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使用复制的模拟社区优化昆虫元编码.

Elzbieta Iwaszkiewicz-Eggebrecht1, Emma Granqvist1, Mateusz Buczek2

  • 1Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.

Methods in ecology and evolution
|October 25, 2023
PubMed
概括
此摘要是机器生成的。

在昆虫群体分析中的metabarcoding性能随着DNA提取而变化. 温和的溶解优于物种存在/不存在,而同质化更好地捕获生物质组成,以准确评估昆虫群落.

关键词:
丰富度估计 丰富度估计麻烦的陷 麻烦的陷均质化 均质化 均质化超级编码元标段编码.模拟社区的模拟社区不具有破坏性的轻度溶解.斯派克 - 进入

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科学领域:

  • 生态生态学 生态生态学
  • 分子生物学分子生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 使用标记基因安普利康的高通量测序进行元编码,是昆虫群体分析的成本效益高的方法.
  • 存在显著的方法差异,阻碍了对物种存在-缺乏,丰度和生物量进行metabarcoding的系统性绩效评估.
  • 在解决昆虫群落的metabarcoding的准确性仍然不清楚.

研究的目的:

  • 评估不同DNA提取协议对昆虫群体的metabarcoding性能的影响.
  • 评估社区概况在复制品之间的一致性.
  • 确定溶解缓冲体,溶解时间和同质化对社区恢复和丰度估计的影响.

主要方法:

  • 利用模拟社区实验,使用不同的DNA提取协议.
  • 使用简单的概率模型来分析结果.
  • 研究了溶解缓冲区选择,溶解持续时间和同质化的影响.
  • 评估了生物尖端引入对物种丰度估计的有用性.

主要成果:

  • 社区估计显示,复制品之间存在显著的变化.
  • 轻度溶解协议更好地重建了物种清单和近似数量.
  • 同质化协议在检索生物质成分方面是优越的.
  • 在 lysates 中更容易检测到小型昆虫;更强硬的物种需要同质化.
  • PCR放大偏差复杂物种计数重建.
  • 在理想条件下,尖端数据允许以~40% (同质物) 到~50% (化物) 的标准误差进行丰度估计.

结论:

  • 非破坏性,温和的溶解方法对存在/不存在描述具有前景,可保存材料进行进一步分析.
  • 同质化协议提供了对社区组成,特别是生物质的优越特征.
  • 优化DNA提取协议对于准确的昆虫元编码至关重要.