甲特拉斯:一个高质量的甲基因组组装器的人类肠道微生物群通过cobarcoding测序阅读读
Yanwei Qi1,2,3, Shengqiang Gu1,4, Yue Zhang1
1BGI-Qingdao BGI-Shenzhen Qingdao China.
iMeta
|June 13, 2024
概括
一种新的方法,MetaTrass,增强了高质量,物种解析的人类肠道微生物基因组的恢复. 这种方法改善了基因组的连续性和完整性,比传统策略显示出更大的遗传多样性.
科学领域:
- 微生物学 微生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 人类肠道微生物基因组在未保存的区域中表现出显著的遗传多样性,因此需要高分辨率的方法来进行物种级别的分析.
- 现有的元基因组分析策略难以满足对高分辨率物种水平变异性阐释的需求.
研究的目的:
- 引入MetaTrass,这是一个高效的分类-首先-然后-组装-以后的策略,用于从元基因组数据中恢复高质量的物种解析基因组.
- 评估MetaTrass的性能与使用模拟和真实人类肠道微生物数据的传统组装-首先-然后-后面策略相比.
主要方法:
- 开发并实施了MetaTrass战略,采用了先装箱,然后装配的方法.
- 使用单管长片段读取 (stLFR) 技术,并具有可读序列的协编码功能.
- 将MetaTrass应用于模拟的微生物群落和四个人类便样本.
主要成果:
- 与基于下一代测序的方法相比,MetaTrass在模拟中显示出更好的基因组连续性 (kb到Mb) 和准确性.
- MetaTrass成功地从人类便样本中获取了178个高质量的基因组,显著优于传统方法 (58个基因组).
- 获取的基因组证实了人类肠道微生物群落内的大量遗传多样性,并使得更深入的见解成为可能.
结论:
- MetaTrass提供了一种卓越的策略,可以从元基因组数据集,特别是通过stLFR技术生成的基因组中组装高质量的物种解析基因组.
- 该方法通过提供更高的空间特征和动态分辨率来增强复杂微生物群落的研究.
- "MetaTrass"可以适应其他可编码库类型,并以开源代码提供.
更多相关视频
11:22Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
27.9K
12:08Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
5.0K
相关概念视频
Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Next-generation Sequencing
88.6K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
88.6K
Sanger Sequencing
754.0K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
754.0K
Genomics
36.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.3K
RNA-seq
9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K
