石珊瑚的DNA条形码研究及其系统发育分析
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摘要
石珊瑚(Scleractinia)属于刺胞动物门(Cnidaria),珊瑚虫纲(Anthozoa),六放珊瑚亚纲(Hexacorallia),石珊瑚目(Scleractinia)。据统计我国的造礁石珊瑚有14科54属174种。珊瑚表型性状的高度相似性使其物种鉴定和分类等存在诸多疑难问题,DNA序列分析可以较好地解决这一问题。目前国内对石珊瑚的系统学研究报道较少,本研究通过比较分析核糖体ITS序列和线粒体COⅢ序列初步探讨海南部分石珊瑚种间、种内遗传距离和分子系统学关系,并对ITS和COⅢ序列是否适宜作为石珊瑚DNA条形码的潜在序列进行了简要评价。研究结果如下：
1.石珊瑚的ITS DNA序列中,ITS1的长度为185bp-250bp, GC含量变化范围为40.1%-63.1%；ITS2序列的长度在188bp-238bp之间,GC含量最高,变化范围为43.7%-74.4%；不同种间的5.8S序列长度也不相同,序列长度在153bp-195bp范围变化。这一结果与其他关于石珊瑚ITS区的研究结果相似。在ITS全序列中,变异位点和简约信息位点都远高于保守位点；碱基的颠换(108)高于转换(89),转换与颠换比(R)为0.82。
2.ITS序列构建的石珊瑚系统分支树结果表明：(1)菌珊瑚科牡丹珊瑚属中的易变牡丹珊瑚、十字牡丹珊瑚和小牡丹珊瑚均聚在一起；(2)滨珊瑚科滨珊瑚属的澄黄滨珊瑚的大部分个体聚为一支；(3)蜂巢珊瑚科扁脑珊瑚属的交替扁脑珊瑚和中华扁脑珊瑚也聚为一支,这一结果与传统的分类学一致；(4)与传统形态学分类不一致的大多数个体属于蜂巢珊瑚科几个属中,主要为同星珊瑚属、刺叶珊瑚属、刺孔珊瑚属和角蜂巢珊瑚属。
3.石珊瑚的COⅢ基因序列中,A、T、C、G核苷酸的平均含量分别为41.1%、21.0%、21.8%和16.1%,A+T含量显著高于C+G含量,且四种碱基在每个个体中的分布比较均匀。COⅢ序列中,保守位点为341,变异位点为176,信息位点为118,自近裔位点为16,单倍型数H=29,单倍型基因多样性指数Hd=0.898,核苷酸多样性指数pi=0.12833,表明石珊瑚含有较高的遗传多样性。三联体密码子中,第三个核苷酸的碱基替换频率较大(0.95)。
4.COⅢ基因构建的系统分支树结果显示：(1)种内个体间的系统发育关系与形态学分类结果比较一致,只有蜂巢珊瑚科小星珊瑚属的紫小星珊瑚个体(L.puYlll)与同科的同星珊瑚属的曲同星珊瑚聚在一起；(2)属内种间的系统发育关系与形态学分类结果也比较一致；(3)科内属间的系统发育关系比较混乱,与形态学分类结果有较大差异,蜂巢珊瑚科的扁脑珊瑚属的交替扁脑与同科的小星珊瑚属的紫小星珊瑚聚在一起,此后却与梳状珊瑚科的刺叶珊瑚属的粗糙刺叶聚在一起,并随后再与裸肋珊瑚科刺柄珊瑚属的腐蚀刺柄聚在一起,最后才与蜂巢珊瑚科的同星珊瑚属和小星珊瑚属聚在一起。
5.以ITSDNA序列和COⅢ基因序列构建的石珊瑚分子系统树结果显示,ITS DNA序列和COIII DNA序列不适合作高阶元的系统发育标记,但可以有效作为物种种内间的分子标记。
Scleractinia belongs to Scleractinia, Hexacorallia, Anthozoa, Cnidaria. It was reported that there were174species of Scleractinia in China, subordinated to54genera of14families. Highly similarity of phenotypic characters among Scleractinia species result into too much difficulty in coral species identification and classification, which can be truly solved with DNA sequence analysis. Up to date, there are just several reports on molecular phylogenic study of Scleractinia. Here, we expect to discover intra-specific and inter-specific genetic distances, and molecular phylogenic relationships among tens of Scleractinia individuals collected from Hainan Island by analyzing DNA sequences of both ribosomal internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase Ⅲ(COⅢ) Besides, the potential possibility for ITS and COⅢ sequences using as DNA barcode in Scleractinia was also discussed. The main results in this study were as following:
1. There are three fragments for ITS sequences, including ITS1,5.8S and ITS2. Among65individuals of Scleractinia, the length of ITS1range from185bp to250bp with the content of GC ranging from40.1%to63.1%, while the length of ITS2range from188bp to238bp with the content of GC ranging from43.7%to74.4%. The length of5.8S also changed among Scleractinia species with a range from153bp to195bp. These results were the same as other reported on study of Scleractinia. Variable sites and information site are much more than conserved sites in ITS sequences. There are more Transversion nucleotides (108) than transition nucleotides (89), namely a ratio of0.82.
2. Phylogenetic trees were constructed based on ITS sequences of Scleractinia. It was show that:(1) For Pavona, a genus of the family of Agariciidae, three species of P. varians, P. decussate and P. minuta were clustered into a branch as expected;(2) For Porites, a genus of the family of Poritidae, most of P. lutea individuals were also clustered into a branch as expected;(3) For Platygyra, a genus of the family of Faviidae, the whole individuals of P. crosslandi and P. sinensis were also clustered together, in line with traditional taxonomy;(4) Most individuals whose cluster results were obviously different from phenotype characters are belong to several genera in Faviidae, especially three genera of Plesiastrea, Echinophyllia, Echinopora and Favites.
3. For COⅢ sequences of Scleractinia, the average content of A, T, C and G are41.1%,21.0%,21.8%and16.1%respectively. The content of A+T is significant higher than that of C+G, and these four fundamental bases are uniform distributed in every individual. There are341conserved sites,176variable sites,118information sites, and16singleton sites in COⅢ DNA sequences of Scleractinia. Furthermore, the number of Haplotype is29, with a Haplotype diversity index of0.898and a nucleotide diversity index of0.12833. Therefore, the genetic diversity of Scleractinia was quite abundant. As concerned from triplet codon, the base substitution frequency of third nucleotide (0.95) was much higher than that of the other two bases.
4. Phylogenetic trees were constructed based on COⅢ DNA sequences of Scleractinia. Results showed that:(1) phylogenetic relationship among intra-specific individuals is consistent with the traditional taxonomy, except that individuals from two different genera, Leptastrea and Plesiastrea of Faviidae, were clustered into a branch;(2) phylogenetic relationship among species within genus was also consistent with the traditional taxonomy.(3) However, phylogenetic relationship among genera within family was quite disorder, obviously inconsistent with results of traditional taxonomy. Platygyra crosslandi (belonging to Platygyra, a genus of Faviidae) was clustered into a branch with Leptastrea purpurea (belonging to Leptastrea, another genus of Faviidae) firstly, but then they were clustered into a branch with Echinophyllia aspera, belonging to Echinophyllia, a genus from another family of Pectiniidae. Subsequently, they were clustered together with Hydnophora exesa (belonging to Hydnophora, a genus from a different family of Merulinidae), and finally clustered into a branch with Plesiastrea and Leptastrea, two genera from the same family of Faviidae.
5. Phylogenetic branch tree of Scleractinia based on ITS DNA sequences and COⅢ sequences showed that ITS and COⅢ sequence is not suitable for phylogeny mark of high taxonomic category, but can be effective as molecular markers in intraspecific.
1.石珊瑚的ITS DNA序列中,ITS1的长度为185bp-250bp, GC含量变化范围为40.1%-63.1%；ITS2序列的长度在188bp-238bp之间,GC含量最高,变化范围为43.7%-74.4%；不同种间的5.8S序列长度也不相同,序列长度在153bp-195bp范围变化。这一结果与其他关于石珊瑚ITS区的研究结果相似。在ITS全序列中,变异位点和简约信息位点都远高于保守位点；碱基的颠换(108)高于转换(89),转换与颠换比(R)为0.82。
2.ITS序列构建的石珊瑚系统分支树结果表明：(1)菌珊瑚科牡丹珊瑚属中的易变牡丹珊瑚、十字牡丹珊瑚和小牡丹珊瑚均聚在一起；(2)滨珊瑚科滨珊瑚属的澄黄滨珊瑚的大部分个体聚为一支；(3)蜂巢珊瑚科扁脑珊瑚属的交替扁脑珊瑚和中华扁脑珊瑚也聚为一支,这一结果与传统的分类学一致；(4)与传统形态学分类不一致的大多数个体属于蜂巢珊瑚科几个属中,主要为同星珊瑚属、刺叶珊瑚属、刺孔珊瑚属和角蜂巢珊瑚属。
3.石珊瑚的COⅢ基因序列中,A、T、C、G核苷酸的平均含量分别为41.1%、21.0%、21.8%和16.1%,A+T含量显著高于C+G含量,且四种碱基在每个个体中的分布比较均匀。COⅢ序列中,保守位点为341,变异位点为176,信息位点为118,自近裔位点为16,单倍型数H=29,单倍型基因多样性指数Hd=0.898,核苷酸多样性指数pi=0.12833,表明石珊瑚含有较高的遗传多样性。三联体密码子中,第三个核苷酸的碱基替换频率较大(0.95)。
4.COⅢ基因构建的系统分支树结果显示：(1)种内个体间的系统发育关系与形态学分类结果比较一致,只有蜂巢珊瑚科小星珊瑚属的紫小星珊瑚个体(L.puYlll)与同科的同星珊瑚属的曲同星珊瑚聚在一起；(2)属内种间的系统发育关系与形态学分类结果也比较一致；(3)科内属间的系统发育关系比较混乱,与形态学分类结果有较大差异,蜂巢珊瑚科的扁脑珊瑚属的交替扁脑与同科的小星珊瑚属的紫小星珊瑚聚在一起,此后却与梳状珊瑚科的刺叶珊瑚属的粗糙刺叶聚在一起,并随后再与裸肋珊瑚科刺柄珊瑚属的腐蚀刺柄聚在一起,最后才与蜂巢珊瑚科的同星珊瑚属和小星珊瑚属聚在一起。
5.以ITSDNA序列和COⅢ基因序列构建的石珊瑚分子系统树结果显示,ITS DNA序列和COIII DNA序列不适合作高阶元的系统发育标记,但可以有效作为物种种内间的分子标记。
Scleractinia belongs to Scleractinia, Hexacorallia, Anthozoa, Cnidaria. It was reported that there were174species of Scleractinia in China, subordinated to54genera of14families. Highly similarity of phenotypic characters among Scleractinia species result into too much difficulty in coral species identification and classification, which can be truly solved with DNA sequence analysis. Up to date, there are just several reports on molecular phylogenic study of Scleractinia. Here, we expect to discover intra-specific and inter-specific genetic distances, and molecular phylogenic relationships among tens of Scleractinia individuals collected from Hainan Island by analyzing DNA sequences of both ribosomal internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase Ⅲ(COⅢ) Besides, the potential possibility for ITS and COⅢ sequences using as DNA barcode in Scleractinia was also discussed. The main results in this study were as following:
1. There are three fragments for ITS sequences, including ITS1,5.8S and ITS2. Among65individuals of Scleractinia, the length of ITS1range from185bp to250bp with the content of GC ranging from40.1%to63.1%, while the length of ITS2range from188bp to238bp with the content of GC ranging from43.7%to74.4%. The length of5.8S also changed among Scleractinia species with a range from153bp to195bp. These results were the same as other reported on study of Scleractinia. Variable sites and information site are much more than conserved sites in ITS sequences. There are more Transversion nucleotides (108) than transition nucleotides (89), namely a ratio of0.82.
2. Phylogenetic trees were constructed based on ITS sequences of Scleractinia. It was show that:(1) For Pavona, a genus of the family of Agariciidae, three species of P. varians, P. decussate and P. minuta were clustered into a branch as expected;(2) For Porites, a genus of the family of Poritidae, most of P. lutea individuals were also clustered into a branch as expected;(3) For Platygyra, a genus of the family of Faviidae, the whole individuals of P. crosslandi and P. sinensis were also clustered together, in line with traditional taxonomy;(4) Most individuals whose cluster results were obviously different from phenotype characters are belong to several genera in Faviidae, especially three genera of Plesiastrea, Echinophyllia, Echinopora and Favites.
3. For COⅢ sequences of Scleractinia, the average content of A, T, C and G are41.1%,21.0%,21.8%and16.1%respectively. The content of A+T is significant higher than that of C+G, and these four fundamental bases are uniform distributed in every individual. There are341conserved sites,176variable sites,118information sites, and16singleton sites in COⅢ DNA sequences of Scleractinia. Furthermore, the number of Haplotype is29, with a Haplotype diversity index of0.898and a nucleotide diversity index of0.12833. Therefore, the genetic diversity of Scleractinia was quite abundant. As concerned from triplet codon, the base substitution frequency of third nucleotide (0.95) was much higher than that of the other two bases.
4. Phylogenetic trees were constructed based on COⅢ DNA sequences of Scleractinia. Results showed that:(1) phylogenetic relationship among intra-specific individuals is consistent with the traditional taxonomy, except that individuals from two different genera, Leptastrea and Plesiastrea of Faviidae, were clustered into a branch;(2) phylogenetic relationship among species within genus was also consistent with the traditional taxonomy.(3) However, phylogenetic relationship among genera within family was quite disorder, obviously inconsistent with results of traditional taxonomy. Platygyra crosslandi (belonging to Platygyra, a genus of Faviidae) was clustered into a branch with Leptastrea purpurea (belonging to Leptastrea, another genus of Faviidae) firstly, but then they were clustered into a branch with Echinophyllia aspera, belonging to Echinophyllia, a genus from another family of Pectiniidae. Subsequently, they were clustered together with Hydnophora exesa (belonging to Hydnophora, a genus from a different family of Merulinidae), and finally clustered into a branch with Plesiastrea and Leptastrea, two genera from the same family of Faviidae.
5. Phylogenetic branch tree of Scleractinia based on ITS DNA sequences and COⅢ sequences showed that ITS and COⅢ sequence is not suitable for phylogeny mark of high taxonomic category, but can be effective as molecular markers in intraspecific.
引文
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