Short rDNA Barcodes for Species Identification in Foraminifera
Short rDNA Barcodes for Species Identification in Foraminifera
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DOI：
10.1111/j.1550-7408.2009.00468.x
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发表时间：
2010-03-01
影响因子：
2.2
通讯作者：
Lecroq, Beatrice
中科院分区：
文献类型：
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作者：
Pawlowski, Jan;Lecroq, Beatrice
核糖体DNA（rDNA）序列已被证明是非常有用的微生物真核生物的鉴定。通常，分析rDNA基因的完整或长的部分序列。然而，新的大规模测序技术的发展产生了大量的相对较短的序列，提出了一个问题，在环境采样的物种区分所需的rDNA片段的最小长度。为了回答这个问题，我们比较了有孔虫小亚基（SSU）rDNA的六个可变区，已知它们具有快速进化的核糖体基因。对于每个区域，我们分析了（1）有孔虫形态种之间和内部的序列差异，（2）种内多态性，以及（3）每个区域识别从较长片段分析推断的序列类型的能力。我们的研究结果表明，虽然不同的分类群体之间的可变区有很大的不同，他们中的大多数都表现得很好的物种标识符。考虑到不同的分析，Helly 37的扩增片段似乎是有孔虫条形码的最佳候选者。我们建议，这个相对较短的区域，平均50-60 nt的长度，可能是一个理想的条形码识别有孔虫在环境样品中使用大规模测序方法。
Ribosomal DNA (rDNA) sequences have been shown to be very useful for identification of microbial eukaryotes. Usually, complete or long partial sequences of the rDNA genes are analysed. However, the development of new massive sequencing technologies producing a large amount of relatively short sequences raises the question about the minimum length of rDNA fragments necessary for species distinction in environmental sampling. To answer this question, we compared six variable regions of the small subunit (SSU) rDNA of foraminifera, known to have rapidly evolving ribosomal genes. For each region, we analysed (1) the sequence divergence between and within foraminiferal morphospecies, (2) the intraspecific polymorphism, and (3) the ability of each region to recognize the phylotypes inferred from analysis of a longer fragment. Our results show that although the variable regions differ considerably between taxonomic groups, most of them perform very well as species identifiers. Taking into account different analyses, the expansion segment of Helix 37 appears to be the best candidate for barcoding foraminifera. We propose that this relatively short region, averaging 50-60 nt in length, could be an ideal barcode for identification of foraminifera in environmental samples using massive sequencing approach.