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一种全长的18S核糖体DNA元编码方法,用于通过纳米孔测序来确定原生体社区的多样性

Chetan C Gaonkar¹, Lisa Campbell^1,2

¹Department of Oceanography Texas A&M University College Station Texas USA.

Ecology and evolution

|April 12, 2024

概括

全长度的18S rDNA测序提供了更高的原生体分类分辨率,而不是在metabarcoding研究中的短读数. 这种方法改善了属的识别,特别是对于具有挑战性的群体,如恐龙鞭动物,提高了生态多样性的评估.

科学领域:

细胞微生物学的微生物学
分子生态学分子生态学
生物多样性评估生物多样性评估

背景情况:

DNA元编码对于原生物种多样性研究至关重要.
18S rDNA标记物的短读测序限制了分类学分辨率.
全长的18S rDNA提供了更高的分辨率,由于保护和超变的区域.

研究的目的:

开发和验证一个全长18S rDNA放大全长的新型原料对.
为了比较全长18S rDNA测序与短读方法 (Illumina MiSeq V4,V8-V9) 的疗效,以评估原生动物的多样性.
评估序列长度对分类学分辨率的影响,特别是对于恐龙鞭毛动物.

主要方法:

使用新的原始对进行全长18SrDNA的放大.
使用纳米孔MinION (长读) 和Illumina MiSeq (短读) 的高通量测序.
生物信息分析用于生成AMPLICON序列变异 (ASV) 并比较分类学注释.

主要成果:

在主要分类学组识别中,长读和短读之间的高度一致性.
与V4 (226/298,76%) 和V8-V9 (213/298,71%) 相比,全长18S rDNA识别了更多的属 (250/298,84%).
全长度测序提高了dinoflagellates的分辨率,与短读数相比检测了更多的属,尽管参考数据库的限制仍然存在.

结论:

全长度的18S rDNA测序是一种可行且有效的方法,用于在实地样本中进行高分辨率的原生虫多样性研究.
这种方法增强了对神秘多样性的检测,特别是在具有挑战性的分类群体内.
需要对参考数据库进行未来的改进,以充分利用长读测序的潜力来识别原生动物.

关键词:

状动物状动物状动物藻类是一种藻类.恐龙旗类动物.微生物多样性的微生物多样性迷你世界迷你世界设计初级设计初级设计

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