茄科植物叶绿体基因组研究进展
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摘要
叶绿体基因组(cpDNA)是与光合作用直接相关的细胞器,其在物种鉴定及系统进化研究中的应用价值已经受到研究者们的广泛关注和逐步认可.茄科作为植物界重要的一科,涵盖了诸多重要的食用及药用植物.本文在整理近年来茄科叶绿体基因组相关研究的基础上,对目前茄科植物叶绿体基因组测序技术的发展、研究现状及今后的发展趋势及应用前景进行了综述.
The chloroplast genome(cpDNA) is an organelle directly related to photosynthesis. The application of cpDNA in species identification and phylogenetic studies has been paid more and more attention and recognition by researchers. Solanaceae, one of the most important members of the plant kingdom, contains many commercially important edible and medicinal plants. In this study, basing on the studies about the chloroplast genome of Solanaceae plants in recent years, the advances, current status, the future development trend and the application prospect of cpDNA sequencing technology were reviewed.
The chloroplast genome(cpDNA) is an organelle directly related to photosynthesis. The application of cpDNA in species identification and phylogenetic studies has been paid more and more attention and recognition by researchers. Solanaceae, one of the most important members of the plant kingdom, contains many commercially important edible and medicinal plants. In this study, basing on the studies about the chloroplast genome of Solanaceae plants in recent years, the advances, current status, the future development trend and the application prospect of cpDNA sequencing technology were reviewed.
引文
[1] JANSEN R K, RUHLMAN T A. Plastid genomes of seed plants[M]//Genomics of chloroplasts and mitochondria. Dordrecht:Springer,2012:103-126.
[2] LI X, YANG Y, HENRY R J, et al. Plant DNA barcoding: from gene to genome[J].Biol Rev Camb Philos Soc,2015,90(1):157-166.
[3] 张韵洁,李德铢.叶绿体系统发育基因组学的研究进展[J].植物分类与资源学报,2011,33(4):365-375.
[4] ZHAO Y, YIN J, GUO H, et al. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng[J].Frontiers in Plant Science,2014,5:696.
[5] SHINOZAKI K, OHME M, TANAKA M, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression[J].The EMBO Journal,1986,5(9):2043-2049.
[6] OHYAMA K, FUKUZAWA H, KOHCHI T, et al. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA[J].Nature,1986,322:572-574.
[7] D'ARCY W G. The Solanaceae since 1976, with a review of its biogeography[M]//HAWKES J G, LESTER R,NEE M, et al. Solanaceae III:Taxonmy, Chemistry, Evolution. Chicago:University of Chicago Press,2000:75-137.
[8] 福建省科学技术委员会《福建植物志》编写组.福建植物志:第5卷[M].福州:福建科学技术出版社,1982:1-30.
[9] 白重炎,刘帆帆.延安前科药用植物野生资源调查[J].安徽农业科学,2011,39(31):19105-19106.
[10] DA SILVA B J M, RODRIGUES A P D, FARIAS L H S, et al. Physalis angulata induces in vitro differentiation of murine bone marrow cells into macrophages[J].BMC Cell Biology,2014,15(1):37.
[11] MAGALHAES H I F, VERAS M L ,TORRES M R, et al. In-vitro and in-vivo antitumour activity of physalins B and D from Physalis angulata[J].Journal of Pharmacy and Pharmacology,2006,58(2):235-241.
[12] BASTOS G N T, SANTOS A R S, FERREIRA V M M, et al. Antinociceptive effect of the aqueous extract obtained from roots of Physalis angulata L. on mice[J].Journal of Ethnopharmacology,2006,103(2):241-245.
[13] BASTOS G N T, SILVEIRA A J A, SALGADO C G, et al. Physalis angulata extract exerts anti-inflammatory effects in rats by inhibiting different pathways[J].Journal of Ethnopharmacology,2008,118(2):246-251.
[14] WHITFELD P R. A method for the determination of nucleotide sequence in polyribonucleotides[J].Biochemical Journal,1954,58(3):390-396.
[15] SANGER F, NICKLEN S, COULSON A R. DNA sequencing with chain-terminating inhibitors[J].Proceedings of the National Academy of Sciences,1977,74(12):5463-5467.
[16] MELAMEDE R J. Automatable process for sequencing nucleotide: U.S,Patent 4,863,849[P].1989-09-05.
[17] MAIER R M,NECKERMANN K, IGLOI GL,et al. Complete sequenceof the maize chloroplast genome: gene content,hotspots of divergence and fine tuning of genetic information by transcript editing[J].Journal of Molecular Biology,1995, 251( 5) :614-628.
[18] CHUNG H J, JUNG J D, PARK H W, et al. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence[J].Plant Cell Reports,2006,25(12):1369-1379.
[19] 刘晶星.宁夏枸杞和黑果枸杞叶绿体全基因组测序及基因注释分析[D].北京:中国科学院大学,2013.
[20] SHIM D, RAVEENDAR S, LEE J R, et al. The complete chloroplast genome of Capsicum frutescens (Solanaceae)[J].Applications in Plant Sciences,2016,4(5):1600002.
[21] GARGANO D, VEZZI A, SCOTTI N, et al. The complete nucleotide sequence genome of potato (Solanum tuberosum cv Désirée) chloroplast DNA[C]//Book of Abstracts of the 2nd Solanaceae Genome Workshop.Ischia:2005:107.
[22] XU X,PAN S K,CHENG S F,et al.Genome sequence and analysis of the tuber crop potato[J].Nature,2011,475(7355):189-195.
[23] WU Z. The completed eight chloroplast genomes of tomato from Solanum genus[J].Mitochondrial DNA Part A,2016,27(6):4155-4157.
[24] KAHLAU S, ASPINALL S, GRAY J C, et al. Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes[J].Journal of Molecular Evolution,2006,63(2):194-207.
[25] YUKAWA M, TSUDZUKI T, SUGIURA M. The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum[J].Molecular Genetics and Genomics,2006,275(4):367-373.
[26] THYSSEN G, SVAB Z, MALIGA P. Cell-to-cell movement of plastids in plants[J].Proceedings of the National Academy of Sciences,2012,109(7):2439-2443.
[27] POCZAI P, AMIRYOUSEFI A, HYVONEN J.Complete chloroplast genome sequence of Coyote tobacco (Nicotiana attenuata, Solanaceae)[J].Mitochondrial DNA Part B:Resources,2017,2(2):761-762.
[28] SCHMITZ-LINNEWEBER C, REGEL R, DU T G, et al. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation[J].Molecular Biology and Evolution,2002,19(9):1602-1612.
[29] SANCHEZ-PUERTA M V, ABBONA C C. The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae)[J].PloS One,2014,9(5):e98353.
[30] RAVEENDAR S, NA Y W, LEE J R, et al. The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing[J].Molecules,2015,20(7):13080-13088.
[31] JO Y D, PARK J, KIM J, et al. Complete sequencing and comparative analyses of the pepper ( Capsicum annuum, L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome[J].Plant Cell Reports,2011,30(2):217-229.
[32] ZENG F C, GAO C W, GAO L Z. The complete chloroplast genome sequence of American bird pepper (Capsicum annuum var. glabriusculum)[J].Mitochondrial Part A,2014,27(1):724-726.
[33] YISILAM G, MAMUT R, LI J,et al.Characterization of the complete chloroplast genome of Lycium ruthenicum (Solanaceae)[J].Mitochondrial DNA Part B:Resources,2018,3(1):361-362.
[34] CLEGG M T,GAUT B S,LEARN G H,et al. Rates and patterns of chloroplast DNA evolution[J].Proceedings of the National Academy of Sciences,1994,91(15):6795-6801.
[35] SHAW J, LICKEY E B, SCHILLING E E, et al. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III[J].American Journal of Botany,2007,94(3):275-288.
[36] YANG M, ZHANG X, LIU G, et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)[J].Plos One,2012,5(9):e12762.
[37] KOLODNER R, TEWARI K K. Inverted repeats in chloroplast DNA from higher plants[J].Proceedings of the National Academy of Sciences of the United States of America,1979,76(1):41-45.
[38] WAKASUGI T, TSUDZUKI T, SUGIURA M. The genomics of land plant chloroplasts: gene content and alteration of genomic information by RNA editing[J].Photosynthesis Research,2001,70(1):107-118.
[39] SHIMDA H, SUGIURO M. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes[J].Nucleic Acids Research,1991,19(5):983-995.
[40] 唐萍,王强,陈建群.茄科植物叶绿体基因组插入,缺失和核苷酸替代的发生方式及影响[J].遗传,2008,30(11):1506-1512.
[41] KELCHNER S A. The evolution of non-coding chloroplast DNA and its application in plant systematics[J]. Ann Missouri Bot Gard,2000,87(4):482-498.
[42] YAMANE K, YANO K, KAWAHARA T. Pattern and rate of indels evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice[J]. DNA Res,2006,13(5):197-204.
[43] DANIELL H, LEE S B, GREVICH J, et al. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes[J].Theoretical and Applied Genetics,2006,112(8):1503-1518.
[44]DAVENPORT L J. Genera Solanacearum: The genera of solanaceae illustrated, arranged according to a new system by Armando T.Hunziker[J].Systematic Botany,2004,29(1):221-223.
[45] MARTINS T R, BARKMAN T J. Reconstruction of Solanaceae phylogeny using the nuclear gene SAMT[J].Systematic Botany,2005,30(2):435-447.
[46] OLMSTEAD R G, SWEERE J A, SPANGLER R E, et al. Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA[J].Solanaceae IV,1999,1(1):1-137.
[47] OLMSTEAD R G, BOHS L, MIGID H A, et al. A molecular phylogeny of the Solanaceae[J].Taxon,2008,57(4):1159-1181.
[48] RUHSAM M, RAI H S, MATHEWS S, et al. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?[J].Molecular Ecology Resources,2015,15(5):1067-1078.
[49] 杨冬之.茄科天仙子族:结构,分化和系统关系[D].北京:中国科学院植物研究所,2002.
[50] 涂铁要.茄科Nolaneae、天仙子族和茄参族的分子系统学与生物地理学研究[D].昆明:中国科学院昆明植物研究所,2008.
[51] JAMIL I, QAMARUNNISA S, AZHAR A, et al. Subfamilial relationships within solanaceae as inferred from Atpβ-rbcL intergenic spacer[J].Pak J Bot,2014,46(2):585-590.
[52] LUTZ K A, KNAPP J E, MALIGA P. Expression of bar in the plastid genome confers herbicide resistance[J].Plant Physiol,2001,125(4):1585-1590.
[53] RUF S, HERMANN M, BERGER I J, et al. Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit[J].Nature Biotechnology,2001,19(9):870-875.
[54] MILLAN F S, ORTIGOSA S M, HERVAS-STUBBS S, et al. Human papillomavirus L1 protein expressed in tobacco chloroplasts self-assembles into virus-like particles that are highly immunogenic[J].Plant Biotechnology Journal,2008,6(5):427-441.
[55] WAHEED M T, THONES N, MULLER M, et al. Transplastomic expression of a modified human papillomavirus L1 protein leading to the assembly of capsomeres in tobacco: a step towards cost-effective second-generation vaccines[J].Transgenic Research,2011,20(2):271-282.
[56] 张景昱.利用转基因植物生产生物可降解塑料(PHB)的研究[D].北京:中国科学院植物研究所,2002.
[57] 张景昱,赵华燕,朱生伟,等.通过叶绿体基因工程表达聚3-羟基丁酸酯合成相关基因[J].科学通报,2002,47(11):845-848.
[2] LI X, YANG Y, HENRY R J, et al. Plant DNA barcoding: from gene to genome[J].Biol Rev Camb Philos Soc,2015,90(1):157-166.
[3] 张韵洁,李德铢.叶绿体系统发育基因组学的研究进展[J].植物分类与资源学报,2011,33(4):365-375.
[4] ZHAO Y, YIN J, GUO H, et al. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng[J].Frontiers in Plant Science,2014,5:696.
[5] SHINOZAKI K, OHME M, TANAKA M, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression[J].The EMBO Journal,1986,5(9):2043-2049.
[6] OHYAMA K, FUKUZAWA H, KOHCHI T, et al. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA[J].Nature,1986,322:572-574.
[7] D'ARCY W G. The Solanaceae since 1976, with a review of its biogeography[M]//HAWKES J G, LESTER R,NEE M, et al. Solanaceae III:Taxonmy, Chemistry, Evolution. Chicago:University of Chicago Press,2000:75-137.
[8] 福建省科学技术委员会《福建植物志》编写组.福建植物志:第5卷[M].福州:福建科学技术出版社,1982:1-30.
[9] 白重炎,刘帆帆.延安前科药用植物野生资源调查[J].安徽农业科学,2011,39(31):19105-19106.
[10] DA SILVA B J M, RODRIGUES A P D, FARIAS L H S, et al. Physalis angulata induces in vitro differentiation of murine bone marrow cells into macrophages[J].BMC Cell Biology,2014,15(1):37.
[11] MAGALHAES H I F, VERAS M L ,TORRES M R, et al. In-vitro and in-vivo antitumour activity of physalins B and D from Physalis angulata[J].Journal of Pharmacy and Pharmacology,2006,58(2):235-241.
[12] BASTOS G N T, SANTOS A R S, FERREIRA V M M, et al. Antinociceptive effect of the aqueous extract obtained from roots of Physalis angulata L. on mice[J].Journal of Ethnopharmacology,2006,103(2):241-245.
[13] BASTOS G N T, SILVEIRA A J A, SALGADO C G, et al. Physalis angulata extract exerts anti-inflammatory effects in rats by inhibiting different pathways[J].Journal of Ethnopharmacology,2008,118(2):246-251.
[14] WHITFELD P R. A method for the determination of nucleotide sequence in polyribonucleotides[J].Biochemical Journal,1954,58(3):390-396.
[15] SANGER F, NICKLEN S, COULSON A R. DNA sequencing with chain-terminating inhibitors[J].Proceedings of the National Academy of Sciences,1977,74(12):5463-5467.
[16] MELAMEDE R J. Automatable process for sequencing nucleotide: U.S,Patent 4,863,849[P].1989-09-05.
[17] MAIER R M,NECKERMANN K, IGLOI GL,et al. Complete sequenceof the maize chloroplast genome: gene content,hotspots of divergence and fine tuning of genetic information by transcript editing[J].Journal of Molecular Biology,1995, 251( 5) :614-628.
[18] CHUNG H J, JUNG J D, PARK H W, et al. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence[J].Plant Cell Reports,2006,25(12):1369-1379.
[19] 刘晶星.宁夏枸杞和黑果枸杞叶绿体全基因组测序及基因注释分析[D].北京:中国科学院大学,2013.
[20] SHIM D, RAVEENDAR S, LEE J R, et al. The complete chloroplast genome of Capsicum frutescens (Solanaceae)[J].Applications in Plant Sciences,2016,4(5):1600002.
[21] GARGANO D, VEZZI A, SCOTTI N, et al. The complete nucleotide sequence genome of potato (Solanum tuberosum cv Désirée) chloroplast DNA[C]//Book of Abstracts of the 2nd Solanaceae Genome Workshop.Ischia:2005:107.
[22] XU X,PAN S K,CHENG S F,et al.Genome sequence and analysis of the tuber crop potato[J].Nature,2011,475(7355):189-195.
[23] WU Z. The completed eight chloroplast genomes of tomato from Solanum genus[J].Mitochondrial DNA Part A,2016,27(6):4155-4157.
[24] KAHLAU S, ASPINALL S, GRAY J C, et al. Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes[J].Journal of Molecular Evolution,2006,63(2):194-207.
[25] YUKAWA M, TSUDZUKI T, SUGIURA M. The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum[J].Molecular Genetics and Genomics,2006,275(4):367-373.
[26] THYSSEN G, SVAB Z, MALIGA P. Cell-to-cell movement of plastids in plants[J].Proceedings of the National Academy of Sciences,2012,109(7):2439-2443.
[27] POCZAI P, AMIRYOUSEFI A, HYVONEN J.Complete chloroplast genome sequence of Coyote tobacco (Nicotiana attenuata, Solanaceae)[J].Mitochondrial DNA Part B:Resources,2017,2(2):761-762.
[28] SCHMITZ-LINNEWEBER C, REGEL R, DU T G, et al. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation[J].Molecular Biology and Evolution,2002,19(9):1602-1612.
[29] SANCHEZ-PUERTA M V, ABBONA C C. The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae)[J].PloS One,2014,9(5):e98353.
[30] RAVEENDAR S, NA Y W, LEE J R, et al. The complete chloroplast genome of Capsicum annuum var. glabriusculum using Illumina sequencing[J].Molecules,2015,20(7):13080-13088.
[31] JO Y D, PARK J, KIM J, et al. Complete sequencing and comparative analyses of the pepper ( Capsicum annuum, L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome[J].Plant Cell Reports,2011,30(2):217-229.
[32] ZENG F C, GAO C W, GAO L Z. The complete chloroplast genome sequence of American bird pepper (Capsicum annuum var. glabriusculum)[J].Mitochondrial Part A,2014,27(1):724-726.
[33] YISILAM G, MAMUT R, LI J,et al.Characterization of the complete chloroplast genome of Lycium ruthenicum (Solanaceae)[J].Mitochondrial DNA Part B:Resources,2018,3(1):361-362.
[34] CLEGG M T,GAUT B S,LEARN G H,et al. Rates and patterns of chloroplast DNA evolution[J].Proceedings of the National Academy of Sciences,1994,91(15):6795-6801.
[35] SHAW J, LICKEY E B, SCHILLING E E, et al. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III[J].American Journal of Botany,2007,94(3):275-288.
[36] YANG M, ZHANG X, LIU G, et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)[J].Plos One,2012,5(9):e12762.
[37] KOLODNER R, TEWARI K K. Inverted repeats in chloroplast DNA from higher plants[J].Proceedings of the National Academy of Sciences of the United States of America,1979,76(1):41-45.
[38] WAKASUGI T, TSUDZUKI T, SUGIURA M. The genomics of land plant chloroplasts: gene content and alteration of genomic information by RNA editing[J].Photosynthesis Research,2001,70(1):107-118.
[39] SHIMDA H, SUGIURO M. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes[J].Nucleic Acids Research,1991,19(5):983-995.
[40] 唐萍,王强,陈建群.茄科植物叶绿体基因组插入,缺失和核苷酸替代的发生方式及影响[J].遗传,2008,30(11):1506-1512.
[41] KELCHNER S A. The evolution of non-coding chloroplast DNA and its application in plant systematics[J]. Ann Missouri Bot Gard,2000,87(4):482-498.
[42] YAMANE K, YANO K, KAWAHARA T. Pattern and rate of indels evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice[J]. DNA Res,2006,13(5):197-204.
[43] DANIELL H, LEE S B, GREVICH J, et al. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes[J].Theoretical and Applied Genetics,2006,112(8):1503-1518.
[44]DAVENPORT L J. Genera Solanacearum: The genera of solanaceae illustrated, arranged according to a new system by Armando T.Hunziker[J].Systematic Botany,2004,29(1):221-223.
[45] MARTINS T R, BARKMAN T J. Reconstruction of Solanaceae phylogeny using the nuclear gene SAMT[J].Systematic Botany,2005,30(2):435-447.
[46] OLMSTEAD R G, SWEERE J A, SPANGLER R E, et al. Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA[J].Solanaceae IV,1999,1(1):1-137.
[47] OLMSTEAD R G, BOHS L, MIGID H A, et al. A molecular phylogeny of the Solanaceae[J].Taxon,2008,57(4):1159-1181.
[48] RUHSAM M, RAI H S, MATHEWS S, et al. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?[J].Molecular Ecology Resources,2015,15(5):1067-1078.
[49] 杨冬之.茄科天仙子族:结构,分化和系统关系[D].北京:中国科学院植物研究所,2002.
[50] 涂铁要.茄科Nolaneae、天仙子族和茄参族的分子系统学与生物地理学研究[D].昆明:中国科学院昆明植物研究所,2008.
[51] JAMIL I, QAMARUNNISA S, AZHAR A, et al. Subfamilial relationships within solanaceae as inferred from Atpβ-rbcL intergenic spacer[J].Pak J Bot,2014,46(2):585-590.
[52] LUTZ K A, KNAPP J E, MALIGA P. Expression of bar in the plastid genome confers herbicide resistance[J].Plant Physiol,2001,125(4):1585-1590.
[53] RUF S, HERMANN M, BERGER I J, et al. Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit[J].Nature Biotechnology,2001,19(9):870-875.
[54] MILLAN F S, ORTIGOSA S M, HERVAS-STUBBS S, et al. Human papillomavirus L1 protein expressed in tobacco chloroplasts self-assembles into virus-like particles that are highly immunogenic[J].Plant Biotechnology Journal,2008,6(5):427-441.
[55] WAHEED M T, THONES N, MULLER M, et al. Transplastomic expression of a modified human papillomavirus L1 protein leading to the assembly of capsomeres in tobacco: a step towards cost-effective second-generation vaccines[J].Transgenic Research,2011,20(2):271-282.
[56] 张景昱.利用转基因植物生产生物可降解塑料(PHB)的研究[D].北京:中国科学院植物研究所,2002.
[57] 张景昱,赵华燕,朱生伟,等.通过叶绿体基因工程表达聚3-羟基丁酸酯合成相关基因[J].科学通报,2002,47(11):845-848.