7,e30531.
Zhang X,Zhou T,Yang J,Sun JJ,Ju MM,Zhao YM,Zhao GF(2018).Comparative analyses of chloroplast genomes of Cucurbitaceae species:lights into selective pressures and phylogenetic relationships.Molecules 23,2165.
唐萍,阮秋燕,彭程(2011).禾本科植物叶绿体基因组结构的系统进化研究.中国农学通报27(30),17.
Baali-Cherif D,Besnard G(2005).High genetic diversity and clonal growth in relict populations of Olea europaea subsp.laperrinei(Oleaceae)from Hoggar,Algeria.Ann Bot 96,823-830.
Benson G(1999).Tandem repeats finder:a program to analyze DNA sequences.Nucleic Acids Res 27,573-580.
Besnard G,de Casas RR,Christin PA,Vargas P(2009).Phylogenetics of Olea(Oleaceae)based on plastid and nuclear ribosomal DNA sequences:tertiary climatic shifts and lineage differentiation times.Ann Bot 104,143-160.
Besnard G,Hernández P,Khadari B,Dorado G,Savolainen V(2011).Genomic profiling of plastid DNA variation in the mediterranean olive tree.BMC Plant Biol 11,80.
Besnard G,Khadari B,Baradat P,BervilléA(2002).Olea europaea(Oleaceae)phylogeography based on chloroplast DNA polymorphism.Theor Appl Genet 104,1353-1361.
Blazier JC,Ruhlman TA,Weng ML,Rehman SK,Sabir JSM,Jansen RK(2016).Divergence of RNA polymeraseαsubunits in angiosperm plastid genomes is mediated by genomic rearrangement.Sci Rep 6,24595.
Chumley TW,Palmer JD,Mower JP,Fourcade HM,Calie PJ,Boore JL,Jansen RK(2006).The complete chloroplast genome sequence of Pelargonium x hortorum:organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.Mol Biol Evol 23,2175-2190.
Darling ACE,Mau B,Blattner FR,Perna ANT(2004).Mauve:multiple alignment of conserved genomic sequence with rearrangements.Genome Res 14,1394-1403.
Dong WP,Xu C,Cheng T,Lin K,Zhou SL(2013).Sequencing angiosperm plastid genomes made easy:a complete set of universal primers and a case study on the phylogeny of Saxifragales.Genome Biol Evol 5,989-997.
Flora of China Editorial Committee(1995).Flora of China,Vol.16.Beijing&St.Louis:Science Press&Missouri Botanical Garden Press.pp.143-188.
Flora of China Editorial Committee(1996).Flora of China,Vol.15.Beijing&St.Louis:Science Press&Missouri Botanical Garden Press.pp.272-319.
Frazer KA,Pachter L,Poliakov A,Rubin EM,Dubchak I(2004).Vista:computational tools for comparative genomics.Nucleic Acids Res 32,W273-W279.
Gao L,Su YJ,Wang T(2010).Plastid genome sequencing,comparative genomics,and phylogenomics:current status and prospects.J Syst Evol 48,77-93.
Gray BN,Ahner BA,Hanson MR(2009).Extensive homologous recombination between introduced and native regulatory plastid DNA elements in transplastomic plants.Transgenic Res 18,559-572.
Greiner S,Wang X,Rauwolf U,Silber MV,Mayer K,Meurer J,Haberer G,Herrmann RG(2008).The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera,subsection Oenothera.I.Sequence evaluation and plastome evolution.Nucleic Acids Res 36,2366-2378.
Guisinger MM,Kuehl JV,Boore JL,Jansen RK(2011).Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae:rearrangements,repeats,and codon usage.Mol Biol Evol 28,583-600.
Hansen DR,Dastidar SG,Cai ZQ,Penaflor C,Kuehl JV,Boore JL,Jansen RK(2007).Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms:Buxus(Buxaceae),Chloranthus(Chloranthaceae),Dioscorea(Dioscoreaceae),and Illicium(Schisandraceae).Mol Phylogenet Evol 45,547-563.
He YX,Liu LX,Yang SH,Dong MF,Yuan WJ,Shang FD(2017).Characterization of the complete chloroplast genome of chinese fringetree(Chionanthus retusus).Conserv Genet Resour 9,431-434.
Hirao T,Watanabe A,Kurita M,Kondo T,Takata K(2008).Complete nucleotide sequence of the Cryptomeria japonica D.Don.chloroplast genome and comparative chloroplast genomics:diversified genomic structure of coniferous species.BMC Plant Biol 8,70.
Hiratsuka J,Shimada H,Whittier R,Ishibashi T,Sakamoto M,Mori M,Kondo C,Honji Y,Sun CR,Meng BY,Li YQ,Kanno A,Nishizawa Y,Hirai A,Shinozaki K,Sugiura M(1989).The complete sequence of the rice(Oryza sativa)chloroplast genome:intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals.Mol Gen Genet 217,185-194.
Hu YC,Zhang Q,Rao GY,Sodmergen(2008).Occurrence of plastids in the sperm cells of Caprifoliaceae:biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance.Plant Cell Physiol 49,958-968.
Huang H,Shi C,Liu Y,Mao SY,Gao LZ(2014).Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing:genome structure and phylogenetic relationships.BMC Evol Biol 14,151.
Jeandroz S,Roy A,Bousquet J(1997).Phylogeny and phylogeography of the circumpolar genus Fraxinus(Oleaceae)based on internal transcribed spacer sequences of nuclear ribosomal DNA.Mol Phylogenet Evol 7,241-251.
Katayama H,Ogihara Y(1996).Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA.Curr Genet 29,572-581.
Khakhlova O,Bock R(2006).Elimination of deleterious mutations in plastid genomes by gene conversion.Plant J46,85-94.
Kim C,Kim HJ,Do HDK,Jung J,Kim JH(2018).Characterization of the complete chloroplast genome of Fraxinus chiisanensis(Oleaceae),an endemic to Korea.Conserv Genet Resour 11,63-66.
Kim HW,Lee HL,Lee DK,Kim KJ(2016).Complete plastid genome sequences of Abeliophyllum distichum Nakai(Oleaceae),a Korea endemic genus.Mitochondr DNAPart B 1,596-598.
Knox EB,Downie SR,Palmer JD(1993).Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors.Mol Biol Evol 10,414-430.
Kurtz S,Choudhuri JV,Ohlebusch E,Schleiermacher C,Stoye J,Giegerich R(2001).Reputer:the manifold applications of repeat analysis on a genomic scale.Nucleic Acids Res 29,4633-4642.
Lee HL,Jansen RK,Chumley TW,Kim KJ(2007).Gene relocations within chloroplast genomes of Jasminum and Menodora(Oleaceae)are due to multiple,overlapping inversions.Mol Biol Evol 24,1161-1180.
Li JH,Alexander JH,Zhang DL(2002).Paraphyletic Syringa(Oleaceae):evidence from sequences of nuclear ribosomal DNA ITS and ETS regions.Syst Bot 27,592-597.
Maier RM,Neckermann K,Igloi GL,K?sel H(1995).Complete sequence of the maize chloroplast genome:gene content,hotspots of divergence and fine tuning of genetic information by transcript editing.J Mol Biol 251,614-628.
Ogihara Y,Terachi T,Sasakuma T(1988).Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species.Proc Natl Acad Sci USA 85,8573-8577.
Palmer JD(1985).Comparative organization of chloroplast genomes.Annu Rev Genet 19,325-354.
Posada D(2008).jModeltest:phylogenetic model averaging.Mol Biol Evol 25,1253-1256.
Ronquist F,Huelsenbeck JP(2003).Mrbayes 3:Bayesian phylogenetic inference under mixed models.Bioinformatics 19,1572-1574.
Stamatakis A,Hoover P,Rougemont J(2008).A rapid bootstrap algorithm for the raxml web servers.Syst Biol57,758-771.
Thiel T,Michalek W,Varshney R,Graner A(2003).Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley(Hordeum vulgare L.).Theor Appl Genet 106,411-422.
Van de Paer C,Bouchez O,Besnard G(2018).Prospects on the evolutionary mitogenomics of plants:a case study on the olive family(Oleaceae).Mol Ecol Res 18,407-423.
Wallander E(2008).Systematics of Fraxinus(Oleaceae)and evolution of dioecy.Plant Syst Evol 273,25-49.
Wallander E,Albert VA(2000).Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data.Am J Bot 87,1827-1841.
Wang WB,Yu H,Wang JH,Lei WJ,Gao JH,Qiu XP,Wang JS(2017).The complete chloroplast genome sequences of the medicinal plant Forsythia suspensa(Oleaceae).Int J Mol Sci 18,2288.
Weng ML,Blazier JC,Govindu M,Jansen RK(2014).Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements,repeats,and nucleotide substitution rates.Mol Biol Evol 31,645-659.
Zhang TW,Fang YJ,Wang XM,Deng X,Zhang XW,Hu SN,Yu J(2012).The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica:insights into the evolution of plant organellar genomes.PLoS One 7,e30531.
Zhang X,Zhou T,Yang J,Sun JJ,Ju MM,Zhao YM,Zhao GF(2018).Comparative analyses of chloroplast genomes of Cucurbitaceae species:lights into selective pressures and phylogenetic relationships.Molecules 23,2165.
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