基因条码（DNA Barcode）在海藻系统学领域中的研究应用
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摘要
我国海岸线漫长，拥有丰富的海藻资源。同时，我国是海藻养殖大国，海藻养殖的基础理论研究也居世界前列。我国海藻产业的进一步发展需要发掘更多的海藻种质资源，特别是我们没有认识或者已经认识但是尚未进一步研究和利用的海藻资源。这项工作的基础是准确的对这些资源分类鉴定。但是，大型海藻其形态特征易受环境因素的影响，发生不同程度地改变；其次在物种水平上，往往形态特征差异微弱不易鉴定或容易出错。再次，我们对于一部分大型海藻的生活史还缺乏必要的了解，也加大了物种鉴定的难度。因此，如果仅仅依赖于形态学特征进行分类鉴定，即便是受过专门训练的藻类学家在工作时也会遇到不少的困难，甚至产生争议。例如龙须菜的归属问题就存在争议。不同的分类学家按照不同的形态学标准，有的将其归为江蓠属，有的认为其应该从江蓠属中划出。同样，底栖硅藻的分类鉴定也存在相类似的问题。
本论文对于海藻的基因条码进行了相关的研究，以便解决这一难题。研究从三个方面入手，内容包括：(1)采集青岛海区潮间带红藻门的样品，对这些样品的COI(细胞色素C氧化酶亚基I), UPA(质体23S rRNA domain V区域)以及ITS(内转录间隔区)序列进行扩增，从中筛选合适的DNA Marker作为红藻标准的基因条码。同时，利用筛选出的基因条码初步研究青岛海区潮下带的红藻资源；(2)分析了我国几种江蓠属海藻的18S rRNA基因、cox2-3间隔区以及RUBISCO间隔区的分子序列，并结合GenBank现有的相关数据进行了分子系统学关系分析，为江蓠属的系统进化，分类提供新的佐证；(3)利用SSU序列和rbcL序列对所分离纯化的底栖硅藻进行初步的鉴定，同时结合形态学方法将样品鉴定到种一级水平。研究结果表明：
(1) COI序列与UPA序列均可以区分红藻到种一级水平。其中，COI序列缺乏通用引物，但是种间种内变异度足够好；UPA序列虽然分辨率相对较低，可能不能准确的鉴定亲缘关系较近的物种，但其具有通用引物。因此，本研究提出在以后的分类鉴定中可将两种序列相结合使用，准确鉴定。而ITS序列在部分样品的扩增中发现了多态性的问题，为避免对后续的工作造成干扰，不推荐ITS序列作为红藻标准的DNA Barcode；在潮下带红藻资源调查中，发现了两种以前从未在青岛海区有过记录的大型红藻，分别为冈村蜈蚣藻和裂膜藻。同时，也发现一些具有重要经济价值藻类，例如紫菜等的野生藻床。这些都是十分宝贵的野生基因资源。
(2)江蓠属分子系统学研究中，基于cox2-3间隔区、以及RUBISCO间隔区序列构建的MP进化树较为相似，而与基于18S rRNA构建的进化树略有不同。这主要是由于18S rRNA更为保守的原因；扁江蓠与脆江蓠在三个系统树中均聚合成支，显示了它们之间具有较近的亲缘关系；龙须菜与江蓠属海藻具有较远的遗传距离，在3个进化树中，龙须菜也均位于进化树的基部，单独成支，证实龙须菜并不隶属于江蓠属，且分化相对较早。
(3)首先使用SSU序列对底栖硅藻样品作初步的鉴定，可以将样品鉴定到属或者科一级的水平，减少错误的产生；对于分离纯化四种底栖硅藻。基于扫描电镜与两个序列的比较，将其鉴定为极小舟形藻,假头舟形藻,不定舟形藻和喙头舟形藻。通过分子生物学分析，我们认为不定舟形藻与极小舟形藻存在较近的亲缘关系。
China has an18000km long coast line and abundant seaweeds resources. Inaddition, China is the dominant nation in world seaweeds culture, and also at the headof basic theory study. In order to get the further development in this field, much moreresources should be researched, including the resources that we do not understand orwe have understood but need further study. However, identifications of seaweeds aresometimes difficult due to their simple and convergent appearance. Morphologicalcharacters of seaweeds are often changeable under various conditions. In some cases,the differences between the species are rare, unknown life cycles also pose moredifficulties in species identification. Even the experts may face problems if theiridentification is solely depending on morphological characteristics. Such asGracilariopsis lemaneiformis, some researchers believe that it belongs to theGracilaria; but other experts proper that the Gracilariopsis lemaneiformis shouldtransfer to other genus, depending on different morphological characteristics. Anoften encountered problem in investigating benthic diatoms is also the accuratebiological identification.
The goal of this research is to study the algae DNA Barcodes for helping solve theidentification difficulties. It included:(1) three DNA Markers, COI (cytochromeoxidase subunit I), UPA (universal plastid amplicon, domain V of23S rRNA), andITS (nuclear internal transcribed spacer) were employed to analyze common speciesof intertidal red seaweeds in Qingdao for selecting proper DNA sequence as standardRhodophyta DNA Barcode. The selected Markers were utilized to research thesubtidal red seaweeds resource in Qingdao;(2) sequences of three molecular markers (18S rRNA, cox2-3intergenic spacer and RUBISCO spacer), in combination withdata from GenBank, were used to analyze the phylogentic relations of Gracilariaspecies collected from the coast of China;(3) the SSU (18S rRNA) and rbcL is usedinitially to help identify the isolated benthic diatoms. The results showed that:
(1): COI and UPA sequences could identify samples to species level. Among them,COI was a sensitive marker. However, not all the tested species gave PCRamplification products due to lack of the universal primers. The second barcode UPAhad effective universal primers but needed to be tested for the effectiveness ofresolving closely related species. For the further identification, the two sequencesshould be combined used. More than one ITS sequence types were found in somespecies in this investigation, which might lead to confusion in further analysis.Therefore ITS sequence is not recommended as a universal barcode for red seaweedsidentification. In subtidal red seaweeds resources research, two species Schizymeniadubyi and Polyopes lancifolius which not recorded in Qingdao were found. Some wildalgal turf, such as Pyropia yezoensis was also found in this study, they were veryimportant in further study.
(2): In phylogenetic analysis of Gracilaria, phylogenetic trees based on cox2-3andRUBISCO spacer sequences exhibited the same pattern but differed slightly from thatof the18S rRNA-based phylogenetic tree due to a higher degree of conservation ofthe latter. Gracilaria textorii was sister to G. chouae in all three trees, showing theclose relationship between the two species. The results further confirmed that theGracilariopsis lemaneiformis did not belong to the genus Gracilaria. Results alsoindicate an earlier evolution status of Gracilariopsis lemaneiformis based on thesethree sequence comparisons.
(3): SSU sequence was recommended to be used initially in most cases todiscriminate samples to genus or family level. Based on scanning electronicmicroscopy (SEM) and sequence comparisons of two genes (SSU, rbcL), the sampleswere identified to be Navicula perminuta, N. pseudacceptata, N. vara and N.rhynchocephala, respectively.
本论文对于海藻的基因条码进行了相关的研究，以便解决这一难题。研究从三个方面入手，内容包括：(1)采集青岛海区潮间带红藻门的样品，对这些样品的COI(细胞色素C氧化酶亚基I), UPA(质体23S rRNA domain V区域)以及ITS(内转录间隔区)序列进行扩增，从中筛选合适的DNA Marker作为红藻标准的基因条码。同时，利用筛选出的基因条码初步研究青岛海区潮下带的红藻资源；(2)分析了我国几种江蓠属海藻的18S rRNA基因、cox2-3间隔区以及RUBISCO间隔区的分子序列，并结合GenBank现有的相关数据进行了分子系统学关系分析，为江蓠属的系统进化，分类提供新的佐证；(3)利用SSU序列和rbcL序列对所分离纯化的底栖硅藻进行初步的鉴定，同时结合形态学方法将样品鉴定到种一级水平。研究结果表明：
(1) COI序列与UPA序列均可以区分红藻到种一级水平。其中，COI序列缺乏通用引物，但是种间种内变异度足够好；UPA序列虽然分辨率相对较低，可能不能准确的鉴定亲缘关系较近的物种，但其具有通用引物。因此，本研究提出在以后的分类鉴定中可将两种序列相结合使用，准确鉴定。而ITS序列在部分样品的扩增中发现了多态性的问题，为避免对后续的工作造成干扰，不推荐ITS序列作为红藻标准的DNA Barcode；在潮下带红藻资源调查中，发现了两种以前从未在青岛海区有过记录的大型红藻，分别为冈村蜈蚣藻和裂膜藻。同时，也发现一些具有重要经济价值藻类，例如紫菜等的野生藻床。这些都是十分宝贵的野生基因资源。
(2)江蓠属分子系统学研究中，基于cox2-3间隔区、以及RUBISCO间隔区序列构建的MP进化树较为相似，而与基于18S rRNA构建的进化树略有不同。这主要是由于18S rRNA更为保守的原因；扁江蓠与脆江蓠在三个系统树中均聚合成支，显示了它们之间具有较近的亲缘关系；龙须菜与江蓠属海藻具有较远的遗传距离，在3个进化树中，龙须菜也均位于进化树的基部，单独成支，证实龙须菜并不隶属于江蓠属，且分化相对较早。
(3)首先使用SSU序列对底栖硅藻样品作初步的鉴定，可以将样品鉴定到属或者科一级的水平，减少错误的产生；对于分离纯化四种底栖硅藻。基于扫描电镜与两个序列的比较，将其鉴定为极小舟形藻,假头舟形藻,不定舟形藻和喙头舟形藻。通过分子生物学分析，我们认为不定舟形藻与极小舟形藻存在较近的亲缘关系。
China has an18000km long coast line and abundant seaweeds resources. Inaddition, China is the dominant nation in world seaweeds culture, and also at the headof basic theory study. In order to get the further development in this field, much moreresources should be researched, including the resources that we do not understand orwe have understood but need further study. However, identifications of seaweeds aresometimes difficult due to their simple and convergent appearance. Morphologicalcharacters of seaweeds are often changeable under various conditions. In some cases,the differences between the species are rare, unknown life cycles also pose moredifficulties in species identification. Even the experts may face problems if theiridentification is solely depending on morphological characteristics. Such asGracilariopsis lemaneiformis, some researchers believe that it belongs to theGracilaria; but other experts proper that the Gracilariopsis lemaneiformis shouldtransfer to other genus, depending on different morphological characteristics. Anoften encountered problem in investigating benthic diatoms is also the accuratebiological identification.
The goal of this research is to study the algae DNA Barcodes for helping solve theidentification difficulties. It included:(1) three DNA Markers, COI (cytochromeoxidase subunit I), UPA (universal plastid amplicon, domain V of23S rRNA), andITS (nuclear internal transcribed spacer) were employed to analyze common speciesof intertidal red seaweeds in Qingdao for selecting proper DNA sequence as standardRhodophyta DNA Barcode. The selected Markers were utilized to research thesubtidal red seaweeds resource in Qingdao;(2) sequences of three molecular markers (18S rRNA, cox2-3intergenic spacer and RUBISCO spacer), in combination withdata from GenBank, were used to analyze the phylogentic relations of Gracilariaspecies collected from the coast of China;(3) the SSU (18S rRNA) and rbcL is usedinitially to help identify the isolated benthic diatoms. The results showed that:
(1): COI and UPA sequences could identify samples to species level. Among them,COI was a sensitive marker. However, not all the tested species gave PCRamplification products due to lack of the universal primers. The second barcode UPAhad effective universal primers but needed to be tested for the effectiveness ofresolving closely related species. For the further identification, the two sequencesshould be combined used. More than one ITS sequence types were found in somespecies in this investigation, which might lead to confusion in further analysis.Therefore ITS sequence is not recommended as a universal barcode for red seaweedsidentification. In subtidal red seaweeds resources research, two species Schizymeniadubyi and Polyopes lancifolius which not recorded in Qingdao were found. Some wildalgal turf, such as Pyropia yezoensis was also found in this study, they were veryimportant in further study.
(2): In phylogenetic analysis of Gracilaria, phylogenetic trees based on cox2-3andRUBISCO spacer sequences exhibited the same pattern but differed slightly from thatof the18S rRNA-based phylogenetic tree due to a higher degree of conservation ofthe latter. Gracilaria textorii was sister to G. chouae in all three trees, showing theclose relationship between the two species. The results further confirmed that theGracilariopsis lemaneiformis did not belong to the genus Gracilaria. Results alsoindicate an earlier evolution status of Gracilariopsis lemaneiformis based on thesethree sequence comparisons.
(3): SSU sequence was recommended to be used initially in most cases todiscriminate samples to genus or family level. Based on scanning electronicmicroscopy (SEM) and sequence comparisons of two genes (SSU, rbcL), the sampleswere identified to be Navicula perminuta, N. pseudacceptata, N. vara and N.rhynchocephala, respectively.
引文
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