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Updated: May 17, 2025

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通过定制的标记基因组来增强微生物的基因组信号

Henry Secaira-Morocho^1,2, Xiaofang Jiang², Qiyun Zhu¹

¹Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.

bioRxiv : the preprint server for biology

|March 31, 2025

概括

从扩展基因家族中选择定制的基因基因标记基因可以提高微生物基因组学的准确性,特别是在基因组组装基因组中. 这种方法增强了家族遗传树的重建,即使有不完整的基因组数据.

科学领域:

微生物基因组学微生物基因组学
人类遗传学是一个学科.
生物信息学是一种生物信息学.

背景情况:

传统的遗传学标记基因选择依赖于有限的,均分布的整个基因组.
大基因组组装基因组 (MAGs) 代表了巨大的微生物多样性,但往往包含新的基因家族.
现有的标志物集与MAGs中发现的不均分布和独特基因家族作斗争.

研究的目的:

系统地评估来自KEGG和EggNOG的基因家族,以改善深层微生物基因组学中的基因信号.
开发一种针对特定基因组数据集 (包括MAG) 量身定制的精确基因标记的选择方法.
介绍一个强大的软件工具,用于自动标记器选择.

主要方法:

来自KEGG和EggNOG数据库的基因家族的系统评估.
使用传统与扩展,量身定制的标记集对遗传树准确性的比较分析.
在整个基因组和MAG的模拟和现实数据集上进行测试.
开发和应用TMarSel软件工具.

主要成果:

从扩展的池中选择并针对输入基因组量身定制的标记物显著提高了家族遗传树的准确性.
在MAG中,即使基因组数据不完整 (缺少开放的读取框架),也保持了增强的标记精度.
选择的标记物包括各种功能,包括新陈代谢,细胞过程,环境信息处理,复制,翻译和转录.

结论:

从更广泛的基因库中进行量身定制的标记物选择可以增强微生物的基因组学,特别是在多样化和不完整的MAG中.
该TMarSel工具提供自动化,灵活和强大的标记物选择,克服了基于专家意见的方法的局限性.
这种方法可以从复杂的基因组数据中准确地重建微生物进化史.

关键词:

转基因组学是指转基因组学.遗传学标志物遗传学标志物人类基因组学是什么?Prokaryotes 是一个原核生物.

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