植物DNA条形码序列筛选与鉴定研究
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摘要
DNA条形码是指用短的、标准的DNA序列作为物种标记来鉴定物种的一种新技术,它是传统形态学分类的有效补充。目前,植物类群中DNA条形码的研究和应用尚处于探索阶段,筛选候选片段、进而确定通用条形码是当前植物条形码研究的首要任务。为了评估候选条形码在植物中的通用性,本文选取了植物主要类群之一裸子植物门作为取样对象进行研究。此外,由于DNA条形码的应用主要集中在属内物种水平,因此本文还专门针对被子植物门中蔷薇科和大戟科两个具体类群进行小范围研究,进而加快植物标准DNA条形码的确定,促进植物完整条形码数据库的建立。综合实验分析结果,得出的主要结论如下：
(1)基于扩增效率、种内种间遗传距离、"DNA barcoding gap"和物种鉴定能力四个筛选标准,本文评估了七个DNA片段(psbA-trnH, rbcL, matK, rpoB, rpoCl,ITS和ITS2)对裸子植物鉴定的有效性。研究结果表明ITS2是所选片段中最适合鉴定裸子植物的条形码。为了进一步验证ITS2对裸子植物的鉴定能力,我们扩大了样本范围对其进行评估。对于涵盖12科80属502种的888个样本,ITS2的正确鉴定效率在种水平和属水平分别达到73%和98%。
(2)以蔷薇科植物为研究对象,本文分别对四个DNA片段(rbcL, matK, rpoCl和ITS2)的扩增成功率、遗传距离差异、"DNA barcoding gap"和物种鉴定能力四个方面进行了评估和比较。研究结果表明ITS2是所评估DNA片段中最有潜力的DNA条形码。为了进一步检验ITS2对蔷薇科植物鉴定的有效性,本文基于一个更大的样本量对其进行验证。对于来自96属893种的1410个样本,ITS2可以将其78%的样本正确鉴定到种,属水平的鉴定成功率可达到100%。此外,本文还专门针对蔷薇科中12个富含密切相关种的属进行了研究。结果表明,除了Amelanchier, Alchemilla和Rosa之外,ITS2对其他九个属均有较高的物种鉴定成功率(69%-97%)。对于含有大于100个物种的属(Cliffortia, Prunus和Rubus),ITS2仍能正确鉴定>70%的物种。
(3)通过对大戟科植物四个DNA条形码候选序列rbcL, matK, ITS和ITS2在种内种间遗传距离差异,"DNA barcoding gap"以及物种鉴定能力等方面的评估和比较,结果表明,ITS/ITS2非常适合鉴定大戟科植物。为了证明ITS/ITS2的鉴定能力,本文在扩大样本量的基础上对这两个片段进行了进一步评估,对于大戟科66属871种的1183个样本,ITS/ITS2可以成功鉴定大于90%的种以及100%的属。此外,本文还专门研究了ITS/ITS2对大戟科中七个属(Andrachne, Mallotus, Euphorbia, Croton, Phyllanthus, Macaranga and Glochidion)的鉴定能力。结果表明,ITS／ITS2对七个属均有较高的物种鉴定成功率(68%-100%)。对于Euphorbia和Croton两个属,每个属的物种数均大于240个,ITS／ITS2仍能正确鉴定88%-99%的物种。
本研究以裸子植物、蔷薇科以及大戟科为例,系统地分析和比较了不同DNA片段作为植物DNA条形码的鉴定有效性。ITS2在所选取的三个植物分类单元中均有较好表现,因而我们的研究结果表明ITS2有潜力成为植物标准DNA条形码之一。该研究将会给其他植物类群DNA条形码研究提供参考并最终促进植物标准DNA条形码的确定。
DNA barcoding is a new technique that uses a short DNA sequence from a standardized and agreed-upon position in the genome as a molecular diagnostic for species-level identification, it is an effective complement for traditional taxonomy based on morphology. At present, the research and application of DNA barcoding in plants is in exploration stage, so the most important task is to select candidate genes or DNA regions and identify a suitable DNA barcode. In this study, we compared different candidate DNA barcodes from gymnosperms to evaluate their universality. In addition, we also aimed at two specific families (Rosaceae and Euphorbiaceae) to test the effectiveness of different candidate barcodes for identifying plants, which will accelerate the determination of universal DNA barcodes for plants and help to build up a comprehensive DNA barcode library. Based on the results of experimental research, the main results are as follows:
1. In order to determine an effective DNA barcode for gymnosperms, seven DNA regions(psbA-trnH, rbcL, matK, rpoB, rpoCl, ITS and ITS2) were evaluated on four criteria including the success rates of PCR amplification, the extent of specific genetic divergence, the DNA barcoding gap and the ability for species discrimination. Our results suggest that ITS2 is most appropriate for barcoding gymnosperms among the seven loci tested. To further evaluate the ability of ITS2 for identifying gymnosperms, we also tested it in 888 gymnosperm samples collected from 502 species of 80 diverse genera in 12 families. ITS2 correctly identified 73% and 98% of them at the species and genus levels, respectively.
2. We tested the applicability of four DNA regions (rbcL, matK, rpoCl and ITS2) as the barcodes for identifying species within Rosaceae. Based on assessments of the success rates of PCR amplification, the extent of specific genetic divergence, the DNA barcoding gap and the ability for species discrimination, our results suggest that ITS2 is the best of the four loci tested for barcoding Rosaceae. We further evaluated the effectiveness of ITS2 for identifying a wide range of species within Rosaceae. Of the 1410 plant samples collected from 893 species in 96 diverse genera, ITS2 successfully identified 78% and 100% of them at the species and genus levels, respectively. Moreover, we also evaluated the species identification ability of the ITS2 region in 12 genera that are rich in closely related species using the BLAST1 method. Although problems were encountered in the genera (Amelanchier, Alchemilla and Rosa), using ITS2 for species identification resulted in an 86%-97% success rate for five genera (Acaena, Polylepis, Pyrus, Malus, and Fragaria) and an 69%-76% success rate for four other genera (Crataegus, Cliffortia, Rubus and Prunus). For three genera(Cliffortia, Prunus and Rubus) with more than 100 species per genus in our samples, ITS2 also performed well with a>70% successful identification rate.
3. We compared the specific genetic divergence, the DNA barcoding gap and the ability for species discrimination of four DNA regions (rbcL, matK, ITS and ITS2) of species within Euphorbiaceae, the present results affirmed that ITS/ITS2 is a potential barcode for Euphorbiaceae species. This study also provided a large-scale test to evaluate the effectiveness of ITS/ITS2 for differentiating species within Euphorbiaceae. For the 1,183 plant samples collected from 871 species in 66 diverse genera, ITS/ITS2 successfully identified>90% and 100% of them at the species and genus levels, respectively. Furthermore, we evaluated the two loci in 7 genera(Andrachne, Mallotus, Euphorbia, Croton, Phyllanthus, Macaranga and Glochidion) within Euphorbiaceae. For the samples collected, using ITS/ITS2 for species identification resulted in an 68-100% success rate for the genera. For two genera(Euphorbia and Croton) with more than 240 species in our sample, ITS/ITS2 also performed well with 88-99% successful identification rates.
The research systematically analyzed and compared the effectiveness of different candidate DNA barcodes for identifying plants using gymnosperms, Rosaceae and Euphorbiaceae. The ITS2 locus is a powerful barcode among all three plant taxa tested, so our results strongly suggest that the ITS2 region should have a great potential to be used as one of the universal barcodes for plants. Our work contributes valuable information for identifying species in other plant taxonomic groups and promotes the determination of the standard DNA barcode for plants.
(1)基于扩增效率、种内种间遗传距离、"DNA barcoding gap"和物种鉴定能力四个筛选标准,本文评估了七个DNA片段(psbA-trnH, rbcL, matK, rpoB, rpoCl,ITS和ITS2)对裸子植物鉴定的有效性。研究结果表明ITS2是所选片段中最适合鉴定裸子植物的条形码。为了进一步验证ITS2对裸子植物的鉴定能力,我们扩大了样本范围对其进行评估。对于涵盖12科80属502种的888个样本,ITS2的正确鉴定效率在种水平和属水平分别达到73%和98%。
(2)以蔷薇科植物为研究对象,本文分别对四个DNA片段(rbcL, matK, rpoCl和ITS2)的扩增成功率、遗传距离差异、"DNA barcoding gap"和物种鉴定能力四个方面进行了评估和比较。研究结果表明ITS2是所评估DNA片段中最有潜力的DNA条形码。为了进一步检验ITS2对蔷薇科植物鉴定的有效性,本文基于一个更大的样本量对其进行验证。对于来自96属893种的1410个样本,ITS2可以将其78%的样本正确鉴定到种,属水平的鉴定成功率可达到100%。此外,本文还专门针对蔷薇科中12个富含密切相关种的属进行了研究。结果表明,除了Amelanchier, Alchemilla和Rosa之外,ITS2对其他九个属均有较高的物种鉴定成功率(69%-97%)。对于含有大于100个物种的属(Cliffortia, Prunus和Rubus),ITS2仍能正确鉴定>70%的物种。
(3)通过对大戟科植物四个DNA条形码候选序列rbcL, matK, ITS和ITS2在种内种间遗传距离差异,"DNA barcoding gap"以及物种鉴定能力等方面的评估和比较,结果表明,ITS/ITS2非常适合鉴定大戟科植物。为了证明ITS/ITS2的鉴定能力,本文在扩大样本量的基础上对这两个片段进行了进一步评估,对于大戟科66属871种的1183个样本,ITS/ITS2可以成功鉴定大于90%的种以及100%的属。此外,本文还专门研究了ITS/ITS2对大戟科中七个属(Andrachne, Mallotus, Euphorbia, Croton, Phyllanthus, Macaranga and Glochidion)的鉴定能力。结果表明,ITS／ITS2对七个属均有较高的物种鉴定成功率(68%-100%)。对于Euphorbia和Croton两个属,每个属的物种数均大于240个,ITS／ITS2仍能正确鉴定88%-99%的物种。
本研究以裸子植物、蔷薇科以及大戟科为例,系统地分析和比较了不同DNA片段作为植物DNA条形码的鉴定有效性。ITS2在所选取的三个植物分类单元中均有较好表现,因而我们的研究结果表明ITS2有潜力成为植物标准DNA条形码之一。该研究将会给其他植物类群DNA条形码研究提供参考并最终促进植物标准DNA条形码的确定。
DNA barcoding is a new technique that uses a short DNA sequence from a standardized and agreed-upon position in the genome as a molecular diagnostic for species-level identification, it is an effective complement for traditional taxonomy based on morphology. At present, the research and application of DNA barcoding in plants is in exploration stage, so the most important task is to select candidate genes or DNA regions and identify a suitable DNA barcode. In this study, we compared different candidate DNA barcodes from gymnosperms to evaluate their universality. In addition, we also aimed at two specific families (Rosaceae and Euphorbiaceae) to test the effectiveness of different candidate barcodes for identifying plants, which will accelerate the determination of universal DNA barcodes for plants and help to build up a comprehensive DNA barcode library. Based on the results of experimental research, the main results are as follows:
1. In order to determine an effective DNA barcode for gymnosperms, seven DNA regions(psbA-trnH, rbcL, matK, rpoB, rpoCl, ITS and ITS2) were evaluated on four criteria including the success rates of PCR amplification, the extent of specific genetic divergence, the DNA barcoding gap and the ability for species discrimination. Our results suggest that ITS2 is most appropriate for barcoding gymnosperms among the seven loci tested. To further evaluate the ability of ITS2 for identifying gymnosperms, we also tested it in 888 gymnosperm samples collected from 502 species of 80 diverse genera in 12 families. ITS2 correctly identified 73% and 98% of them at the species and genus levels, respectively.
2. We tested the applicability of four DNA regions (rbcL, matK, rpoCl and ITS2) as the barcodes for identifying species within Rosaceae. Based on assessments of the success rates of PCR amplification, the extent of specific genetic divergence, the DNA barcoding gap and the ability for species discrimination, our results suggest that ITS2 is the best of the four loci tested for barcoding Rosaceae. We further evaluated the effectiveness of ITS2 for identifying a wide range of species within Rosaceae. Of the 1410 plant samples collected from 893 species in 96 diverse genera, ITS2 successfully identified 78% and 100% of them at the species and genus levels, respectively. Moreover, we also evaluated the species identification ability of the ITS2 region in 12 genera that are rich in closely related species using the BLAST1 method. Although problems were encountered in the genera (Amelanchier, Alchemilla and Rosa), using ITS2 for species identification resulted in an 86%-97% success rate for five genera (Acaena, Polylepis, Pyrus, Malus, and Fragaria) and an 69%-76% success rate for four other genera (Crataegus, Cliffortia, Rubus and Prunus). For three genera(Cliffortia, Prunus and Rubus) with more than 100 species per genus in our samples, ITS2 also performed well with a>70% successful identification rate.
3. We compared the specific genetic divergence, the DNA barcoding gap and the ability for species discrimination of four DNA regions (rbcL, matK, ITS and ITS2) of species within Euphorbiaceae, the present results affirmed that ITS/ITS2 is a potential barcode for Euphorbiaceae species. This study also provided a large-scale test to evaluate the effectiveness of ITS/ITS2 for differentiating species within Euphorbiaceae. For the 1,183 plant samples collected from 871 species in 66 diverse genera, ITS/ITS2 successfully identified>90% and 100% of them at the species and genus levels, respectively. Furthermore, we evaluated the two loci in 7 genera(Andrachne, Mallotus, Euphorbia, Croton, Phyllanthus, Macaranga and Glochidion) within Euphorbiaceae. For the samples collected, using ITS/ITS2 for species identification resulted in an 68-100% success rate for the genera. For two genera(Euphorbia and Croton) with more than 240 species in our sample, ITS/ITS2 also performed well with 88-99% successful identification rates.
The research systematically analyzed and compared the effectiveness of different candidate DNA barcodes for identifying plants using gymnosperms, Rosaceae and Euphorbiaceae. The ITS2 locus is a powerful barcode among all three plant taxa tested, so our results strongly suggest that the ITS2 region should have a great potential to be used as one of the universal barcodes for plants. Our work contributes valuable information for identifying species in other plant taxonomic groups and promotes the determination of the standard DNA barcode for plants.
引文
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