Becker Sven, Hanner Robert, Steinke Dirk
Department of Integrative Biology, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ont, Canada.
Mitochondrial DNA. 2011 Oct;22 Suppl 1:3-9. doi: 10.3109/19401736.2010.535528. Epub 2011 Jan 27.
The Fish Barcode of Life Initiative (FISH-BOL) is a concerted global research project launched in 2005, with the goal to collect and assemble standardized DNA barcode sequences and associated voucher provenance data in a curated reference sequence library to aid the molecular identification of all fish species. This article is a detailed progress report (July 2010) on the number of fish species that have been assigned a DNA barcode. Of the approximately 31,000 currently known fish species, 25% have been processed successfully, with at least one species from 89% of all families barcoded; in this report we give a progress overview by taxonomy and geographic region. Using standard analytical protocols, differences in the barcoding completion rate between orders and families are observed, suggesting a potential PCR amplification bias. Overall, between 3 and 9% of the species analyzed failed to yield a "BARCODE compliant" sequence, depending upon how the data are filtered. When species with only a single representative specimen are included, the failure rate was 9%. This might derive from several sources such as mismatched primers and degraded DNA templates. In an attempt to account for the latter, when the analysis is restricted to species with at least two specimens examined, the observed failure rate is significantly lower (3%), suggesting that template quality is a source of concern for FISH-BOL. We, therefore, conclude that using a standard protocol with several specimens per species and PCR primer cocktails is an efficient and successful approach because failures were evenly distributed among orders and families. Only six orders with low species numbers (Pristiformes, Torpediniformes, Albuliformes, Batrachoidiformes, Gobiesociformes, and Petromyzontiformes) showed failure rates between 10 and 33%. Besides outlining an overarching approach for FISH-BOL data curation, the goal of the present article is to give guidance in directing sampling campaigns toward neglected or underrepresented families in order to complete the FISH-BOL campaign most efficiently.
鱼类生命条形码计划（FISH - BOL）是一项于2005年启动的全球协同研究项目，其目标是在一个经过整理的参考序列库中收集和整合标准化的DNA条形码序列以及相关凭证来源数据，以辅助对所有鱼类物种进行分子鉴定。本文是一份关于已被赋予DNA条形码的鱼类物种数量的详细进展报告（2010年7月）。在目前已知的约31000种鱼类中，25%已成功进行了处理，所有科中有89%至少有一个物种被条形码化；在本报告中，我们按分类学和地理区域给出了进展概述。使用标准分析方案时，观察到目和科之间条形码完成率存在差异，这表明存在潜在的PCR扩增偏差。总体而言，根据数据过滤方式的不同，所分析物种中有3%至9%未能产生“符合条形码标准”的序列。当纳入只有单个代表性标本的物种时，失败率为9%。这可能源于多种原因，如引物不匹配和DNA模板降解。为了解决后者的问题，当分析仅限于至少检查了两个标本的物种时，观察到的失败率显著降低（3%），这表明模板质量是FISH - BOL需要关注的一个问题。因此，我们得出结论，对每个物种使用多个标本和PCR引物混合物的标准方案是一种有效且成功的方法，因为失败情况在目和科之间均匀分布。只有六个物种数量较少的目（锯鲨目、电鳐目、北梭鱼目、蟾鱼目、喉盘鱼目和七鳃鳗目）的失败率在10%至33%之间。除了概述FISH - BOL数据管理的总体方法外，本文的目的是为指导采样活动提供指导，使其针对被忽视或代表性不足的科，以便最有效地完成FISH - BOL项目。
