基于nrDNA ITS序列对忍冬属部分植物系统发育关系的研究
摘要
在进行植物分子系统学研究过程中,选择进化速率适宜的基因或DNA片段对于系统发育关系的推断十分重要。由于植物细胞核核糖体内转录间隔区(nrDNA ITS)进化速率较快,可以提供较丰富的信息位点,目前已被广泛应用于研究被子植物近缘属间、种间等分类阶元的系统发育关系。国内外学者在忍冬属内各分类群间的系统发育问题上存在较多的分歧,因此有必要进行深入的探讨。
本研究以nrDNA ITS序列为研究对象,对分布于新疆的8个种及引进的7种的忍冬属(Lonicera L.)植物ITS区全序列进行了测定,利用系统发育分析软件MEGA3.1对测得的数据及GenBank中已经发表的5个忍冬属ITS序列数据进行了分析。并对测序的15种忍冬属植物及1个外类群进行了37个形态性状的数量分类分析。所得结果如下:
1.通过引物设计、PCR、克隆、测序、序列的同源性比对及聚类分析,得到新疆8个种及引进的7种忍冬属的ITS序列,并进行了相应的系统发育分析。
2.在本研究中的15种忍冬属植物中,ITS转录间隔区(包括ITS1和ITS2)内信息位点达到11.7%。在对包括5种GenBank中已发表的忍冬属植物所有ITS区序列进行综合分析时,数据的信息位点达到11.0%,由此可见,在整个忍冬属内,ITS区序列信息位点相对比较丰富。从分支分析的结果来看,忍冬属内部分类群的划分与形态划分具有较高的一致性,证明ITS区可以为解决忍冬属植物的系统发育问题提供较强的证据,数量分类的结果也与ITS区分析结果基本一致,由此也证明了ITS区在忍冬属植物分类中可行性。
3.从ITS序列分析得到的各聚类图以及数量分类聚类图中,阿尔泰忍冬(L.caerulea var.altaic)、蓝果忍冬(L. caerulea var. caerulea)、蓝靛果(L.caerulea var.edulis)聚为一支,自展支持率高达90%以上,ITS数据、数量分类数据说明蓝靛果忍冬与蓝果忍冬、阿尔泰忍冬同属蓝果亚组(Sect.Caeruleae),与传统分类相符,故不支持将蓝靛果另立新属。
4.在对20种忍冬属植物的分析中,基于ITS序列数据的系统树,支持传统分类中对忍冬属空枝组(Sect. Coeloxylosteum )、忍冬组(Sect. Nintooa)、蓝果亚组的划分,获得较高的自展支持率(bootstrap>90%),而其余组的划分需增加研究类群进行进一步的研究。
5.在对15种忍冬属植物的ITS序列构建的系统树中,以及包括GenBank中所发表的ITS区序列的20种忍冬属的系ITS序列构建的NJ系统树中(有根树),忍冬属内各组没有一组表现出首先从基部分出,所以没有形成系统树的基部分支,忍属内各组形成姐妹群关系,表现出平行进化的趋势。
In carries on the plant member systematic research process, the choice of suitable evolution speed of the gene or the DNA fragment is extremely important regarding the system growth relations inference. Because plant ribose the gap area (nrDNA ITS) in the cell nucleus evolves the speed very quick, may provide the richer information bit spot.At present it has been widely applied to the research angiosperm, inter-species and so on.The domestic and foreign scholars have more differences in the Lonicera phylogenetic, therefore, there has the necessary to carry on the discussion.
This research take the nrDNA ITS sequence as the object, to mensurate ITS area complete sequences of Lonicera plant in Xinjiang's 8 kind and the introduction 7 kind, 5 Lonicera plant ITS sequences data obtained in GenBank which using system growth analysis software MEGA3.1 to carry on the analysis, and has carried on 37 shapescharacters quantity classification analysis to above 15 kind of Lonicera plant and 1 out-group. Obtained result as follows:
1.The nrDNA ITS sequences of the 15 Lonicera plant and one out-group were obtained by primer designing, PCR, cloning and sequencing, which subsequently were used to analyze the phylogenetic relationships in the genus by homologous blast and clade analysis.
2.In the data set of 15 Lonicera plant, the percentage of phylogenetically informative sites is 11.7% in ITS regions (including two spacers, without 5.8S spacers).In the data set including the ITS sequences downloaded from GenBank, the percentage of phylogenetically informative sites is 11.0%. According to the above statistics, there ate relatively abundant informative sites in the ITS sequences of genus Lonicera. The phylogenetix analyses based on the ITS sequence are in consensus with the morphological classification of the group within the genus to a degree, which proved that the ITS regions are valuable to resolve the phylogenetic relationships in Lonicera.The quantity classification result basic is also consistent with the ITS area analysis result, from this has also proven the ITS area in the Lonicera plant classification the feasibility.
3.Obtains from the ITS sequence analysis respectively gathers charts and quantity classified collection class chart, L.caerulea var. altaic, L. caerulea var.caerulea and L. caerulea var. edulis gather in one branch, Bootstrap reach as high as above 90%, the ITS data, the quantity classified data showed that L. caerulea var. edulis, L. caerulea var. altaic and L. caerulea var. caerulea to be the Sect.Caeruleae, tallies with the traditional classification, therefore will not support L. caerulea var. edulis to stand newly is.
4.In to 20 kind of Loniceras plants' analysis, based on the ITS sequence data genealogical tree, supports in the traditional classification to the Lonicera Sect.Coeloxylosteum, Sect.Nintooa and Subsect.caerulea the division, obtains high Bootstrap (bootstrap> 90%), other three groups’divisions must increase the research texons to conduct the further research.
5.In the genealogical tree which constructs to 15 kind of Lonicera plants ITS sequence, in the NJ genealogical tree which including GenBank in as well as which publishes ITS the area sequence 20 kind of Lonicera department ITS sequences construct (to have a tree), in the Lonicera an each group of group has not displayed first branches out from the base, therefore has not formed the genealogical tree the base branch in, endures to be each group to form the sisters group relations, displays the parallel evolution the tendency.
本研究以nrDNA ITS序列为研究对象,对分布于新疆的8个种及引进的7种的忍冬属(Lonicera L.)植物ITS区全序列进行了测定,利用系统发育分析软件MEGA3.1对测得的数据及GenBank中已经发表的5个忍冬属ITS序列数据进行了分析。并对测序的15种忍冬属植物及1个外类群进行了37个形态性状的数量分类分析。所得结果如下:
1.通过引物设计、PCR、克隆、测序、序列的同源性比对及聚类分析,得到新疆8个种及引进的7种忍冬属的ITS序列,并进行了相应的系统发育分析。
2.在本研究中的15种忍冬属植物中,ITS转录间隔区(包括ITS1和ITS2)内信息位点达到11.7%。在对包括5种GenBank中已发表的忍冬属植物所有ITS区序列进行综合分析时,数据的信息位点达到11.0%,由此可见,在整个忍冬属内,ITS区序列信息位点相对比较丰富。从分支分析的结果来看,忍冬属内部分类群的划分与形态划分具有较高的一致性,证明ITS区可以为解决忍冬属植物的系统发育问题提供较强的证据,数量分类的结果也与ITS区分析结果基本一致,由此也证明了ITS区在忍冬属植物分类中可行性。
3.从ITS序列分析得到的各聚类图以及数量分类聚类图中,阿尔泰忍冬(L.caerulea var.altaic)、蓝果忍冬(L. caerulea var. caerulea)、蓝靛果(L.caerulea var.edulis)聚为一支,自展支持率高达90%以上,ITS数据、数量分类数据说明蓝靛果忍冬与蓝果忍冬、阿尔泰忍冬同属蓝果亚组(Sect.Caeruleae),与传统分类相符,故不支持将蓝靛果另立新属。
4.在对20种忍冬属植物的分析中,基于ITS序列数据的系统树,支持传统分类中对忍冬属空枝组(Sect. Coeloxylosteum )、忍冬组(Sect. Nintooa)、蓝果亚组的划分,获得较高的自展支持率(bootstrap>90%),而其余组的划分需增加研究类群进行进一步的研究。
5.在对15种忍冬属植物的ITS序列构建的系统树中,以及包括GenBank中所发表的ITS区序列的20种忍冬属的系ITS序列构建的NJ系统树中(有根树),忍冬属内各组没有一组表现出首先从基部分出,所以没有形成系统树的基部分支,忍属内各组形成姐妹群关系,表现出平行进化的趋势。
In carries on the plant member systematic research process, the choice of suitable evolution speed of the gene or the DNA fragment is extremely important regarding the system growth relations inference. Because plant ribose the gap area (nrDNA ITS) in the cell nucleus evolves the speed very quick, may provide the richer information bit spot.At present it has been widely applied to the research angiosperm, inter-species and so on.The domestic and foreign scholars have more differences in the Lonicera phylogenetic, therefore, there has the necessary to carry on the discussion.
This research take the nrDNA ITS sequence as the object, to mensurate ITS area complete sequences of Lonicera plant in Xinjiang's 8 kind and the introduction 7 kind, 5 Lonicera plant ITS sequences data obtained in GenBank which using system growth analysis software MEGA3.1 to carry on the analysis, and has carried on 37 shapescharacters quantity classification analysis to above 15 kind of Lonicera plant and 1 out-group. Obtained result as follows:
1.The nrDNA ITS sequences of the 15 Lonicera plant and one out-group were obtained by primer designing, PCR, cloning and sequencing, which subsequently were used to analyze the phylogenetic relationships in the genus by homologous blast and clade analysis.
2.In the data set of 15 Lonicera plant, the percentage of phylogenetically informative sites is 11.7% in ITS regions (including two spacers, without 5.8S spacers).In the data set including the ITS sequences downloaded from GenBank, the percentage of phylogenetically informative sites is 11.0%. According to the above statistics, there ate relatively abundant informative sites in the ITS sequences of genus Lonicera. The phylogenetix analyses based on the ITS sequence are in consensus with the morphological classification of the group within the genus to a degree, which proved that the ITS regions are valuable to resolve the phylogenetic relationships in Lonicera.The quantity classification result basic is also consistent with the ITS area analysis result, from this has also proven the ITS area in the Lonicera plant classification the feasibility.
3.Obtains from the ITS sequence analysis respectively gathers charts and quantity classified collection class chart, L.caerulea var. altaic, L. caerulea var.caerulea and L. caerulea var. edulis gather in one branch, Bootstrap reach as high as above 90%, the ITS data, the quantity classified data showed that L. caerulea var. edulis, L. caerulea var. altaic and L. caerulea var. caerulea to be the Sect.Caeruleae, tallies with the traditional classification, therefore will not support L. caerulea var. edulis to stand newly is.
4.In to 20 kind of Loniceras plants' analysis, based on the ITS sequence data genealogical tree, supports in the traditional classification to the Lonicera Sect.Coeloxylosteum, Sect.Nintooa and Subsect.caerulea the division, obtains high Bootstrap (bootstrap> 90%), other three groups’divisions must increase the research texons to conduct the further research.
5.In the genealogical tree which constructs to 15 kind of Lonicera plants ITS sequence, in the NJ genealogical tree which including GenBank in as well as which publishes ITS the area sequence 20 kind of Lonicera department ITS sequences construct (to have a tree), in the Lonicera an each group of group has not displayed first branches out from the base, therefore has not formed the genealogical tree the base branch in, endures to be each group to form the sisters group relations, displays the parallel evolution the tendency.
引文
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