五加科植物叶绿体基因组结构与进化分析
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摘要
目的获取五加科叶绿体基因组的结构特征以及进化关系。方法以已测序完成的10个属的20种五加科植物叶绿体基因组为研究对象,系统比较基因组间的差异,分析4个IR边界扩张与收缩情况,并以近缘物种当归为外类群,使用MEGA 4.0构建系统进化树,分析物种间的亲缘关系。结果 20种五加科植物的叶绿体基因组大小差异较小,最大差仅1 909bp。各物种均出现基因替换现象,由cem A基因替换ycf10基因,且数量存在一定差异,主要由t RNA引起。通过比较发现,五加科物种的4个IR边界比较保守,仅野三七、三七和穗序鹅掌柴的边界基因进入IR区的长度与其他物种的差异较大。以当归为外类构建的系统进化树,各节点的支持率较高,清晰地反映了各物种间的亲缘关系。结论叶绿体基因组涵盖的信息量大,可以用于分析关系较近与进化较快物种的系统发生问题。
Objective To obtain the structural characteristics and phylogentic relationships of the chloroplast genome in Araliaceae species. Methods we used 20 chloroplast genomes which have sequenced as materials, they were from 20 species belonging to 10 genus of Araliaceae. Analysis the differences of genomes and the dilation or shrink of four boundaries for IR, we used MEGA 4.0 to build the phylogenetic tree with Angelica gigas of sibling species as the outgroup and analysis their phylogentic relationships. ResultsThere was a small difference among the chloroplast genomes size, and the largest difference is 1 909 bp. All of species had existed gene replacements, cem A replaced ycf10, and number of genes existed some differences, they were mainly caused by t RNA. The four boundaries of IR was relatively conservative, only Panax vietnamensi, Panax notoginseng and Schefflera delavayi were special, their boundary genes were in IR. All nodes of the phylogenetic tree of Araliaceae which was based on Angelica gigas were of high supports, and the tree had good resolution to reflect the genetic relationships among Araliaceae. Conclusion Chloroplast genomes have a lot of information, it can be used to analysis phylogeny among the species which are affinity or faster evolution.
Objective To obtain the structural characteristics and phylogentic relationships of the chloroplast genome in Araliaceae species. Methods we used 20 chloroplast genomes which have sequenced as materials, they were from 20 species belonging to 10 genus of Araliaceae. Analysis the differences of genomes and the dilation or shrink of four boundaries for IR, we used MEGA 4.0 to build the phylogenetic tree with Angelica gigas of sibling species as the outgroup and analysis their phylogentic relationships. ResultsThere was a small difference among the chloroplast genomes size, and the largest difference is 1 909 bp. All of species had existed gene replacements, cem A replaced ycf10, and number of genes existed some differences, they were mainly caused by t RNA. The four boundaries of IR was relatively conservative, only Panax vietnamensi, Panax notoginseng and Schefflera delavayi were special, their boundary genes were in IR. All nodes of the phylogenetic tree of Araliaceae which was based on Angelica gigas were of high supports, and the tree had good resolution to reflect the genetic relationships among Araliaceae. Conclusion Chloroplast genomes have a lot of information, it can be used to analysis phylogeny among the species which are affinity or faster evolution.
引文
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[14]唐萍,阮秋燕,彭程.禾本科植物叶绿体基因组结构的系统进化分析[J].中国农学通报,2011,27(30):171-176.
[15]Chang C C,Lin H C,Lin I P,et al.The chloroplast genome of Phalaenopsis aphrodite(Orchidaceae):Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications[J].Mol Biol Evol,2006,23(2):279-291.
[16]Li R,Ma P,Wen J,et al.Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications[J].PLo S One,2013,8(10):e78568.
[2]王玲,董文攀,周世良.被子植物叶绿体基因组的结构变异研究进展[J].西北植物学报,2012,32(6):1282-1288.
[3]Zhang T,Fang Y,Wang X,et al.The complete chloroplast and mitochondrial genome sequences of Boea hygrometrice:Insight into the evolution of plant organellar genomes[J].PLo S One,2012,7:e30531.
[4]任玉新,金立弟,韩宇.五加科植物多糖的药理作用研究进展[J].中国药业,2012,21(6):83-86.
[5]Nock C J,Waters D J,Edwards M A,et al.Chloroplast genome sequence from total DNA for plant identification[J].Plant Biotechnol J,2011,9(3):328-333.
[6]邢少辰,Clarke J L.叶绿体基因组研究进展[J].生物化学与生物物理进展,2008,31(1):21-28.
[7]田欣,李德铢.DNA序列在植物系统学研究中的应用[J].云南植物研究,2002,2(2):170-184.
[8]Khakhlova O,Bock R.Elimination of deleterious mutations in plastid genome by gene conversion[J].Plant J,2006,46(1):85-94.
[9]Chumley T W,Plamer J D,Mower J P,et al.The complete chloroplast genome sequence of Pelargonium×hortorum:Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants[J].Mol Biol Evol,2006,23(11):2175-2190.
[10]Hirao T,Watanabe A,Kurita M,et al.Complete nucleotide sequence of the Cryptomeria japonica D.Don.chloroplast genome and comparative chloroplast genomics:Diversified genomic structure of coniferous species[J].BMC Plant Biol,2008,8:70.
[11]Saski C,Lee S B,Daniell H,et al.Complete chloroplast genome sequence of Glycine max and comparative analysis with other legume genomes[J].Plant Mol Biol,2005,59(2):309-322.
[12]Yao X H,Tang P,Li Z Z,et al.The first complete chloroplast genome sequence in Actinidiaceae:Genome structure and comparative analysis[J].PLo S One,2015,10(6):e0129347.
[13]李岩,吕光辉,张雪妮,等.十字花科植物叶绿体基因组结构及变异分析[J].西北植物学报,2017,37(6):1090-1101.
[14]唐萍,阮秋燕,彭程.禾本科植物叶绿体基因组结构的系统进化分析[J].中国农学通报,2011,27(30):171-176.
[15]Chang C C,Lin H C,Lin I P,et al.The chloroplast genome of Phalaenopsis aphrodite(Orchidaceae):Comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications[J].Mol Biol Evol,2006,23(2):279-291.
[16]Li R,Ma P,Wen J,et al.Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications[J].PLo S One,2013,8(10):e78568.