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Abstract：
OBJECTIVE: DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants.
METHODS: To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants.
RESULTS: Performance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession.
CONCLUSIONS: Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.
METHODS: To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants.
RESULTS: Performance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession.
CONCLUSIONS: Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.
摘要：
目的：DNA可以在非常寒冷或干燥的环境中保存数千年，土壤和浅层水生沉积物中的植物组织碎片和花粉非常适合过去植物区系的分子表征。然而,这一研究领域的一个障碍是生物信息学分类中的限制性偏差，植物的复杂基因组。
方法：为了建立一个可能的基线方案，用于快速分类短阅读鸟枪宏基因组数据，以重建植物群落，阅读分类程序Kraken，离心机,和MegaBLAST在模拟和古代数据上进行了测试，并针对针对植物的参考数据库进行了分类。
结果：对模拟数据的性能测试表明，Kraken和Centrifge的性能优于MegaBLAST。Kraken往往是最保守的高精度方法，而离心机具有更高的灵敏度。对来自北美的13,000年古代沉积DNA的重新分析表征了潜在的冰川后植被演替。
结论：分类方法的选择对性能和结果的任何下游解释都有影响。对冰川湖沉积物中古代DNA的重新分析产生了植被历史，这些植被历史因方法而异，从分子证据中得出的潜在改变的古生态学结论。
方法：为了建立一个可能的基线方案，用于快速分类短阅读鸟枪宏基因组数据，以重建植物群落，阅读分类程序Kraken，离心机,和MegaBLAST在模拟和古代数据上进行了测试，并针对针对植物的参考数据库进行了分类。
结果：对模拟数据的性能测试表明，Kraken和Centrifge的性能优于MegaBLAST。Kraken往往是最保守的高精度方法，而离心机具有更高的灵敏度。对来自北美的13,000年古代沉积DNA的重新分析表征了潜在的冰川后植被演替。
结论：分类方法的选择对性能和结果的任何下游解释都有影响。对冰川湖沉积物中古代DNA的重新分析产生了植被历史，这些植被历史因方法而异，从分子证据中得出的潜在改变的古生态学结论。
